Add files using upload-large-folder tool

llmeval-env/lib/python3.10/site-packages/transformers/models/bloom/__init__.py

@@ -0,0 +1,103 @@
+# Copyright 2022 The HuggingFace Team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from typing import TYPE_CHECKING
+
+from ...utils import (
+    OptionalDependencyNotAvailable,
+    _LazyModule,
+    is_flax_available,
+    is_tokenizers_available,
+    is_torch_available,
+)
+
+
+_import_structure = {
+    "configuration_bloom": ["BLOOM_PRETRAINED_CONFIG_ARCHIVE_MAP", "BloomConfig", "BloomOnnxConfig"],
+}
+try:
+    if not is_tokenizers_available():
+        raise OptionalDependencyNotAvailable()
+except OptionalDependencyNotAvailable:
+    pass
+else:
+    _import_structure["tokenization_bloom_fast"] = ["BloomTokenizerFast"]
+
+try:
+    if not is_torch_available():
+        raise OptionalDependencyNotAvailable()
+except OptionalDependencyNotAvailable:
+    pass
+else:
+    _import_structure["modeling_bloom"] = [
+        "BLOOM_PRETRAINED_MODEL_ARCHIVE_LIST",
+        "BloomForCausalLM",
+        "BloomModel",
+        "BloomPreTrainedModel",
+        "BloomForSequenceClassification",
+        "BloomForTokenClassification",
+        "BloomForQuestionAnswering",
+    ]
+
+try:
+    if not is_flax_available():
+        raise OptionalDependencyNotAvailable()
+except OptionalDependencyNotAvailable:
+    pass
+else:
+    _import_structure["modeling_flax_bloom"] = [
+        "FlaxBloomForCausalLM",
+        "FlaxBloomModel",
+        "FlaxBloomPreTrainedModel",
+    ]
+
+
+if TYPE_CHECKING:
+    from .configuration_bloom import BLOOM_PRETRAINED_CONFIG_ARCHIVE_MAP, BloomConfig, BloomOnnxConfig
+
+    try:
+        if not is_tokenizers_available():
+            raise OptionalDependencyNotAvailable()
+    except OptionalDependencyNotAvailable:
+        pass
+    else:
+        from .tokenization_bloom_fast import BloomTokenizerFast
+
+    try:
+        if not is_torch_available():
+            raise OptionalDependencyNotAvailable()
+    except OptionalDependencyNotAvailable:
+        pass
+    else:
+        from .modeling_bloom import (
+            BLOOM_PRETRAINED_MODEL_ARCHIVE_LIST,
+            BloomForCausalLM,
+            BloomForQuestionAnswering,
+            BloomForSequenceClassification,
+            BloomForTokenClassification,
+            BloomModel,
+            BloomPreTrainedModel,
+        )
+
+    try:
+        if not is_flax_available():
+            raise OptionalDependencyNotAvailable()
+    except OptionalDependencyNotAvailable:
+        pass
+    else:
+        from .modeling_flax_bloom import FlaxBloomForCausalLM, FlaxBloomModel, FlaxBloomPreTrainedModel
+else:
+    import sys
+
+    sys.modules[__name__] = _LazyModule(__name__, globals()["__file__"], _import_structure, module_spec=__spec__)

llmeval-env/lib/python3.10/site-packages/transformers/models/bloom/configuration_bloom.py

@@ -0,0 +1,236 @@
+# coding=utf-8
+# Copyright 2022 the Big Science Workshop and HuggingFace Inc. team.  All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+""" Bloom configuration"""
+from collections import OrderedDict
+from typing import TYPE_CHECKING, Any, List, Mapping, Optional
+
+from packaging import version
+
+
+if TYPE_CHECKING:
+    from ... import PreTrainedTokenizer, TensorType
+
+from ...configuration_utils import PretrainedConfig
+from ...onnx import OnnxConfigWithPast, PatchingSpec
+from ...utils import is_torch_available, logging
+
+
+logger = logging.get_logger(__name__)
+
+
+from ..deprecated._archive_maps import BLOOM_PRETRAINED_CONFIG_ARCHIVE_MAP  # noqa: F401, E402
+
+
+class BloomConfig(PretrainedConfig):
+    """
+    This is the configuration class to store the configuration of a [`BloomModel`]. It is used to instantiate a Bloom
+    model according to the specified arguments, defining the model architecture. Instantiating a configuration with the
+    defaults will yield a similar configuration to the Bloom architecture
+    [bigscience/bloom](https://huggingface.co/bigscience/bloom).
+
+    Configuration objects inherit from [`PretrainedConfig`] and can be used to control the model outputs. Read the
+    documentation from [`PretrainedConfig`] for more information.
+
+
+    Args:
+        vocab_size (`int`, *optional*, defaults to 250880):
+            Vocabulary size of the Bloom model. Defines the maximum number of different tokens that can be represented
+            by the `inputs_ids` passed when calling [`BloomModel`]. Check [this
+            discussion](https://huggingface.co/bigscience/bloom/discussions/120#633d28389addb8530b406c2a) on how the
+            `vocab_size` has been defined.
+        hidden_size (`int`, *optional*, defaults to 64):
+            Dimensionality of the embeddings and hidden states.
+        n_layer (`int`, *optional*, defaults to 2):
+            Number of hidden layers in the Transformer encoder.
+        n_head (`int`, *optional*, defaults to 8):
+            Number of attention heads for each attention layer in the Transformer encoder.
+        layer_norm_epsilon (`float`, *optional*, defaults to 1e-5):
+            The epsilon to use in the layer normalization layers.
+        initializer_range (`float`, *optional*, defaults to 0.02):
+            The standard deviation of the truncated_normal_initializer for initializing all weight matrices.
+        apply_residual_connection_post_layernorm (`bool`, *optional*, defaults to `False`):
+            If enabled, use the layer norm of the hidden states as the residual in the transformer blocks
+        hidden_dropout (`float`, *optional*, defaults to 0.1):
+            Dropout rate of the dropout function on the bias dropout.
+        attention_dropout (`float`, *optional*, defaults to 0.1):
+            Dropout rate applied to the attention probs
+        use_cache (`bool`, *optional*, defaults to `True`):
+            Whether or not the model should return the last key/values attentions (not used by all models).
+        pretraining_tp (`int`, *optional*, defaults to `1`):
+            Experimental feature. Tensor parallelism rank used during pretraining with Megatron. Please refer to [this
+            document](https://huggingface.co/docs/transformers/parallelism) to understand more about it. This value is
+            necessary to ensure exact reproducibility of the pretraining results. Please refer to [this
+            issue](https://github.com/pytorch/pytorch/issues/76232). Note also that this is enabled only when
+            `slow_but_exact=True`.
+        slow_but_exact (`bool`, *optional*, defaults to `False`):
+            Experimental feature. Whether to use slow but exact implementation of the attention mechanism. While
+            merging the TP rank tensors, due to slicing operations the results may be slightly different between the
+            model trained on Megatron and our model. Please refer to [this
+            issue](https://github.com/pytorch/pytorch/issues/76232). A solution to obtain more accurate results is to
+            enable this feature. Enabling this will hurt the computational time of the inference. Will be probably
+            resolved in the future once the main model has been fine-tuned with TP_rank=1.
+
+    Example:
+
+    ```python
+    >>> from transformers import BloomConfig, BloomModel
+
+    >>> # Initializing a Bloom configuration
+    >>> configuration = BloomConfig()
+
+    >>> # Initializing a model (with random weights) from the configuration
+    >>> model = BloomModel(configuration)
+
+    >>> # Accessing the model configuration
+    >>> configuration = model.config
+    ```"""
+
+    model_type = "bloom"
+    keys_to_ignore_at_inference = ["past_key_values"]
+    attribute_map = {
+        "num_hidden_layers": "n_layer",
+        "num_attention_heads": "n_head",
+    }
+
+    def __init__(
+        self,
+        vocab_size=250880,
+        hidden_size=64,
+        n_layer=2,
+        n_head=8,
+        layer_norm_epsilon=1e-5,
+        initializer_range=0.02,
+        use_cache=True,
+        bos_token_id=1,
+        eos_token_id=2,
+        apply_residual_connection_post_layernorm=False,
+        hidden_dropout=0.0,
+        attention_dropout=0.0,
+        pretraining_tp=1,  # TP rank used when training with megatron
+        slow_but_exact=False,
+        **kwargs,
+    ):
+        self.vocab_size = vocab_size
+        # Backward compatibility with n_embed kwarg
+        n_embed = kwargs.pop("n_embed", None)
+        self.hidden_size = hidden_size if n_embed is None else n_embed
+        self.n_layer = n_layer
+        self.n_head = n_head
+        self.layer_norm_epsilon = layer_norm_epsilon
+        self.initializer_range = initializer_range
+        self.use_cache = use_cache
+        self.pretraining_tp = pretraining_tp
+        self.apply_residual_connection_post_layernorm = apply_residual_connection_post_layernorm
+        self.hidden_dropout = hidden_dropout
+        self.attention_dropout = attention_dropout
+
+        self.bos_token_id = bos_token_id
+        self.eos_token_id = eos_token_id
+        self.slow_but_exact = slow_but_exact
+
+        super().__init__(bos_token_id=bos_token_id, eos_token_id=eos_token_id, **kwargs)
+
+
+class BloomOnnxConfig(OnnxConfigWithPast):
+    torch_onnx_minimum_version = version.parse("1.12")
+
+    def __init__(
+        self,
+        config: PretrainedConfig,
+        task: str = "default",
+        patching_specs: List[PatchingSpec] = None,
+        use_past: bool = False,
+    ):
+        super().__init__(config, task=task, patching_specs=patching_specs, use_past=use_past)
+        if not getattr(self._config, "pad_token_id", None):
+            # TODO: how to do that better?
+            self._config.pad_token_id = 0
+
+    @property
+    def inputs(self) -> Mapping[str, Mapping[int, str]]:
+        common_inputs = OrderedDict({"input_ids": {0: "batch", 1: "sequence"}})
+        if self.use_past:
+            # BLOOM stores values on dynamic axis 2. For more details see: https://github.com/huggingface/transformers/pull/18344
+            self.fill_with_past_key_values_(common_inputs, direction="inputs", inverted_values_shape=True)
+            common_inputs["attention_mask"] = {0: "batch", 1: "past_sequence + sequence"}
+        else:
+            common_inputs["attention_mask"] = {0: "batch", 1: "sequence"}
+
+        return common_inputs
+
+    @property
+    def num_layers(self) -> int:
+        return self._config.n_layer
+
+    @property
+    def num_attention_heads(self) -> int:
+        return self._config.n_head
+
+    @property
+    def atol_for_validation(self) -> float:
+        return 1e-3
+
+    def generate_dummy_inputs(
+        self,
+        tokenizer: "PreTrainedTokenizer",
+        batch_size: int = -1,
+        seq_length: int = -1,
+        is_pair: bool = False,
+        framework: Optional["TensorType"] = None,
+    ) -> Mapping[str, Any]:
+        common_inputs = super(OnnxConfigWithPast, self).generate_dummy_inputs(
+            tokenizer, batch_size=batch_size, seq_length=seq_length, is_pair=is_pair, framework=framework
+        )
+
+        # We need to order the input in the way they appears in the forward()
+        ordered_inputs = OrderedDict({"input_ids": common_inputs["input_ids"]})
+
+        # Need to add the past_keys
+        if self.use_past:
+            if not is_torch_available():
+                raise ValueError("Cannot generate dummy past_keys inputs without PyTorch installed.")
+            else:
+                import torch
+
+                batch, seqlen = common_inputs["input_ids"].shape
+                # Not using the same length for past_key_values
+                past_key_values_length = seqlen + 2
+                head_dim = self._config.hidden_size // self.num_attention_heads
+                past_key_shape = (
+                    batch * self.num_attention_heads,
+                    head_dim,
+                    past_key_values_length,
+                )
+                past_value_shape = (
+                    batch * self.num_attention_heads,
+                    past_key_values_length,
+                    head_dim,
+                )
+                ordered_inputs["past_key_values"] = [
+                    (torch.zeros(past_key_shape), torch.zeros(past_value_shape)) for _ in range(self.num_layers)
+                ]
+
+        ordered_inputs["attention_mask"] = common_inputs["attention_mask"]
+        if self.use_past:
+            mask_dtype = ordered_inputs["attention_mask"].dtype
+            ordered_inputs["attention_mask"] = torch.cat(
+                [ordered_inputs["attention_mask"], torch.ones(batch, past_key_values_length, dtype=mask_dtype)], dim=1
+            )
+
+        return ordered_inputs
+
+    @property
+    def default_onnx_opset(self) -> int:
+        return 13

llmeval-env/lib/python3.10/site-packages/transformers/models/bloom/convert_bloom_original_checkpoint_to_pytorch.py

@@ -0,0 +1,255 @@
+# coding=utf-8
+# Copyright 2022 The HuggingFace Inc. team.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Convert BigScience BLOOM checkpoint."""
+
+
+import argparse
+import json
+import os
+import re
+
+import torch
+
+from transformers import BloomConfig, BloomModel
+from transformers.file_utils import CONFIG_NAME, WEIGHTS_NAME
+from transformers.utils import logging
+
+
+logging.set_verbosity_info()
+
+WEIGHTS_TO_AVERAGE_ENDSWITH = [
+    "word_embeddings_layernorm.weight",
+    "word_embeddings_layernorm.bias",
+    "input_layernorm.weight",
+    "input_layernorm.bias",
+    "post_attention_layernorm.weight",
+    "post_attention_layernorm.bias",
+    "self_attention.dense.bias",
+    "mlp.dense_4h_to_h.bias",
+    "ln_f.weight",
+    "ln_f.bias",
+]
+
+WEIGHTS_WITH_ROW_PARALLELISM_CONTAIN = [
+    "mlp.dense_4h_to_h.weight",
+    "self_attention.dense.weight",
+]
+
+
+def layer_name_mapping(key, file):
+    """Convert Megatron-DeepSpeed TP/PP weights mapping in transformers PP only"""
+    # Handle first and last layers
+    layer_rename_map = {
+        "word_embeddings.weight": "word_embeddings.weight",
+        "word_embeddings.norm.weight": "word_embeddings_layernorm.weight",
+        "word_embeddings.norm.bias": "word_embeddings_layernorm.bias",
+        "weight": "ln_f.weight",
+        "bias": "ln_f.bias",
+    }
+
+    if key in layer_rename_map:
+        return layer_rename_map[key]
+
+    # Handle transformer blocks
+    layer_number = int(re.match(r".*layer_(\d*).*", file)[1])
+    layer_number -= 3
+    return f"h.{layer_number}." + key
+
+
+def get_dtype_size(dtype):
+    if dtype == torch.bool:
+        return 1 / 8
+    bit_search = re.search(r"[^\d](\d+)$", str(dtype))
+    if bit_search is None:
+        raise ValueError(f"`dtype` is not a valid dtype: {dtype}.")
+    bit_size = int(bit_search.groups()[0])
+    return bit_size // 8
+
+
+def convert_bloom_checkpoint_to_pytorch(
+    bloom_checkpoint_path, bloom_config_file, pytorch_dump_folder_path, shard_model, pretraining_tp
+):
+    # Construct model
+    if bloom_config_file == "":
+        config = BloomConfig()
+    else:
+        config = BloomConfig.from_json_file(bloom_config_file)
+
+    if shard_model:
+        file_names = os.listdir(bloom_checkpoint_path)
+        file_names = sorted(filter(lambda s: s.startswith("layer") and "model_00" in s, file_names))
+
+        index_dict = {"weight_map": {}, "metadata": {}}
+        total_size = 0
+
+        missing_keys = None
+
+        config = BloomConfig()
+
+        for j, file in enumerate(file_names):
+            print("Processing file: {}".format(file))
+            tensors = None
+
+            for i in range(pretraining_tp):
+                # load all TP files
+                f_name = file.replace("model_00", f"model_0{i}")
+                temp = torch.load(os.path.join(bloom_checkpoint_path, f_name), map_location="cpu")
+
+                # Rename keys in the transformers names
+                keys = list(temp.keys())
+                for key in keys:
+                    temp[layer_name_mapping(key, file)] = temp.pop(key)
+
+                if tensors is None:
+                    tensors = temp
+                else:
+                    for key in tensors.keys():
+                        if any(key.endswith(end) for end in WEIGHTS_TO_AVERAGE_ENDSWITH):
+                            # We average (sum and then divide) some weights accross TP ranks (see https://github.com/bigscience-workshop/Megatron-DeepSpeed/blob/olruwase/sync_layer_norms/megatron/training.py#L425)
+                            tensors[key] += temp[key]
+                        else:
+                            # Some weights are RowParallelLinear in Megatron-Deepspeed, others are ColumnParallel
+                            cat_dim = 1 if any(text in key for text in WEIGHTS_WITH_ROW_PARALLELISM_CONTAIN) else 0
+                            # We concatenate these weights accross TP ranks
+                            tensors[key] = torch.cat([tensors[key], temp[key]], dim=cat_dim)
+
+            # Divide by the number of TP the weights we want to average
+            for key in tensors.keys():
+                if any(key.endswith(end) for end in WEIGHTS_TO_AVERAGE_ENDSWITH):
+                    tensors[key] = tensors[key] / pretraining_tp
+            torch.save(
+                tensors,
+                os.path.join(
+                    pytorch_dump_folder_path,
+                    "pytorch_model_{}-of-{}.bin".format(str(j + 1).zfill(5), str(len(file_names)).zfill(5)),
+                ),
+            )
+
+            for key in tensors.keys():
+                value = tensors[key]
+                total_size += value.numel() * get_dtype_size(value.dtype)
+                if key not in index_dict["weight_map"]:
+                    index_dict["weight_map"][key] = "pytorch_model_{}-of-{}.bin".format(
+                        str(j + 1).zfill(5), str(len(file_names)).zfill(5)
+                    )
+
+        config = BloomConfig()
+        pytorch_config_dump_path = pytorch_dump_folder_path + "/" + CONFIG_NAME
+        index_dict["metadata"]["total_size"] = total_size
+        with open(pytorch_config_dump_path, "w", encoding="utf-8") as f:
+            f.write(config.to_json_string())
+        with open(os.path.join(pytorch_dump_folder_path, WEIGHTS_NAME + ".index.json"), "w", encoding="utf-8") as f:
+            json_config = json.dumps(index_dict, indent=2, sort_keys=True) + "\n"
+            f.write(json_config)
+    else:
+        model = BloomModel(config)
+
+        file_names = os.listdir(bloom_checkpoint_path)
+        file_names = sorted(filter(lambda s: s.startswith("layer") and "model_00" in s, file_names))
+
+        missing_keys = None
+        for i, file in enumerate(file_names):
+            tensors = None
+            for i in range(pretraining_tp):
+                # load all TP files
+                f_name = file.replace("model_00", f"model_0{i}")
+                temp = torch.load(os.path.join(bloom_checkpoint_path, f_name), map_location="cpu")
+
+                # Rename keys in the transformers names
+                keys = list(temp.keys())
+                for key in keys:
+                    temp[layer_name_mapping(key, file)] = temp.pop(key)
+
+                if tensors is None:
+                    tensors = temp
+                else:
+                    for key in tensors.keys():
+                        # We average (sum and then divide) some weights accross TP ranks (see https://github.com/bigscience-workshop/Megatron-DeepSpeed/blob/olruwase/sync_layer_norms/megatron/training.py#L425)
+                        if any(key.endswith(end) for end in WEIGHTS_TO_AVERAGE_ENDSWITH):
+                            tensors[key] += temp[key]
+                        else:
+                            # Some weights are RowParallelLinear in Megatron-Deepspeed, others are ColumnParallel
+                            cat_dim = 1 if any(text in key for text in WEIGHTS_WITH_ROW_PARALLELISM_CONTAIN) else 0
+                            # We concatenate these weights accross TP ranks
+                            tensors[key] = torch.cat([tensors[key], temp[key]], dim=cat_dim)
+
+            # Divide by the number of TP the weights we want to average
+            for key in tensors.keys():
+                if any(key.endswith(end) for end in WEIGHTS_TO_AVERAGE_ENDSWITH):
+                    tensors[key] = tensors[key] / pretraining_tp
+
+            other_keys = model.load_state_dict(tensors, strict=False)
+            assert not other_keys.unexpected_keys, f"The keys {other_keys.unexpected_keys} are unexpected"
+            if missing_keys is None:
+                missing_keys = set(other_keys.missing_keys)
+            else:
+                missing_keys = missing_keys.intersection(set(other_keys.missing_keys))
+
+        assert not missing_keys, f"The keys {missing_keys} are missing"
+
+        # Save pytorch-model
+        os.makedirs(pytorch_dump_folder_path, exist_ok=True)
+        pytorch_weights_dump_path = pytorch_dump_folder_path + "/" + WEIGHTS_NAME
+        pytorch_config_dump_path = pytorch_dump_folder_path + "/" + CONFIG_NAME
+        print(f"Save PyTorch model to {pytorch_weights_dump_path} with dtype {config.torch_dtype}")
+        if config.torch_dtype is not None:
+            model = model.to(config.torch_dtype)
+        torch.save(model.state_dict(), pytorch_weights_dump_path)
+        print(f"Save configuration file to {pytorch_config_dump_path}")
+        with open(pytorch_config_dump_path, "w", encoding="utf-8") as f:
+            f.write(config.to_json_string())
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    # Required parameters
+    parser.add_argument(
+        "--bloom_checkpoint_path",
+        default=None,
+        type=str,
+        required=True,
+        help="Path to the Megatron-LM checkpoint path.",
+    )
+    parser.add_argument(
+        "--pytorch_dump_folder_path", default=None, type=str, required=True, help="Path to the output PyTorch model."
+    )
+    parser.add_argument(
+        "--bloom_config_file",
+        default="",
+        type=str,
+        help=(
+            "An optional config json file corresponding to the pre-trained model. \n"
+            "This specifies the model architecture."
+        ),
+    )
+    parser.add_argument(
+        "--shard_model",
+        action="store_true",
+        help="An optional setting to shard the output model \nThis enables sharding the converted checkpoint",
+    )
+    parser.add_argument(
+        "--pretraining_tp",
+        default=4,
+        type=int,
+        help="Pretraining TP rank that has been used when training the model in Megatron-LM \n",
+    )
+    args = parser.parse_args()
+    convert_bloom_checkpoint_to_pytorch(
+        args.bloom_checkpoint_path,
+        args.bloom_config_file,
+        args.pytorch_dump_folder_path,
+        args.shard_model,
+        args.pretraining_tp,
+    )

llmeval-env/lib/python3.10/site-packages/transformers/models/bloom/modeling_bloom.py

@@ -0,0 +1,1243 @@
+# coding=utf-8
+# Copyright 2022 HuggingFace Inc. team and BigScience workshop.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""PyTorch BLOOM model."""
+
+import math
+import warnings
+from typing import Optional, Tuple, Union
+
+import torch
+import torch.utils.checkpoint
+from torch import nn
+from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, LayerNorm, MSELoss
+from torch.nn import functional as F
+
+from ...file_utils import add_code_sample_docstrings, add_start_docstrings, add_start_docstrings_to_model_forward
+from ...modeling_attn_mask_utils import _prepare_4d_causal_attention_mask
+from ...modeling_outputs import (
+    BaseModelOutputWithPastAndCrossAttentions,
+    CausalLMOutputWithCrossAttentions,
+    QuestionAnsweringModelOutput,
+    SequenceClassifierOutputWithPast,
+    TokenClassifierOutput,
+)
+from ...modeling_utils import PreTrainedModel
+from ...utils import logging
+from .configuration_bloom import BloomConfig
+
+
+logger = logging.get_logger(__name__)
+
+_CHECKPOINT_FOR_DOC = "bigscience/bloom-560m"
+_CONFIG_FOR_DOC = "BloomConfig"
+
+
+from ..deprecated._archive_maps import BLOOM_PRETRAINED_MODEL_ARCHIVE_LIST  # noqa: F401, E402
+
+
+def build_alibi_tensor(attention_mask: torch.Tensor, num_heads: int, dtype: torch.dtype) -> torch.Tensor:
+    """
+    Link to paper: https://arxiv.org/abs/2108.12409 Alibi tensor is not causal as the original paper mentions, it
+    relies on a translation invariance of softmax for quick implementation: with l being a tensor, and a fixed value
+    `softmax(l+a) = softmax(l)`. Based on
+    https://github.com/ofirpress/attention_with_linear_biases/blob/a35aaca144e0eb6b789dfcb46784c4b8e31b7983/fairseq/models/transformer.py#L742
+    TODO @thomasw21 this doesn't work as nicely due to the masking strategy, and so masking varies slightly.
+
+    Args:
+    Returns tensor shaped (batch_size * num_heads, 1, max_seq_len)
+        attention_mask (`torch.Tensor`):
+            Token-wise attention mask, this should be of shape (batch_size, max_seq_len).
+        num_heads (`int`, *required*):
+            number of heads
+        dtype (`torch.dtype`, *optional*, default=`torch.bfloat16`):
+            dtype of the output tensor
+    """
+    batch_size, seq_length = attention_mask.shape
+    closest_power_of_2 = 2 ** math.floor(math.log2(num_heads))
+    base = torch.tensor(
+        2 ** (-(2 ** -(math.log2(closest_power_of_2) - 3))), device=attention_mask.device, dtype=torch.float32
+    )
+    powers = torch.arange(1, 1 + closest_power_of_2, device=attention_mask.device, dtype=torch.int32)
+    slopes = torch.pow(base, powers)
+
+    if closest_power_of_2 != num_heads:
+        extra_base = torch.tensor(
+            2 ** (-(2 ** -(math.log2(2 * closest_power_of_2) - 3))), device=attention_mask.device, dtype=torch.float32
+        )
+        num_remaining_heads = min(closest_power_of_2, num_heads - closest_power_of_2)
+        extra_powers = torch.arange(1, 1 + 2 * num_remaining_heads, 2, device=attention_mask.device, dtype=torch.int32)
+        slopes = torch.cat([slopes, torch.pow(extra_base, extra_powers)], dim=0)
+
+    # Note: alibi will added to the attention bias that will be applied to the query, key product of attention
+    # => therefore alibi will have to be of shape (batch_size, num_heads, query_length, key_length)
+    # => here we set (batch_size=1, num_heads=num_heads, query_length=1, key_length=max_length)
+    # => the query_length dimension will then be broadcasted correctly
+    # This is more or less identical to T5's relative position bias:
+    # https://github.com/huggingface/transformers/blob/f681437203baa7671de3174b0fa583c349d9d5e1/src/transformers/models/t5/modeling_t5.py#L527
+    arange_tensor = ((attention_mask.cumsum(dim=-1) - 1) * attention_mask)[:, None, :]
+    alibi = slopes[..., None] * arange_tensor
+    return alibi.reshape(batch_size * num_heads, 1, seq_length).to(dtype)
+
+
+def dropout_add(x: torch.Tensor, residual: torch.Tensor, prob: float, training: bool) -> torch.Tensor:
+    """
+    Dropout add function
+
+    Args:
+        x (`torch.tensor`, *required*):
+            input tensor
+        residual (`torch.tensor`, *required*):
+            residual tensor
+        prob (`float`, *required*):
+            dropout probability
+        training (`bool`, *required*):
+            training mode
+    """
+    out = F.dropout(x, p=prob, training=training)
+    out = residual + out
+    return out
+
+
+def bloom_gelu_forward(x: torch.Tensor) -> torch.Tensor:
+    """
+    Custom bias GELU function. Adapted from Megatron-DeepSpeed code. Here we use a simple implementation (inference) to
+    make the model jitable.
+
+    Args:
+        x (`torch.tensor`, *required*):
+            input hidden states
+    """
+    return x * 0.5 * (1.0 + torch.tanh(0.79788456 * x * (1 + 0.044715 * x * x)))
+
+
+def bloom_gelu_back(g: torch.Tensor, x: torch.Tensor) -> torch.Tensor:
+    """
+    gradient of tanh approximation of gelu gradient of actual gelu is: 0.5 * (1. + torch.erf(x * 0.70710678)) +
+    0.3989423 * x * torch.exp(-0.5 * x * x)
+
+    Args:
+        g (`torch.tensor`, *required*):
+            gradient output tensor
+        x (`torch.tensor`, *required*):
+            input tensor
+    """
+    x = x[0]  # x is a tuple of 1 element, needs to unpack it first
+    tanh_out = torch.tanh(0.79788456 * x * (1 + 0.044715 * x * x))
+    # sqrt(2/pi) * 3 * 0.044715 -> 0.1070322243
+    ff = 0.5 * x * ((1 - tanh_out * tanh_out) * (0.79788456 + 0.1070322243 * x * x)) + 0.5 * (1 + tanh_out)
+    return ff * g
+
+
+class GeLUFunction(torch.autograd.Function):
+    @staticmethod
+    def forward(ctx, input: torch.Tensor) -> torch.Tensor:
+        ctx.save_for_backward(input)
+        return bloom_gelu_forward(input)
+
+    @staticmethod
+    def backward(ctx, grad_output: torch.Tensor) -> torch.Tensor:
+        input = ctx.saved_tensors
+        tmp = bloom_gelu_back(grad_output, input)
+        return tmp
+
+
+class BloomGelu(nn.Module):
+    """
+    BloomBiasGelu wrapper function that make use of the simple function on inference mode to make the model
+    torchscriptable and use the autograd function in training mode to get the accurate results of the gradients Partly
+    copied from Megatron-DeepSpeed code and adapted for our needs
+
+    See here why autograd functions are not torchscriptable: https://github.com/pytorch/pytorch/issues/22329
+    """
+
+    def __init__(self):
+        super().__init__()
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        if self.training:
+            return GeLUFunction.apply(x)
+        else:
+            return bloom_gelu_forward(x)
+
+
+class BloomAttention(nn.Module):
+    def __init__(self, config: BloomConfig):
+        super().__init__()
+
+        self.pretraining_tp = config.pretraining_tp
+        self.slow_but_exact = config.slow_but_exact
+
+        self.hidden_size = config.hidden_size
+        self.num_heads = config.n_head
+        self.head_dim = self.hidden_size // self.num_heads
+        self.split_size = self.hidden_size
+        self.hidden_dropout = config.hidden_dropout
+
+        if self.head_dim * self.num_heads != self.hidden_size:
+            raise ValueError(
+                f"`hidden_size` must be divisible by num_heads (got `hidden_size`: {self.hidden_size} and `num_heads`:"
+                f" {self.num_heads})."
+            )
+
+        # Layer-wise attention scaling
+        self.inv_norm_factor = 1.0 / math.sqrt(self.head_dim)
+        self.beta = 1.0
+
+        self.query_key_value = nn.Linear(self.hidden_size, 3 * self.hidden_size, bias=True)
+        self.dense = nn.Linear(self.hidden_size, self.hidden_size)
+        self.attention_dropout = nn.Dropout(config.attention_dropout)
+
+    def _split_heads(self, fused_qkv: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]:
+        """
+        Split the last dimension into (num_heads, head_dim) without making any copies, results share same memory
+        storage as `fused_qkv`
+
+        Args:
+            fused_qkv (`torch.tensor`, *required*): [batch_size, seq_length, num_heads * 3 * head_dim]
+
+        Returns:
+            query: [batch_size, seq_length, num_heads, head_dim] key: [batch_size, seq_length, num_heads, head_dim]
+            value: [batch_size, seq_length, num_heads, head_dim]
+        """
+        batch_size, seq_length, three_times_hidden_size = fused_qkv.shape
+        fused_qkv = fused_qkv.view(batch_size, seq_length, self.num_heads, 3, self.head_dim)
+        return fused_qkv[..., 0, :], fused_qkv[..., 1, :], fused_qkv[..., 2, :]
+
+    def _merge_heads(self, x: torch.Tensor) -> torch.Tensor:
+        """
+        Merge heads together over the last dimension
+
+        Args:
+            x (`torch.tensor`, *required*): [batch_size * num_heads, seq_length, head_dim]
+
+        Returns:
+            torch.tensor: [batch_size, seq_length, num_heads * head_dim]
+        """
+        # What we want to achieve is:
+        # batch_size * num_heads, seq_length, head_dim -> batch_size, seq_length, num_heads * head_dim
+        batch_size_and_num_heads, seq_length, _ = x.shape
+        batch_size = batch_size_and_num_heads // self.num_heads
+
+        # First view to decompose the batch size
+        # batch_size * num_heads, seq_length, head_dim -> batch_size, num_heads, seq_length, head_dim
+        x = x.view(batch_size, self.num_heads, seq_length, self.head_dim)
+
+        # batch_size, num_heads, seq_length, head_dim -> batch_size, seq_length, num_heads, head_dim
+        x = x.permute(0, 2, 1, 3)
+
+        # batch_size, seq_length, num_heads, head_dim -> batch_size, seq_length, num_heads * head_dim
+        return x.reshape(batch_size, seq_length, self.num_heads * self.head_dim)
+
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        residual: torch.Tensor,
+        alibi: torch.Tensor,
+        attention_mask: torch.Tensor,
+        layer_past: Optional[Tuple[torch.Tensor, torch.Tensor]] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        use_cache: bool = False,
+        output_attentions: bool = False,
+    ):
+        fused_qkv = self.query_key_value(hidden_states)  # [batch_size, seq_length, 3 x hidden_size]
+
+        # 3 x [batch_size, seq_length, num_heads, head_dim]
+        (query_layer, key_layer, value_layer) = self._split_heads(fused_qkv)
+
+        batch_size, q_length, _, _ = query_layer.shape
+
+        query_layer = query_layer.transpose(1, 2).reshape(batch_size * self.num_heads, q_length, self.head_dim)
+        key_layer = key_layer.permute(0, 2, 3, 1).reshape(batch_size * self.num_heads, self.head_dim, q_length)
+        value_layer = value_layer.transpose(1, 2).reshape(batch_size * self.num_heads, q_length, self.head_dim)
+        if layer_past is not None:
+            past_key, past_value = layer_past
+            # concatenate along seq_length dimension:
+            #  - key: [batch_size * self.num_heads, head_dim, kv_length]
+            #  - value: [batch_size * self.num_heads, kv_length, head_dim]
+            key_layer = torch.cat((past_key, key_layer), dim=2)
+            value_layer = torch.cat((past_value, value_layer), dim=1)
+
+        _, _, kv_length = key_layer.shape
+
+        if use_cache is True:
+            present = (key_layer, value_layer)
+        else:
+            present = None
+
+        # [batch_size * num_heads, q_length, kv_length]
+        # we use `torch.Tensor.baddbmm` instead of `torch.baddbmm` as the latter isn't supported by TorchScript v1.11
+        matmul_result = alibi.baddbmm(
+            batch1=query_layer,
+            batch2=key_layer,
+            beta=self.beta,
+            alpha=self.inv_norm_factor,
+        )
+
+        # change view to [batch_size, num_heads, q_length, kv_length]
+        attention_scores = matmul_result.view(batch_size, self.num_heads, q_length, kv_length)
+
+        # cast attention scores to fp32, compute scaled softmax and cast back to initial dtype - [batch_size, num_heads, q_length, kv_length]
+        input_dtype = attention_scores.dtype
+        # `float16` has a minimum value of -65504.0, whereas `bfloat16` and `float32` have a minimum value of `-3.4e+38`
+        if input_dtype == torch.float16:
+            attention_scores = attention_scores.to(torch.float)
+        attn_weights = torch.masked_fill(attention_scores, attention_mask, torch.finfo(attention_scores.dtype).min)
+        attention_probs = F.softmax(attn_weights, dim=-1, dtype=torch.float32).to(input_dtype)
+
+        # [batch_size, num_heads, q_length, kv_length]
+        attention_probs = self.attention_dropout(attention_probs)
+
+        if head_mask is not None:
+            attention_probs = attention_probs * head_mask
+
+        # change view [batch_size x num_heads, q_length, kv_length]
+        attention_probs_reshaped = attention_probs.view(batch_size * self.num_heads, q_length, kv_length)
+
+        # matmul: [batch_size * num_heads, q_length, head_dim]
+        context_layer = torch.bmm(attention_probs_reshaped, value_layer)
+
+        # change view [batch_size, q_length, num_heads * head_dim]
+        context_layer = self._merge_heads(context_layer)
+
+        # aggregate results across tp ranks. See here: https://github.com/pytorch/pytorch/issues/76232
+        if self.pretraining_tp > 1 and self.slow_but_exact:
+            slices = self.hidden_size / self.pretraining_tp
+            output_tensor = torch.zeros_like(context_layer)
+            for i in range(self.pretraining_tp):
+                output_tensor = output_tensor + F.linear(
+                    context_layer[:, :, int(i * slices) : int((i + 1) * slices)],
+                    self.dense.weight[:, int(i * slices) : int((i + 1) * slices)],
+                )
+        else:
+            output_tensor = self.dense(context_layer)
+
+        output_tensor = dropout_add(output_tensor, residual, self.hidden_dropout, self.training)
+
+        outputs = (output_tensor, present)
+        if output_attentions:
+            outputs += (attention_probs,)
+
+        return outputs
+
+
+class BloomMLP(nn.Module):
+    def __init__(self, config: BloomConfig):
+        super().__init__()
+        hidden_size = config.hidden_size
+
+        self.pretraining_tp = config.pretraining_tp
+        self.slow_but_exact = config.slow_but_exact
+        self.dense_h_to_4h = nn.Linear(hidden_size, 4 * hidden_size)
+        self.gelu_impl = BloomGelu()
+        self.dense_4h_to_h = nn.Linear(4 * hidden_size, hidden_size)
+        self.hidden_dropout = config.hidden_dropout
+
+    def forward(self, hidden_states: torch.Tensor, residual: torch.Tensor) -> torch.Tensor:
+        hidden_states = self.gelu_impl(self.dense_h_to_4h(hidden_states))
+
+        if self.pretraining_tp > 1 and self.slow_but_exact:
+            intermediate_output = torch.zeros_like(residual)
+            slices = self.dense_4h_to_h.weight.shape[-1] / self.pretraining_tp
+            for i in range(self.pretraining_tp):
+                intermediate_output = intermediate_output + F.linear(
+                    hidden_states[:, :, int(i * slices) : int((i + 1) * slices)],
+                    self.dense_4h_to_h.weight[:, int(i * slices) : int((i + 1) * slices)],
+                )
+        else:
+            intermediate_output = self.dense_4h_to_h(hidden_states)
+
+        output = dropout_add(intermediate_output, residual, self.hidden_dropout, self.training)
+
+        return output
+
+
+class BloomBlock(nn.Module):
+    def __init__(self, config: BloomConfig):
+        super().__init__()
+        hidden_size = config.hidden_size
+
+        self.input_layernorm = LayerNorm(hidden_size, eps=config.layer_norm_epsilon)
+        self.num_heads = config.n_head
+        self.self_attention = BloomAttention(config)
+        self.post_attention_layernorm = LayerNorm(hidden_size, eps=config.layer_norm_epsilon)
+
+        self.mlp = BloomMLP(config)
+
+        self.apply_residual_connection_post_layernorm = config.apply_residual_connection_post_layernorm
+        self.hidden_dropout = config.hidden_dropout
+
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        alibi: torch.Tensor,
+        attention_mask: torch.Tensor,
+        layer_past: Optional[Tuple[torch.Tensor, torch.Tensor]] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        use_cache: bool = False,
+        output_attentions: bool = False,
+    ):
+        # hidden_states: [batch_size, seq_length, hidden_size]
+
+        # Layer norm at the beginning of the transformer layer.
+        layernorm_output = self.input_layernorm(hidden_states)
+
+        # Layer norm post the self attention.
+        if self.apply_residual_connection_post_layernorm:
+            residual = layernorm_output
+        else:
+            residual = hidden_states
+
+        # Self attention.
+        attn_outputs = self.self_attention(
+            layernorm_output,
+            residual,
+            layer_past=layer_past,
+            attention_mask=attention_mask,
+            alibi=alibi,
+            head_mask=head_mask,
+            use_cache=use_cache,
+            output_attentions=output_attentions,
+        )
+
+        attention_output = attn_outputs[0]
+
+        outputs = attn_outputs[1:]
+
+        layernorm_output = self.post_attention_layernorm(attention_output)
+
+        # Get residual
+        if self.apply_residual_connection_post_layernorm:
+            residual = layernorm_output
+        else:
+            residual = attention_output
+
+        # MLP.
+        output = self.mlp(layernorm_output, residual)
+
+        if use_cache:
+            outputs = (output,) + outputs
+        else:
+            outputs = (output,) + outputs[1:]
+
+        return outputs  # hidden_states, present, attentions
+
+
+class BloomPreTrainedModel(PreTrainedModel):
+    config_class = BloomConfig
+    base_model_prefix = "transformer"
+    supports_gradient_checkpointing = True
+    _no_split_modules = ["BloomBlock"]
+    _skip_keys_device_placement = "past_key_values"
+
+    def __init__(self, *inputs, **kwargs):
+        super().__init__(*inputs, **kwargs)
+
+    def _init_weights(self, module: nn.Module):
+        """Initialize the weights."""
+        if isinstance(module, nn.Linear):
+            # Slightly different from the TF version which uses truncated_normal for initialization
+            # cf https://github.com/pytorch/pytorch/pull/5617
+            module.weight.data.normal_(mean=0.0, std=self.config.initializer_range)
+            if module.bias is not None:
+                module.bias.data.zero_()
+        elif isinstance(module, nn.Embedding):
+            module.weight.data.normal_(mean=0.0, std=self.config.initializer_range)
+            if module.padding_idx is not None:
+                module.weight.data[module.padding_idx].zero_()
+        elif isinstance(module, LayerNorm):
+            module.bias.data.zero_()
+            module.weight.data.fill_(1.0)
+
+    @staticmethod
+    def _convert_to_standard_cache(
+        past_key_value: Tuple[Tuple[torch.Tensor, torch.Tensor]], batch_size: int
+    ) -> Tuple[Tuple[torch.Tensor, torch.Tensor]]:
+        """
+        Standardizes the format of the cache so as to match most implementations, i.e. to tuple(tuple([batch_size,
+        num_heads, ...]))
+        """
+        batch_size_times_num_heads, head_dim, seq_length = past_key_value[0][0].shape
+        num_heads = batch_size_times_num_heads // batch_size
+        # key: [batch_size * num_heads, head_dim, seq_length] -> [batch_size, num_heads, head_dim, seq_length]
+        # value: [batch_size * num_heads, seq_length, head_dim] -> [batch_size, num_heads, seq_length, head_dim]
+        return tuple(
+            (
+                layer_past[0].view(batch_size, num_heads, head_dim, seq_length),
+                layer_past[1].view(batch_size, num_heads, seq_length, head_dim),
+            )
+            for layer_past in past_key_value
+        )
+
+    @staticmethod
+    def _convert_to_bloom_cache(
+        past_key_value: Tuple[Tuple[torch.Tensor, torch.Tensor]],
+    ) -> Tuple[Tuple[torch.Tensor, torch.Tensor]]:
+        """
+        Converts the cache to the format expected by Bloom, i.e. to tuple(tuple([batch_size * num_heads, ...]))
+        """
+        batch_size, num_heads, head_dim, seq_length = past_key_value[0][0].shape
+        batch_size_times_num_heads = batch_size * num_heads
+        # key:  [batch_size, num_heads, head_dim, seq_length] -> [batch_size * num_heads, head_dim, seq_length]
+        # value: [batch_size, num_heads, seq_length, head_dim] -> [batch_size * num_heads, seq_length, head_dim]
+        return tuple(
+            (
+                layer_past[0].view(batch_size_times_num_heads, head_dim, seq_length),
+                layer_past[1].view(batch_size_times_num_heads, seq_length, head_dim),
+            )
+            for layer_past in past_key_value
+        )
+
+
+BLOOM_START_DOCSTRING = r"""
+
+    This model inherits from [`PreTrainedModel`]. Check the superclass documentation for the generic methods the
+    library implements for all its model (such as downloading or saving, resizing the input embeddings etc.)
+
+    This model is also a PyTorch [torch.nn.Module](https://pytorch.org/docs/stable/nn.html#torch.nn.Module) subclass.
+    Use it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage
+    and behavior.
+
+    Parameters:
+        config ([`BloomConfig`]): Model configuration class with all the parameters of the model.
+            Initializing with a config file does not load the weights associated with the model, only the
+            configuration. Check out the [`~PreTrainedModel.from_pretrained`] method to load the model weights.
+"""
+
+BLOOM_INPUTS_DOCSTRING = r"""
+    Args:
+        input_ids (`torch.LongTensor` of shape `(batch_size, input_ids_length)`):
+            `input_ids_length` = `sequence_length` if `past_key_values` is `None` else `past_key_values[0][0].shape[2]`
+            (`sequence_length` of input past key value states). Indices of input sequence tokens in the vocabulary.
+
+            If `past_key_values` is used, only `input_ids` that do not have their past calculated should be passed as
+            `input_ids`.
+
+            Indices can be obtained using [`AutoTokenizer`]. See [`PreTrainedTokenizer.encode`] and
+            [`PreTrainedTokenizer.__call__`] for details.
+
+            [What are input IDs?](../glossary#input-ids)
+        past_key_values (`Tuple[Tuple[torch.Tensor]]` of length `config.n_layers`):
+            Contains precomputed hidden-states (key and values in the attention blocks) as computed by the model (see
+            `past_key_values` output below). Can be used to speed up sequential decoding. The `input_ids` which have
+            their past given to this model should not be passed as `input_ids` as they have already been computed.
+
+            Each element of `past_key_values` is a tuple (past_key, past_value):
+            - past_key: [batch_size * num_heads, head_dim, kv_length]
+            - past_value: [batch_size * num_heads, kv_length, head_dim]
+        attention_mask (`torch.FloatTensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Mask to avoid performing attention on padding token indices. Mask values selected in `[0, 1]`:
+
+            - 1 for tokens that are **not masked**,
+            - 0 for tokens that are **masked**.
+
+            [What are attention masks?](../glossary#attention-mask)
+        head_mask (`torch.FloatTensor` of shape `(num_heads,)` or `(num_layers, num_heads)`, *optional*):
+            Mask to nullify selected heads of the self-attention modules. Mask values selected in `[0, 1]`:
+
+            - 1 indicates the head is **not masked**,
+            - 0 indicates the head is **masked**.
+
+        inputs_embeds (`torch.FloatTensor` of shape `(batch_size, sequence_length, hidden_size)`, *optional*):
+            Optionally, instead of passing `input_ids` you can choose to directly pass an embedded representation. This
+            is useful if you want more control over how to convert `input_ids` indices into associated vectors than the
+            model's internal embedding lookup matrix.
+
+            If `past_key_values` is used, optionally only the last `inputs_embeds` have to be input (see
+            `past_key_values`).
+        use_cache (`bool`, *optional*):
+            If set to `True`, `past_key_values` key value states are returned and can be used to speed up decoding (see
+            `past_key_values`).
+        output_attentions (`bool`, *optional*):
+            Whether or not to return the attentions tensors of all attention layers. See `attentions` under returned
+            tensors for more detail.
+        output_hidden_states (`bool`, *optional*):
+            Whether or not to return the hidden states of all layers. See `hidden_states` under returned tensors for
+            more detail.
+        return_dict (`bool`, *optional*):
+            Whether or not to return a [`~file_utils.ModelOutput`] instead of a plain tuple.
+"""
+
+
+@add_start_docstrings(
+    "The bare Bloom Model transformer outputting raw hidden-states without any specific head on top.",
+    BLOOM_START_DOCSTRING,
+)
+class BloomModel(BloomPreTrainedModel):
+    def __init__(self, config: BloomConfig):
+        super().__init__(config)
+
+        self.embed_dim = config.hidden_size
+        self.num_heads = config.n_head
+
+        # Embedding + LN Embedding
+        self.word_embeddings = nn.Embedding(config.vocab_size, self.embed_dim)
+        self.word_embeddings_layernorm = LayerNorm(self.embed_dim, eps=config.layer_norm_epsilon)
+
+        # Transformer blocks
+        self.h = nn.ModuleList([BloomBlock(config) for _ in range(config.num_hidden_layers)])
+
+        # Final Layer Norm
+        self.ln_f = LayerNorm(self.embed_dim, eps=config.layer_norm_epsilon)
+
+        self.gradient_checkpointing = False
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    def build_alibi_tensor(self, attention_mask: torch.Tensor, num_heads: int, dtype: torch.dtype) -> torch.Tensor:
+        return build_alibi_tensor(attention_mask, num_heads, dtype)
+
+    def get_input_embeddings(self):
+        return self.word_embeddings
+
+    def set_input_embeddings(self, new_embeddings: torch.Tensor):
+        self.word_embeddings = new_embeddings
+
+    @add_start_docstrings_to_model_forward(BLOOM_INPUTS_DOCSTRING)
+    @add_code_sample_docstrings(
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=BaseModelOutputWithPastAndCrossAttentions,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        past_key_values: Optional[Tuple[Tuple[torch.Tensor, torch.Tensor], ...]] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        head_mask: Optional[torch.LongTensor] = None,
+        inputs_embeds: Optional[torch.LongTensor] = None,
+        use_cache: Optional[bool] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+        **deprecated_arguments,
+    ) -> Union[Tuple[torch.Tensor, ...], BaseModelOutputWithPastAndCrossAttentions]:
+        if deprecated_arguments.pop("position_ids", False) is not False:
+            # `position_ids` could have been `torch.Tensor` or `None` so defaulting pop to `False` allows to detect if users were passing explicitly `None`
+            warnings.warn(
+                "`position_ids` have no functionality in BLOOM and will be removed in v5.0.0. You can safely ignore"
+                " passing `position_ids`.",
+                FutureWarning,
+            )
+        if len(deprecated_arguments) > 0:
+            raise ValueError(f"Got unexpected arguments: {deprecated_arguments}")
+
+        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
+        output_hidden_states = (
+            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
+        )
+        use_cache = use_cache if use_cache is not None else self.config.use_cache
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        if input_ids is not None and inputs_embeds is not None:
+            raise ValueError("You cannot specify both input_ids and inputs_embeds at the same time")
+        elif input_ids is not None:
+            batch_size, seq_length = input_ids.shape
+        elif inputs_embeds is not None:
+            batch_size, seq_length, _ = inputs_embeds.shape
+        else:
+            raise ValueError("You have to specify either input_ids or inputs_embeds")
+
+        if past_key_values is None:
+            past_key_values = tuple([None] * len(self.h))
+
+        # Prepare head mask if needed
+        # 1.0 in head_mask indicate we keep the head
+        # attention_probs has shape batch_size x num_heads x N x N
+        # head_mask has shape n_layer x batch x num_heads x N x N
+        head_mask = self.get_head_mask(head_mask, self.config.n_layer)
+
+        if inputs_embeds is None:
+            inputs_embeds = self.word_embeddings(input_ids)
+
+        hidden_states = self.word_embeddings_layernorm(inputs_embeds)
+
+        presents = () if use_cache else None
+        all_self_attentions = () if output_attentions else None
+        all_hidden_states = () if output_hidden_states else None
+
+        if self.gradient_checkpointing and self.training:
+            if use_cache:
+                logger.warning_once(
+                    "`use_cache=True` is incompatible with gradient checkpointing. Setting `use_cache=False`..."
+                )
+                use_cache = False
+
+        # Compute alibi tensor: check build_alibi_tensor documentation
+        seq_length_with_past = seq_length
+        past_key_values_length = 0
+        if past_key_values[0] is not None:
+            past_key_values_length = past_key_values[0][0].shape[2]
+            seq_length_with_past = seq_length_with_past + past_key_values_length
+        if attention_mask is None:
+            attention_mask = torch.ones((batch_size, seq_length_with_past), device=hidden_states.device)
+        else:
+            attention_mask = attention_mask.to(hidden_states.device)
+
+        alibi = self.build_alibi_tensor(attention_mask, self.num_heads, dtype=hidden_states.dtype)
+
+        causal_mask = _prepare_4d_causal_attention_mask(
+            attention_mask,
+            input_shape=(batch_size, seq_length),
+            inputs_embeds=inputs_embeds,
+            past_key_values_length=past_key_values_length,
+        )
+        causal_mask = causal_mask.bool()
+
+        for i, (block, layer_past) in enumerate(zip(self.h, past_key_values)):
+            if output_hidden_states:
+                all_hidden_states = all_hidden_states + (hidden_states,)
+
+            if self.gradient_checkpointing and self.training:
+                outputs = self._gradient_checkpointing_func(
+                    block.__call__,
+                    hidden_states,
+                    alibi,
+                    causal_mask,
+                    layer_past,
+                    head_mask[i],
+                    use_cache,
+                    output_attentions,
+                )
+            else:
+                outputs = block(
+                    hidden_states,
+                    layer_past=layer_past,
+                    attention_mask=causal_mask,
+                    head_mask=head_mask[i],
+                    use_cache=use_cache,
+                    output_attentions=output_attentions,
+                    alibi=alibi,
+                )
+
+            hidden_states = outputs[0]
+            if use_cache is True:
+                presents = presents + (outputs[1],)
+
+            if output_attentions:
+                all_self_attentions = all_self_attentions + (outputs[2 if use_cache else 1],)
+
+        # Add last hidden state
+        hidden_states = self.ln_f(hidden_states)
+
+        if output_hidden_states:
+            all_hidden_states = all_hidden_states + (hidden_states,)
+
+        if not return_dict:
+            return tuple(v for v in [hidden_states, presents, all_hidden_states, all_self_attentions] if v is not None)
+
+        return BaseModelOutputWithPastAndCrossAttentions(
+            last_hidden_state=hidden_states,
+            past_key_values=presents,
+            hidden_states=all_hidden_states,
+            attentions=all_self_attentions,
+        )
+
+
+@add_start_docstrings(
+    """
+    The Bloom Model transformer with a language modeling head on top (linear layer with weights tied to the input
+    embeddings).
+    """,
+    BLOOM_START_DOCSTRING,
+)
+class BloomForCausalLM(BloomPreTrainedModel):
+    _tied_weights_keys = ["lm_head.weight"]
+
+    def __init__(self, config: BloomConfig):
+        super().__init__(config)
+        self.transformer = BloomModel(config)
+        self.lm_head = nn.Linear(config.hidden_size, config.vocab_size, bias=False)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    def get_output_embeddings(self):
+        return self.lm_head
+
+    def set_output_embeddings(self, new_embeddings: torch.Tensor):
+        self.lm_head = new_embeddings
+
+    def prepare_inputs_for_generation(
+        self,
+        input_ids: torch.LongTensor,
+        past_key_values: Optional[torch.Tensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.Tensor] = None,
+        **kwargs,
+    ) -> dict:
+        # only last tokens for input_ids if past is not None
+        if past_key_values is not None:
+            past_length = past_key_values[0][0].shape[2]
+
+            # Some generation methods already pass only the last input ID
+            if input_ids.shape[1] > past_length:
+                remove_prefix_length = past_length
+            else:
+                # Default to old behavior: keep only final ID
+                remove_prefix_length = input_ids.shape[1] - 1
+
+            input_ids = input_ids[:, remove_prefix_length:]
+
+            # the cache may be in the stardard format (e.g. in contrastive search), convert to bloom's format if needed
+            if past_key_values[0][0].shape[0] == input_ids.shape[0]:
+                past_key_values = self._convert_to_bloom_cache(past_key_values)
+
+        # if `inputs_embeds` are passed, we only want to use them in the 1st generation step
+        if inputs_embeds is not None and past_key_values is None:
+            model_inputs = {"inputs_embeds": inputs_embeds}
+        else:
+            model_inputs = {"input_ids": input_ids}
+
+        model_inputs.update(
+            {
+                "past_key_values": past_key_values,
+                "use_cache": kwargs.get("use_cache"),
+                "attention_mask": attention_mask,
+            }
+        )
+        return model_inputs
+
+    @add_start_docstrings_to_model_forward(BLOOM_INPUTS_DOCSTRING)
+    @add_code_sample_docstrings(
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=CausalLMOutputWithCrossAttentions,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        past_key_values: Optional[Tuple[Tuple[torch.Tensor, torch.Tensor], ...]] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.Tensor] = None,
+        labels: Optional[torch.Tensor] = None,
+        use_cache: Optional[bool] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+        **deprecated_arguments,
+    ) -> Union[Tuple[torch.Tensor], CausalLMOutputWithCrossAttentions]:
+        r"""
+        labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Labels for language modeling. Note that the labels **are shifted** inside the model, i.e. you can set
+            `labels = input_ids` Indices are selected in `[-100, 0, ..., config.vocab_size]` All labels set to `-100`
+            are ignored (masked), the loss is only computed for labels in `[0, ..., config.vocab_size]`
+        """
+        if deprecated_arguments.pop("position_ids", False) is not False:
+            # `position_ids` could have been `torch.Tensor` or `None` so defaulting pop to `False` allows to detect if users were passing explicitly `None`
+            warnings.warn(
+                "`position_ids` have no functionality in BLOOM and will be removed in v5.0.0. You can safely ignore"
+                " passing `position_ids`.",
+                FutureWarning,
+            )
+        if len(deprecated_arguments) > 0:
+            raise ValueError(f"Got unexpected arguments: {deprecated_arguments}")
+
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        transformer_outputs = self.transformer(
+            input_ids,
+            past_key_values=past_key_values,
+            attention_mask=attention_mask,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            use_cache=use_cache,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+        hidden_states = transformer_outputs[0]
+
+        lm_logits = self.lm_head(hidden_states)
+
+        loss = None
+        if labels is not None:
+            # move labels to correct device to enable model parallelism
+            labels = labels.to(lm_logits.device)
+            # Shift so that tokens < n predict n
+            shift_logits = lm_logits[..., :-1, :].contiguous()
+            shift_labels = labels[..., 1:].contiguous()
+            batch_size, seq_length, vocab_size = shift_logits.shape
+            # Flatten the tokens
+            loss_fct = CrossEntropyLoss()
+            loss = loss_fct(
+                shift_logits.view(batch_size * seq_length, vocab_size), shift_labels.view(batch_size * seq_length)
+            )
+
+        if not return_dict:
+            output = (lm_logits,) + transformer_outputs[1:]
+            return ((loss,) + output) if loss is not None else output
+
+        return CausalLMOutputWithCrossAttentions(
+            loss=loss,
+            logits=lm_logits,
+            past_key_values=transformer_outputs.past_key_values,
+            hidden_states=transformer_outputs.hidden_states,
+            attentions=transformer_outputs.attentions,
+        )
+
+    def _reorder_cache(
+        self, past: Tuple[Tuple[torch.Tensor, torch.Tensor], ...], beam_idx: torch.LongTensor
+    ) -> Tuple[Tuple[torch.Tensor, torch.Tensor], ...]:
+        """
+        This function is used to re-order the `past_key_values` cache if [`~PreTrainedModel.beam_search`] or
+        [`~PreTrainedModel.beam_sample`] is called. This is required to match `past_key_values` with the correct
+        beam_idx at every generation step.
+
+        Output shares the same memory storage as `past`.
+        """
+        standardized_past = self._convert_to_standard_cache(past, batch_size=len(beam_idx))
+
+        # Get a copy of `beam_idx` on all the devices where we need those indices.
+        device_to_beam_idx = {
+            past_state.device: beam_idx.to(past_state.device) for layer_past in past for past_state in layer_past
+        }
+        reordered_past = tuple(
+            (
+                layer_past[0].index_select(0, device_to_beam_idx[layer_past[0].device]),
+                layer_past[1].index_select(0, device_to_beam_idx[layer_past[0].device]),
+            )
+            for layer_past in standardized_past
+        )
+        return self._convert_to_bloom_cache(reordered_past)
+
+
+@add_start_docstrings(
+    """
+    The Bloom Model transformer with a sequence classification head on top (linear layer).
+
+    [`BloomForSequenceClassification`] uses the last token in order to do the classification, as other causal models
+    (e.g. GPT-1) do.
+
+    Since it does classification on the last token, it requires to know the position of the last token. If a
+    `pad_token_id` is defined in the configuration, it finds the last token that is not a padding token in each row. If
+    no `pad_token_id` is defined, it simply takes the last value in each row of the batch. Since it cannot guess the
+    padding tokens when `inputs_embeds` are passed instead of `input_ids`, it does the same (take the last value in
+    each row of the batch).
+    """,
+    BLOOM_START_DOCSTRING,
+)
+class BloomForSequenceClassification(BloomPreTrainedModel):
+    def __init__(self, config: BloomConfig):
+        super().__init__(config)
+        self.num_labels = config.num_labels
+        self.transformer = BloomModel(config)
+        self.score = nn.Linear(config.hidden_size, config.num_labels, bias=False)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    @add_start_docstrings_to_model_forward(BLOOM_INPUTS_DOCSTRING)
+    @add_code_sample_docstrings(
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=SequenceClassifierOutputWithPast,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        past_key_values: Optional[Tuple[Tuple[torch.Tensor, torch.Tensor], ...]] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.Tensor] = None,
+        labels: Optional[torch.Tensor] = None,
+        use_cache: Optional[bool] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+        **deprecated_arguments,
+    ) -> Union[Tuple[torch.Tensor], SequenceClassifierOutputWithPast]:
+        r"""
+        labels (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
+            Labels for computing the sequence classification/regression loss. Indices should be in `[0, ...,
+            config.num_labels - 1]`. If `config.num_labels == 1` a regression loss is computed (Mean-Square loss), If
+            `config.num_labels > 1` a classification loss is computed (Cross-Entropy).
+        """
+        if deprecated_arguments.pop("position_ids", False) is not False:
+            # `position_ids` could have been `torch.Tensor` or `None` so defaulting pop to `False` allows to detect if users were passing explicitly `None`
+            warnings.warn(
+                "`position_ids` have no functionality in BLOOM and will be removed in v5.0.0. You can safely ignore"
+                " passing `position_ids`.",
+                FutureWarning,
+            )
+        if len(deprecated_arguments) > 0:
+            raise ValueError(f"Got unexpected arguments: {deprecated_arguments}")
+
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        transformer_outputs = self.transformer(
+            input_ids,
+            past_key_values=past_key_values,
+            attention_mask=attention_mask,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            use_cache=use_cache,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        hidden_states = transformer_outputs[0]
+        logits = self.score(hidden_states)
+
+        if input_ids is not None:
+            batch_size = input_ids.shape[0]
+        else:
+            batch_size = inputs_embeds.shape[0]
+
+        if self.config.pad_token_id is None and batch_size != 1:
+            raise ValueError("Cannot handle batch sizes > 1 if no padding token is defined.")
+        if self.config.pad_token_id is None:
+            sequence_lengths = -1
+        else:
+            if input_ids is not None:
+                # if no pad token found, use modulo instead of reverse indexing for ONNX compatibility
+                sequence_lengths = torch.eq(input_ids, self.config.pad_token_id).int().argmax(-1) - 1
+                sequence_lengths = sequence_lengths % input_ids.shape[-1]
+                sequence_lengths = sequence_lengths.to(logits.device)
+            else:
+                sequence_lengths = -1
+                logger.warning(
+                    f"{self.__class__.__name__} will not detect padding tokens in `inputs_embeds`. Results may be "
+                    "unexpected if using padding tokens in conjunction with `inputs_embeds.`"
+                )
+
+        pooled_logits = logits[torch.arange(batch_size, device=logits.device), sequence_lengths]
+
+        loss = None
+        if labels is not None:
+            if self.config.problem_type is None:
+                if self.num_labels == 1:
+                    self.config.problem_type = "regression"
+                elif self.num_labels > 1 and (labels.dtype == torch.long or labels.dtype == torch.int):
+                    self.config.problem_type = "single_label_classification"
+                else:
+                    self.config.problem_type = "multi_label_classification"
+
+            if self.config.problem_type == "regression":
+                loss_fct = MSELoss()
+                if self.num_labels == 1:
+                    loss = loss_fct(pooled_logits.squeeze(), labels.squeeze())
+                else:
+                    loss = loss_fct(pooled_logits, labels)
+            elif self.config.problem_type == "single_label_classification":
+                loss_fct = CrossEntropyLoss()
+                loss = loss_fct(pooled_logits, labels)
+            elif self.config.problem_type == "multi_label_classification":
+                loss_fct = BCEWithLogitsLoss()
+                loss = loss_fct(pooled_logits, labels)
+        if not return_dict:
+            output = (pooled_logits,) + transformer_outputs[1:]
+            return ((loss,) + output) if loss is not None else output
+
+        return SequenceClassifierOutputWithPast(
+            loss=loss,
+            logits=pooled_logits,
+            past_key_values=transformer_outputs.past_key_values,
+            hidden_states=transformer_outputs.hidden_states,
+            attentions=transformer_outputs.attentions,
+        )
+
+
+@add_start_docstrings(
+    """
+    Bloom Model with a token classification head on top (a linear layer on top of the hidden-states output) e.g. for
+    Named-Entity-Recognition (NER) tasks.
+    """,
+    BLOOM_START_DOCSTRING,
+)
+class BloomForTokenClassification(BloomPreTrainedModel):
+    def __init__(self, config: BloomConfig):
+        super().__init__(config)
+        self.num_labels = config.num_labels
+
+        self.transformer = BloomModel(config)
+        if hasattr(config, "classifier_dropout") and config.classifier_dropout is not None:
+            classifier_dropout = config.classifier_dropout
+        elif hasattr(config, "hidden_dropout") and config.hidden_dropout is not None:
+            classifier_dropout = config.hidden_dropout
+        else:
+            classifier_dropout = 0.1
+        self.dropout = nn.Dropout(classifier_dropout)
+        self.classifier = nn.Linear(config.hidden_size, config.num_labels)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    @add_start_docstrings_to_model_forward(BLOOM_INPUTS_DOCSTRING)
+    @add_code_sample_docstrings(
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=TokenClassifierOutput,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        past_key_values: Optional[Tuple[Tuple[torch.Tensor, torch.Tensor], ...]] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.Tensor] = None,
+        labels: Optional[torch.Tensor] = None,
+        use_cache: Optional[bool] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+        **deprecated_arguments,
+    ) -> Union[Tuple[torch.Tensor], TokenClassifierOutput]:
+        r"""
+        labels (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
+            Labels for computing the sequence classification/regression loss. Indices should be in `[0, ...,
+            config.num_labels - 1]`. If `config.num_labels == 1` a regression loss is computed (Mean-Square loss), If
+            `config.num_labels > 1` a classification loss is computed (Cross-Entropy).
+        """
+        if deprecated_arguments.pop("position_ids", False) is not False:
+            # `position_ids` could have been `torch.Tensor` or `None` so defaulting pop to `False` allows to detect if users were passing explicitly `None`
+            warnings.warn(
+                "`position_ids` have no functionality in BLOOM and will be removed in v5.0.0. You can safely ignore"
+                " passing `position_ids`.",
+                FutureWarning,
+            )
+        if len(deprecated_arguments) > 0:
+            raise ValueError(f"Got unexpected arguments: {deprecated_arguments}")
+
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        transformer_outputs = self.transformer(
+            input_ids,
+            past_key_values=past_key_values,
+            attention_mask=attention_mask,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            use_cache=use_cache,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        hidden_states = transformer_outputs[0]
+        hidden_states = self.dropout(hidden_states)
+        logits = self.classifier(hidden_states)
+
+        loss = None
+        if labels is not None:
+            # move labels to correct device to enable model parallelism
+            labels = labels.to(logits.device)
+            batch_size, seq_length = labels.shape
+            loss_fct = CrossEntropyLoss()
+            loss = loss_fct(
+                logits.view(batch_size * seq_length, self.num_labels), labels.view(batch_size * seq_length)
+            )
+
+        if not return_dict:
+            output = (logits,) + transformer_outputs[2:]
+            return ((loss,) + output) if loss is not None else output
+
+        return TokenClassifierOutput(
+            loss=loss,
+            logits=logits,
+            hidden_states=transformer_outputs.hidden_states,
+            attentions=transformer_outputs.attentions,
+        )
+
+
+@add_start_docstrings(
+    """
+    The BLOOM Model transformer with a span classification head on top for extractive question-answering tasks like
+    SQuAD (a linear layers on top of the hidden-states output to compute `span start logits` and `span end logits`).
+    """,
+    BLOOM_START_DOCSTRING,
+)
+class BloomForQuestionAnswering(BloomPreTrainedModel):
+    def __init__(self, config):
+        super().__init__(config)
+        self.transformer = BloomModel(config)
+        self.qa_outputs = nn.Linear(config.hidden_size, 2)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    @add_start_docstrings_to_model_forward(BLOOM_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        start_positions: Optional[torch.LongTensor] = None,
+        end_positions: Optional[torch.LongTensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple, QuestionAnsweringModelOutput]:
+        r"""
+        start_positions (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
+            Labels for position (index) of the start of the labelled span for computing the token classification loss.
+            Positions are clamped to the length of the sequence (`sequence_length`). Position outside of the sequence
+            are not taken into account for computing the loss.
+        end_positions (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
+            Labels for position (index) of the end of the labelled span for computing the token classification loss.
+            Positions are clamped to the length of the sequence (`sequence_length`). Position outside of the sequence
+            are not taken into account for computing the loss.
+        """
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.transformer(
+            input_ids,
+            attention_mask=attention_mask,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        sequence_output = outputs[0]
+
+        logits = self.qa_outputs(sequence_output)
+        start_logits, end_logits = logits.split(1, dim=-1)
+        start_logits = start_logits.squeeze(-1).contiguous()
+        end_logits = end_logits.squeeze(-1).contiguous()
+
+        total_loss = None
+        if start_positions is not None and end_positions is not None:
+            # If we are on multi-GPU, split add a dimension
+            if len(start_positions.size()) > 1:
+                start_positions = start_positions.squeeze(-1)
+            if len(end_positions.size()) > 1:
+                end_positions = end_positions.squeeze(-1)
+            # sometimes the start/end positions are outside our model inputs, we ignore these terms
+            ignored_index = start_logits.size(1)
+            start_positions = start_positions.clamp(0, ignored_index)
+            end_positions = end_positions.clamp(0, ignored_index)
+
+            loss_fct = CrossEntropyLoss(ignore_index=ignored_index)
+            start_loss = loss_fct(start_logits, start_positions)
+            end_loss = loss_fct(end_logits, end_positions)
+            total_loss = (start_loss + end_loss) / 2
+
+        if not return_dict:
+            output = (start_logits, end_logits) + outputs[2:]
+            return ((total_loss,) + output) if total_loss is not None else output
+
+        return QuestionAnsweringModelOutput(
+            loss=total_loss,
+            start_logits=start_logits,
+            end_logits=end_logits,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )

llmeval-env/lib/python3.10/site-packages/transformers/models/bloom/modeling_flax_bloom.py

@@ -0,0 +1,734 @@
+# coding=utf-8
+# Copyright 2023 HuggingFace Inc. Team and Bigscience Workshop. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Flax BLOOM model."""
+
+import math
+from functools import partial
+from typing import Optional, Tuple
+
+import flax.linen as nn
+import jax
+import jax.numpy as jnp
+from flax.core.frozen_dict import FrozenDict, freeze, unfreeze
+from flax.linen import combine_masks, dot_product_attention_weights, make_causal_mask
+from flax.linen.activation import tanh
+from flax.traverse_util import flatten_dict, unflatten_dict
+from jax import lax
+
+from ...modeling_flax_outputs import (
+    FlaxBaseModelOutput,
+    FlaxBaseModelOutputWithPastAndCrossAttentions,
+    FlaxCausalLMOutput,
+)
+from ...modeling_flax_utils import FlaxPreTrainedModel, append_call_sample_docstring
+from ...utils import add_start_docstrings, add_start_docstrings_to_model_forward, logging
+from .configuration_bloom import BloomConfig
+
+
+logger = logging.get_logger(__name__)
+
+_CHECKPOINT_FOR_DOC = "bigscience/bloom"
+_CONFIG_FOR_DOC = "BloomConfig"
+
+
+BLOOM_START_DOCSTRING = r"""
+
+    This model inherits from [`FlaxPreTrainedModel`]. Check the superclass documentation for the generic methods the
+    library implements for all its model (such as downloading or saving, resizing the input embeddings, pruning heads
+    etc.)
+
+    This model is also a Flax Linen
+    [flax.nn.Module](https://flax.readthedocs.io/en/latest/_autosummary/flax.nn.module.html) subclass. Use it as a
+    regular Flax Module and refer to the Flax documentation for all matter related to general usage and behavior.
+
+    Finally, this model supports inherent JAX features such as:
+
+    - [Just-In-Time (JIT) compilation](https://jax.readthedocs.io/en/latest/jax.html#just-in-time-compilation-jit)
+    - [Automatic Differentiation](https://jax.readthedocs.io/en/latest/jax.html#automatic-differentiation)
+    - [Vectorization](https://jax.readthedocs.io/en/latest/jax.html#vectorization-vmap)
+    - [Parallelization](https://jax.readthedocs.io/en/latest/jax.html#parallelization-pmap)
+
+    Parameters:
+        config ([`BloomConfig`]): Model configuration class with all the parameters of the model.
+            Initializing with a config file does not load the weights associated with the model, only the
+            configuration. Check out the [`~FlaxPreTrainedModel.from_pretrained`] method to load the model weights.
+        dtype (`jax.numpy.dtype`, *optional*, defaults to `jax.numpy.float32`):
+            The data type of the computation. Can be one of `jax.numpy.float32`, `jax.numpy.float16` (on GPUs) and
+            `jax.numpy.bfloat16` (on TPUs).
+
+            This can be used to enable mixed-precision training or half-precision inference on GPUs or TPUs. If
+            specified all the computation will be performed with the given `dtype`.
+
+            **Note that this only specifies the dtype of the computation and does not influence the dtype of model
+            parameters.**
+
+            If you wish to change the dtype of the model parameters, see [`~FlaxPreTrainedModel.to_fp16`] and
+            [`~FlaxPreTrainedModel.to_bf16`].
+"""
+
+BLOOM_INPUTS_DOCSTRING = r"""
+    Args:
+        input_ids (`numpy.ndarray` of shape `(batch_size, input_ids_length)`):
+            `input_ids_length` = `sequence_length`. Indices of input sequence tokens in the vocabulary.
+
+            Indices can be obtained using [`BloomTokenizer`]. See [`PreTrainedTokenizer.encode`] and
+            [`PreTrainedTokenizer.__call__`] for details.
+
+            [What are input IDs?](../glossary#input-ids)
+        attention_mask (`numpy.ndarray` of shape `(batch_size, sequence_length)`, *optional*):
+            Mask to avoid performing attention on padding token indices. Mask values selected in `[0, 1]`:
+
+            - 1 for tokens that are **not masked**,
+            - 0 for tokens that are **masked**.
+
+            [What are attention masks?](../glossary#attention-mask)
+        past_key_values (`Dict[str, np.ndarray]`, *optional*, returned by `init_cache` or when passing previous `past_key_values`):
+            Dictionary of pre-computed hidden-states (key and values in the attention blocks) that can be used for fast
+            auto-regressive decoding. Pre-computed key and value hidden-states are of shape *[batch_size, max_length]*.
+        output_attentions (`bool`, *optional*):
+            Whether or not to return the attentions tensors of all attention layers. See `attentions` under returned
+            tensors for more detail.
+        output_hidden_states (`bool`, *optional*):
+            Whether or not to return the hidden states of all layers. See `hidden_states` under returned tensors for
+            more detail.
+        return_dict (`bool`, *optional*):
+            Whether or not to return a [`~utils.ModelOutput`] instead of a plain tuple.
+"""
+
+
+def build_alibi_tensor(attention_mask: jnp.ndarray, num_heads: int, dtype: Optional[jnp.dtype] = jnp.float32):
+    """
+    Flax implementation of the BLOOM Alibi tensor. BLOOM Alibi tensor is not causal as the original paper mentions, it
+    relies on a translation invariance of softmax for quick implementation: with l being a tensor, and a fixed value
+    `softmax(l+a) = softmax(l)`. Based on
+    https://github.com/ofirpress/attention_with_linear_biases/blob/a35aaca144e0eb6b789dfcb46784c4b8e31b7983/fairseq/models/transformer.py#L742
+    Link to paper: https://arxiv.org/abs/2108.12409
+
+    Args:
+        attention_mask (`jnp.ndarray`):
+            Token-wise attention mask, this should be of shape `(batch_size, max_seq_len)`.
+        num_heads (`int`):
+            Number of attention heads.
+        dtype (`jnp.dtype`, *optional*, defaults to `jnp.float32`):
+            The data type (dtype) of the output tensor.
+
+    Returns: Alibi tensor of shape `(batch_size * num_heads, 1, max_seq_len)`.
+    """
+    batch_size, seq_length = attention_mask.shape
+    closest_power_of_2 = 2 ** math.floor(math.log2(num_heads))
+    base = jnp.array(2 ** (-(2 ** -(math.log2(closest_power_of_2) - 3))), dtype=jnp.float32)
+    powers = jnp.arange(1, 1 + closest_power_of_2, dtype=jnp.float32)
+    slopes = jax.lax.pow(base, powers)
+
+    if closest_power_of_2 != num_heads:
+        extra_base = jnp.array(2 ** (-(2 ** -(math.log2(2 * closest_power_of_2) - 3))), dtype=jnp.float32)
+        num_remaining_heads = min(closest_power_of_2, num_heads - closest_power_of_2)
+        extra_powers = jnp.arange(1, 1 + 2 * num_remaining_heads, 2, dtype=jnp.float32)
+        slopes = jnp.cat([slopes, jax.lax.pow(extra_base, extra_powers)], axis=0)
+
+    # Note: the Alibi tensor will added to the attention bias that will be applied to the query, key product of attention
+    # therefore, Alibi will have to be of shape (batch_size, num_heads, query_length, key_length)
+    # => here we set (batch_size=1, num_heads=num_heads, query_length=1, key_length=max_length)
+    # so that the query_length dimension will then be broadcast correctly.
+    # This is more or less identical to T5's relative position bias:
+    # https://github.com/huggingface/transformers/blob/f681437203baa7671de3174b0fa583c349d9d5e1/src/transformers/models/t5/modeling_t5.py#L527
+    arange_tensor = ((attention_mask.cumsum(axis=-1) - 1) * attention_mask)[:, None, :]
+    alibi = slopes[..., None] * arange_tensor
+    alibi = jnp.expand_dims(alibi, axis=2)
+    return jnp.asarray(alibi, dtype)
+
+
+class FlaxBloomAttention(nn.Module):
+    config: BloomConfig
+    dtype: jnp.dtype = jnp.float32
+
+    def setup(self):
+        self.hidden_size = self.config.hidden_size
+        self.num_heads = self.config.n_head
+        self.head_dim = self.hidden_size // self.num_heads
+        self.attention_softmax_in_fp32 = self.dtype is not jnp.float32
+
+        if self.head_dim * self.num_heads != self.hidden_size:
+            raise ValueError(
+                f"`hidden_size` must be divisible by `num_heads` (got `hidden_size`: {self.hidden_size} and "
+                f"`num_heads`: {self.num_heads})."
+            )
+
+        dense = partial(
+            nn.Dense,
+            dtype=self.dtype,
+            kernel_init=jax.nn.initializers.normal(self.config.initializer_range),
+        )
+
+        self.query_key_value = dense(self.hidden_size * 3)
+        self.dense = dense(self.hidden_size)
+        self.resid_dropout = nn.Dropout(rate=self.config.hidden_dropout)
+
+    def _split_heads(self, hidden_states):
+        return hidden_states.reshape(hidden_states.shape[:-1] + (self.num_heads, self.head_dim * 3))
+
+    def _merge_heads(self, hidden_states):
+        return hidden_states.reshape(hidden_states.shape[:2] + (self.hidden_size,))
+
+    @nn.compact
+    # Copied from transformers.models.gptj.modeling_flax_gptj.FlaxGPTJAttention._concatenate_to_cache
+    def _concatenate_to_cache(self, key, value, query, attention_mask):
+        """
+        This function takes projected key, value states from a single input token and concatenates the states to cached
+        states from previous steps. This function is slighly adapted from the official Flax repository:
+        https://github.com/google/flax/blob/491ce18759622506588784b4fca0e4bf05f8c8cd/flax/linen/attention.py#L252
+        """
+        # detect if we're initializing by absence of existing cache data.
+        is_initialized = self.has_variable("cache", "cached_key")
+        cached_key = self.variable("cache", "cached_key", jnp.zeros, key.shape, key.dtype)
+        cached_value = self.variable("cache", "cached_value", jnp.zeros, value.shape, value.dtype)
+        cache_index = self.variable("cache", "cache_index", lambda: jnp.array(0, dtype=jnp.int32))
+
+        if is_initialized:
+            *batch_dims, max_length, num_heads, depth_per_head = cached_key.value.shape
+            # update key, value caches with our new 1d spatial slices
+            cur_index = cache_index.value
+            indices = (0,) * len(batch_dims) + (cur_index, 0, 0)
+            key = lax.dynamic_update_slice(cached_key.value, key, indices)
+            value = lax.dynamic_update_slice(cached_value.value, value, indices)
+            cached_key.value = key
+            cached_value.value = value
+            num_updated_cache_vectors = query.shape[1]
+            cache_index.value = cache_index.value + num_updated_cache_vectors
+            # causal mask for cached decoder self-attention: our single query position should only attend to those key
+            # positions that have already been generated and cached, not the remaining zero elements.
+            pad_mask = jnp.broadcast_to(
+                jnp.arange(max_length) < cur_index + num_updated_cache_vectors,
+                tuple(batch_dims) + (1, num_updated_cache_vectors, max_length),
+            )
+            attention_mask = combine_masks(pad_mask, attention_mask)
+        return key, value, attention_mask
+
+    def __call__(
+        self,
+        hidden_states,
+        residual,
+        alibi,
+        attention_mask=None,
+        deterministic: bool = True,
+        init_cache: bool = False,
+        output_attentions: bool = False,
+    ):
+        batch_size, seq_length = hidden_states.shape[:2]
+
+        # proj q, k, v
+        fused_qkv = self.query_key_value(hidden_states)
+        fused_qkv = self._split_heads(fused_qkv)
+        query, key, value = jnp.split(fused_qkv, 3, axis=-1)
+
+        causal_attention_mask = make_causal_mask(attention_mask, dtype="bool")
+
+        # for fast decoding causal attention mask should be shifted
+        causal_attention_mask_shift = (
+            self.variables["cache"]["cache_index"] if self.has_variable("cache", "cached_key") else 0
+        )
+
+        # fast decoding for generate requires special attention_mask
+        if self.has_variable("cache", "cached_key"):
+            max_decoder_length = self.variables["cache"]["cached_key"].shape[1]
+            causal_attention_mask = jax.lax.dynamic_slice(
+                causal_attention_mask,
+                (0, 0, causal_attention_mask_shift, 0),
+                (1, 1, seq_length, max_decoder_length),
+            )
+
+        # broadcast causal attention mask & attention mask to fit for merge
+        causal_attention_mask = jnp.broadcast_to(
+            causal_attention_mask, (batch_size,) + causal_attention_mask.shape[1:]
+        )
+        attention_mask = jnp.broadcast_to(jnp.expand_dims(attention_mask, axis=(-3, -2)), causal_attention_mask.shape)
+        attention_mask = combine_masks(attention_mask, causal_attention_mask)
+
+        dropout_rng = None
+        if not deterministic and self.config.attention_dropout > 0.0:
+            dropout_rng = self.make_rng("dropout")
+
+        # During fast autoregressive decoding, we feed one position at a time,
+        # and cache the keys and values step by step.
+        if self.has_variable("cache", "cached_key") or init_cache:
+            key, value, attention_mask = self._concatenate_to_cache(key, value, query, attention_mask)
+
+        # transform boolean mask into float mask
+        mask_value = jnp.finfo(self.dtype).min
+        attention_bias = lax.select(
+            attention_mask > 0,
+            jnp.full(attention_mask.shape, 0.0).astype(self.dtype),
+            jnp.full(attention_mask.shape, mask_value).astype(self.dtype),
+        )
+
+        attention_bias = attention_bias + alibi
+
+        # Cast in fp32 if the original dtype is different from fp32
+        attention_dtype = jnp.float32 if self.attention_softmax_in_fp32 else self.dtype
+
+        attn_weights = dot_product_attention_weights(
+            query,
+            key,
+            bias=attention_bias,
+            dropout_rng=dropout_rng,
+            dropout_rate=self.config.attention_dropout,
+            deterministic=deterministic,
+            dtype=attention_dtype,
+        )
+
+        # Cast back in the original dtype if the native dtype is not fp32
+        if self.attention_softmax_in_fp32:
+            attn_weights = attn_weights.astype(self.dtype)
+
+        attn_output = jnp.einsum("...hqk,...khd->...qhd", attn_weights, value)
+        attn_output = self._merge_heads(attn_output)
+        attn_output = self.dense(attn_output)
+        attn_output = self.resid_dropout(attn_output, deterministic=deterministic)
+
+        attn_output = attn_output + residual
+
+        outputs = (attn_output, attn_weights) if output_attentions else (attn_output,)
+        return outputs
+
+
+class BloomGELU(nn.Module):
+    def setup(self):
+        self.dtype = jnp.float32
+
+    def __call__(self, x):
+        return x * 0.5 * (1.0 + tanh(0.79788456 * x * (1 + 0.044715 * x * x)))
+
+
+class FlaxBloomMLP(nn.Module):
+    config: BloomConfig
+    dtype: jnp.dtype = jnp.float32
+
+    def setup(self):
+        hidden_size = self.config.hidden_size
+
+        kernel_init = jax.nn.initializers.normal(self.config.initializer_range)
+
+        self.dense_h_to_4h = nn.Dense(4 * hidden_size, dtype=self.dtype, kernel_init=kernel_init)
+        self.dense_4h_to_h = nn.Dense(hidden_size, dtype=self.dtype, kernel_init=kernel_init)
+        self.hidden_dropout = nn.Dropout(self.config.hidden_dropout)
+        self.act = BloomGELU()
+
+    def __call__(self, hidden_states, residual, deterministic: bool = True):
+        hidden_states = self.dense_h_to_4h(hidden_states)
+        hidden_states = self.act(hidden_states)
+
+        intermediate_output = self.dense_4h_to_h(hidden_states)
+
+        intermediate_output = intermediate_output + residual
+        hidden_states = self.hidden_dropout(intermediate_output, deterministic=deterministic)
+
+        return hidden_states
+
+
+class FlaxBloomBlock(nn.Module):
+    config: BloomConfig
+    dtype: jnp.dtype = jnp.float32
+
+    def setup(self):
+        self.input_layernorm = nn.LayerNorm(epsilon=self.config.layer_norm_epsilon, dtype=self.dtype)
+
+        self.self_attention = FlaxBloomAttention(self.config, dtype=self.dtype)
+        self.post_attention_layernorm = nn.LayerNorm(epsilon=self.config.layer_norm_epsilon, dtype=self.dtype)
+
+        self.mlp = FlaxBloomMLP(self.config, dtype=self.dtype)
+
+        self.apply_residual_connection_post_layernorm = self.config.apply_residual_connection_post_layernorm
+        self.hidden_dropout = self.config.hidden_dropout
+
+    def __call__(
+        self,
+        hidden_states,
+        alibi,
+        attention_mask=None,
+        deterministic: bool = True,
+        init_cache: bool = False,
+        output_attentions: bool = False,
+    ):
+        layernorm_output = self.input_layernorm(hidden_states)
+
+        # layer norm before saving residual if config calls for it
+        if self.apply_residual_connection_post_layernorm:
+            residual = layernorm_output
+        else:
+            residual = hidden_states
+
+        # self-attention
+        attn_outputs = self.self_attention(
+            layernorm_output,
+            residual=residual,
+            alibi=alibi,
+            attention_mask=attention_mask,
+            deterministic=deterministic,
+            init_cache=init_cache,
+            output_attentions=output_attentions,
+        )
+
+        attention_output = attn_outputs[0]
+
+        outputs = attn_outputs[1:]
+
+        post_layernorm = self.post_attention_layernorm(attention_output)
+
+        # set residual based on config
+        if self.apply_residual_connection_post_layernorm:
+            residual = post_layernorm
+        else:
+            residual = attention_output
+
+        output = self.mlp(post_layernorm, residual, deterministic=deterministic)
+
+        outputs = (output,) + outputs
+
+        return outputs
+
+
+class FlaxBloomPreTrainedModel(FlaxPreTrainedModel):
+    """
+    An abstract class to handle weights initialization and a simple interface for downloading and loading pretrained
+    models.
+    """
+
+    config_class = BloomConfig
+    base_model_prefix = "transformer"
+    module_class: nn.Module = None
+
+    def __init__(
+        self,
+        config: BloomConfig,
+        input_shape: Tuple = (1, 1),
+        seed: int = 0,
+        dtype: jnp.dtype = jnp.float32,
+        _do_init: bool = True,
+        **kwargs,
+    ):
+        module = self.module_class(config=config, dtype=dtype, **kwargs)
+        super().__init__(config, module, input_shape=input_shape, seed=seed, dtype=dtype, _do_init=_do_init)
+
+    def init_weights(self, rng: jax.random.PRNGKey, input_shape: Tuple, params: FrozenDict = None) -> FrozenDict:
+        # init input tensors
+        input_ids = jnp.zeros(input_shape, dtype="i4")
+        attention_mask = jnp.ones_like(input_ids)
+        params_rng, dropout_rng = jax.random.split(rng)
+        rngs = {"params": params_rng, "dropout": dropout_rng}
+
+        random_params = self.module.init(rngs, input_ids, attention_mask, return_dict=False)["params"]
+
+        if params is not None:
+            random_params = flatten_dict(unfreeze(random_params))
+            params = flatten_dict(unfreeze(params))
+            for missing_key in self._missing_keys:
+                params[missing_key] = random_params[missing_key]
+            self._missing_keys = set()
+            return freeze(unflatten_dict(params))
+        else:
+            return random_params
+
+    def init_cache(self, batch_size, max_length):
+        r"""
+        Args:
+            batch_size (`int`):
+                batch_size used for fast auto-regressive decoding. Defines the batch size of the initialized cache.
+            max_length (`int`):
+                maximum possible length for auto-regressive decoding. Defines the sequence length of the initialized
+                cache.
+        """
+        # init input variables to retrieve cache
+        input_ids = jnp.ones((batch_size, max_length), dtype="i4")
+        attention_mask = jnp.ones_like(input_ids)
+
+        init_variables = self.module.init(
+            jax.random.PRNGKey(0), input_ids, attention_mask, return_dict=False, init_cache=True
+        )
+        return unfreeze(init_variables["cache"])
+
+    @add_start_docstrings_to_model_forward(BLOOM_INPUTS_DOCSTRING)
+    def __call__(
+        self,
+        input_ids,
+        attention_mask=None,
+        past_key_values: dict = None,
+        params: dict = None,
+        dropout_rng: jax.random.PRNGKey = None,
+        train: bool = False,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ):
+        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
+        output_hidden_states = (
+            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
+        )
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        batch_size, sequence_length = input_ids.shape
+
+        if attention_mask is None:
+            attention_mask = jnp.ones((batch_size, sequence_length))
+
+        # Handle any PRNG if needed
+        rngs = {}
+        if dropout_rng is not None:
+            rngs["dropout"] = dropout_rng
+
+        inputs = {"params": params or self.params}
+
+        # If past_key_values are passed then cache is already initialized a private flag init_cache has to be passed
+        # down to ensure cache is used. It has to be made sure that cache is marked as mutable so that it can be
+        # changed by FlaxBloomAttention module
+        if past_key_values:
+            inputs["cache"] = past_key_values
+            mutable = ["cache"]
+        else:
+            mutable = False
+
+        outputs = self.module.apply(
+            inputs,
+            jnp.array(input_ids, dtype="i4"),
+            jnp.array(attention_mask, dtype="i4"),
+            not train,
+            False,
+            output_attentions,
+            output_hidden_states,
+            return_dict,
+            rngs=rngs,
+            mutable=mutable,
+        )
+
+        # add updated cache to model output
+        if past_key_values is not None and return_dict:
+            outputs, past_key_values = outputs
+            outputs["past_key_values"] = unfreeze(past_key_values["cache"])
+            return outputs
+        elif past_key_values is not None and not return_dict:
+            outputs, past_key_values = outputs
+            outputs = outputs[:1] + (unfreeze(past_key_values["cache"]),) + outputs[1:]
+
+        return outputs
+
+
+class FlaxBloomBlockCollection(nn.Module):
+    config: BloomConfig
+    dtype: jnp.dtype = jnp.float32
+
+    def setup(self):
+        self.layers = [
+            FlaxBloomBlock(self.config, name=str(layer_number), dtype=self.dtype)
+            for layer_number in range(self.config.num_hidden_layers)
+        ]
+
+    def __call__(
+        self,
+        hidden_states,
+        alibi,
+        attention_mask=None,
+        deterministic: bool = True,
+        init_cache: bool = False,
+        output_attentions: bool = False,
+        output_hidden_states: bool = False,
+    ):
+        all_attentions = () if output_attentions else None
+        all_hidden_states = () if output_hidden_states else None
+
+        for layer_number in range(self.config.num_hidden_layers):
+            if output_hidden_states:
+                all_hidden_states += (hidden_states,)
+
+            layer_outputs = self.layers[layer_number](
+                hidden_states,
+                alibi=alibi,
+                attention_mask=attention_mask,
+                deterministic=deterministic,
+                init_cache=init_cache,
+                output_attentions=output_attentions,
+            )
+            hidden_states = layer_outputs[0]
+
+            if output_attentions:
+                all_attentions += (layer_outputs[1],)
+
+        # this contains possible `None` values - `FlaxBloomModule` will filter them out
+        outputs = (hidden_states, all_hidden_states, all_attentions)
+
+        return outputs
+
+
+class FlaxBloomModule(nn.Module):
+    config: BloomConfig
+    dtype: jnp.dtype = jnp.float32
+
+    def setup(self):
+        self.embed_dim = self.config.hidden_size
+
+        # word embeddings (no positional embedding layer)
+        self.word_embeddings = nn.Embed(
+            self.config.vocab_size,
+            self.embed_dim,
+            embedding_init=jax.nn.initializers.normal(stddev=self.config.initializer_range),
+            dtype=self.dtype,
+        )
+
+        # post-embedding layernorm
+        self.word_embeddings_layernorm = nn.LayerNorm(epsilon=self.config.layer_norm_epsilon, dtype=self.dtype)
+
+        # transformer layers
+        self.h = FlaxBloomBlockCollection(self.config, dtype=self.dtype)
+
+        # final layernorm
+        self.ln_f = nn.LayerNorm(epsilon=self.config.layer_norm_epsilon, dtype=self.dtype)
+
+    def __call__(
+        self,
+        input_ids=None,
+        attention_mask=None,
+        deterministic=True,
+        init_cache: bool = False,
+        output_attentions: bool = False,
+        output_hidden_states: bool = False,
+        return_dict: bool = True,
+    ):
+        inputs_embeds = self.word_embeddings(input_ids)
+        # do post-embedding layernorm
+        hidden_states = self.word_embeddings_layernorm(inputs_embeds)
+
+        # build alibi depending on `attention_mask`
+        alibi = build_alibi_tensor(attention_mask, self.config.n_head, dtype=hidden_states.dtype)
+
+        outputs = self.h(
+            hidden_states,
+            alibi=alibi,
+            attention_mask=attention_mask,
+            deterministic=deterministic,
+            init_cache=init_cache,
+            output_hidden_states=output_hidden_states,
+            output_attentions=output_attentions,
+        )
+
+        hidden_states = outputs[0]
+        hidden_states = self.ln_f(hidden_states)
+
+        if output_hidden_states:
+            all_hidden_states = outputs[1] + (hidden_states,)
+            outputs = (hidden_states, all_hidden_states) + outputs[2:]
+        else:
+            outputs = (hidden_states,) + outputs[1:]
+
+        if not return_dict:
+            return tuple(v for v in [outputs[0], outputs[-1]] if v is not None)
+
+        return FlaxBaseModelOutputWithPastAndCrossAttentions(
+            last_hidden_state=hidden_states,
+            hidden_states=outputs[1],
+            attentions=outputs[-1],
+        )
+
+
+@add_start_docstrings(
+    "The bare Bloom Model transformer outputting raw hidden-states without any specific head on top.",
+    BLOOM_START_DOCSTRING,
+)
+# Copied from transformers.models.gpt_neo.modeling_flax_gpt_neo.FlaxGPTNeoModel with GPTNeo->Bloom
+class FlaxBloomModel(FlaxBloomPreTrainedModel):
+    module_class = FlaxBloomModule
+
+
+append_call_sample_docstring(FlaxBloomModel, _CHECKPOINT_FOR_DOC, FlaxBaseModelOutput, _CONFIG_FOR_DOC)
+
+
+class FlaxBloomForCausalLMModule(nn.Module):
+    config: BloomConfig
+    dtype: jnp.dtype = jnp.float32
+
+    def setup(self):
+        self.transformer = FlaxBloomModule(self.config, dtype=self.dtype)
+        self.lm_head = nn.Dense(
+            self.config.vocab_size,
+            use_bias=False,
+            dtype=self.dtype,
+            kernel_init=jax.nn.initializers.normal(stddev=self.config.initializer_range),
+        )
+
+    def __call__(
+        self,
+        input_ids,
+        attention_mask,
+        deterministic: bool = True,
+        init_cache: bool = False,
+        output_attentions: bool = False,
+        output_hidden_states: bool = False,
+        return_dict: bool = True,
+    ):
+        outputs = self.transformer(
+            input_ids,
+            attention_mask=attention_mask,
+            deterministic=deterministic,
+            init_cache=init_cache,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        hidden_states = outputs[0]
+
+        if self.config.tie_word_embeddings:
+            shared_kernel = self.transformer.variables["params"]["word_embeddings"]["embedding"].T
+            lm_logits = self.lm_head.apply({"params": {"kernel": shared_kernel}}, hidden_states)
+        else:
+            lm_logits = self.lm_head(hidden_states)
+
+        if not return_dict:
+            return (lm_logits,) + outputs[1:]
+
+        return FlaxCausalLMOutput(logits=lm_logits, hidden_states=outputs.hidden_states, attentions=outputs.attentions)
+
+
+@add_start_docstrings(
+    """
+    The Bloom Model transformer with a language modeling head on top (linear layer with weights tied to the input
+    embeddings).
+    """,
+    BLOOM_START_DOCSTRING,
+)
+class FlaxBloomForCausalLM(FlaxBloomPreTrainedModel):
+    module_class = FlaxBloomForCausalLMModule
+
+    def prepare_inputs_for_generation(self, input_ids, max_length, attention_mask: Optional[jax.Array] = None):
+        # initializing the cache
+        batch_size, seq_length = input_ids.shape
+
+        past_key_values = self.init_cache(batch_size, max_length)
+        # Note that usually one would have to put 0's in the attention_mask for
+        # x > input_ids.shape[-1] and x < cache_length. But since Bloom uses a causal mask,
+        # those positions are masked anyway. Thus, we can create a single static attention_mask here,
+        # which is more efficient for compilation
+        extended_attention_mask = jnp.ones((batch_size, max_length), dtype="i4")
+        if attention_mask is not None:
+            extended_attention_mask = lax.dynamic_update_slice(extended_attention_mask, attention_mask, (0, 0))
+
+        return {
+            "past_key_values": past_key_values,
+            "attention_mask": extended_attention_mask,
+        }
+
+    def update_inputs_for_generation(self, model_outputs, model_kwargs):
+        model_kwargs["past_key_values"] = model_outputs.past_key_values
+        return model_kwargs
+
+
+append_call_sample_docstring(FlaxBloomForCausalLM, _CHECKPOINT_FOR_DOC, FlaxCausalLMOutput, _CONFIG_FOR_DOC)

llmeval-env/lib/python3.10/site-packages/transformers/models/bloom/tokenization_bloom_fast.py

@@ -0,0 +1,164 @@
+# coding=utf-8
+# Copyright 2022 The HuggingFace Inc. team.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Tokenization classes for Bloom."""
+
+
+import pickle
+from typing import Optional, Tuple
+
+from ...tokenization_utils_base import BatchEncoding
+from ...tokenization_utils_fast import PreTrainedTokenizerFast
+from ...utils import logging
+
+
+logger = logging.get_logger(__name__)
+
+VOCAB_FILES_NAMES = {"tokenizer_file": "tokenizer.json"}
+
+
+class BloomTokenizerFast(PreTrainedTokenizerFast):
+    """
+    Construct a "fast" Bloom tokenizer (backed by HuggingFace's *tokenizers* library). Based on byte-level
+    Byte-Pair-Encoding.
+
+    This tokenizer has been trained to treat spaces like parts of the tokens (a bit like sentencepiece) so a word will
+    be encoded differently whether it is at the beginning of the sentence (without space) or not:
+
+    ```python
+    >>> from transformers import BloomTokenizerFast
+
+    >>> tokenizer = BloomTokenizerFast.from_pretrained("bigscience/bloom")
+    >>> tokenizer("Hello world")["input_ids"]
+    [59414, 8876]
+
+    >>> tokenizer(" Hello world")["input_ids"]
+    [86153, 8876]
+    ```
+
+    You can get around that behavior by passing `add_prefix_space=True` when instantiating this tokenizer, but since
+    the model was not pretrained this way, it might yield a decrease in performance.
+
+    <Tip>
+
+    When used with `is_split_into_words=True`, this tokenizer needs to be instantiated with `add_prefix_space=True`.
+
+    </Tip>
+
+    This tokenizer inherits from [`PreTrainedTokenizerFast`] which contains most of the main methods. Users should
+    refer to this superclass for more information regarding those methods.
+
+    Args:
+        vocab_file (`str`):
+            Path to the vocabulary file.
+        merges_file (`str`):
+            Path to the merges file.
+        errors (`str`, *optional*, defaults to `"replace"`):
+            Paradigm to follow when decoding bytes to UTF-8. See
+            [bytes.decode](https://docs.python.org/3/library/stdtypes.html#bytes.decode) for more information.
+        unk_token (`str`, *optional*, defaults to `<|endoftext|>`):
+            The unknown token. A token that is not in the vocabulary cannot be converted to an ID and is set to be this
+            token instead.
+        bos_token (`str`, *optional*, defaults to `<|endoftext|>`):
+            The beginning of sequence token.
+        eos_token (`str`, *optional*, defaults to `<|endoftext|>`):
+            The end of sequence token.
+        add_prefix_space (`bool`, *optional*, defaults to `False`):
+            Whether or not to add an initial space to the input. This allows to treat the leading word just as any
+            other word. (Bloom tokenizer detect beginning of words by the preceding space).
+        trim_offsets (`bool`, *optional*, defaults to `True`):
+            Whether or not the post-processing step should trim offsets to avoid including whitespaces.
+    """
+
+    vocab_files_names = VOCAB_FILES_NAMES
+    model_input_names = ["input_ids", "attention_mask"]
+    slow_tokenizer_class = None
+    # No `max_model_input_sizes` as BLOOM uses ALiBi positional embeddings
+
+    def __init__(
+        self,
+        vocab_file=None,
+        merges_file=None,
+        tokenizer_file=None,
+        unk_token="<unk>",
+        bos_token="<s>",
+        eos_token="</s>",
+        pad_token="<pad>",
+        add_prefix_space=False,
+        clean_up_tokenization_spaces=False,
+        **kwargs,
+    ):
+        super().__init__(
+            vocab_file,
+            merges_file,
+            tokenizer_file=tokenizer_file,
+            unk_token=unk_token,
+            bos_token=bos_token,
+            eos_token=eos_token,
+            pad_token=pad_token,
+            add_prefix_space=add_prefix_space,
+            clean_up_tokenization_spaces=clean_up_tokenization_spaces,
+            **kwargs,
+        )
+        # TODO @ArthurZucker this can only work one way for now, to update later-on. Tests should also properly
+        # check this as they were green before.
+        pre_tok_state = pickle.dumps(self.backend_tokenizer.pre_tokenizer)
+        decoder_state = pickle.dumps(self.backend_tokenizer.decoder)
+
+        if add_prefix_space:
+            pre_tok_state = pre_tok_state.replace(b'"add_prefix_space":false', b'"add_prefix_space": true')
+            decoder_state = decoder_state.replace(b'"add_prefix_space":false', b'"add_prefix_space": true')
+        self.backend_tokenizer.pre_tokenizer = pickle.loads(pre_tok_state)
+        self.backend_tokenizer.decoder = pickle.loads(decoder_state)
+
+        self.add_prefix_space = add_prefix_space
+
+    def _batch_encode_plus(self, *args, **kwargs) -> BatchEncoding:
+        is_split_into_words = kwargs.get("is_split_into_words", False)
+        if not (self.add_prefix_space or not is_split_into_words):
+            raise Exception(
+                f"You need to instantiate {self.__class__.__name__} with add_prefix_space=True to use it with"
+                " pretokenized inputs."
+            )
+
+        return super()._batch_encode_plus(*args, **kwargs)
+
+    def _encode_plus(self, *args, **kwargs) -> BatchEncoding:
+        is_split_into_words = kwargs.get("is_split_into_words", False)
+
+        if not (self.add_prefix_space or not is_split_into_words):
+            raise Exception(
+                f"You need to instantiate {self.__class__.__name__} with add_prefix_space=True to use it with"
+                " pretokenized inputs."
+            )
+
+        return super()._encode_plus(*args, **kwargs)
+
+    def save_vocabulary(self, save_directory: str, filename_prefix: Optional[str] = None) -> Tuple[str]:
+        files = self._tokenizer.model.save(save_directory, name=filename_prefix)
+        return tuple(files)
+
+    @property
+    # Copied from transformers.models.gpt2.tokenization_gpt2.GPT2Tokenizer.default_chat_template
+    def default_chat_template(self):
+        """
+        A simple chat template that ignores role information and just concatenates messages with EOS tokens.
+        """
+        logger.warning_once(
+            "\nNo chat template is defined for this tokenizer - using the default template "
+            f"for the {self.__class__.__name__} class. If the default is not appropriate for "
+            "your model, please set `tokenizer.chat_template` to an appropriate template. "
+            "See https://huggingface.co/docs/transformers/main/chat_templating for more information.\n"
+        )
+        return "{% for message in messages %}" "{{ message.content }}{{ eos_token }}" "{% endfor %}"

llmeval-env/lib/python3.10/site-packages/transformers/models/esm/__init__.py

@@ -0,0 +1,94 @@
+# Copyright 2022 Facebook and The HuggingFace Team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+from typing import TYPE_CHECKING
+
+from ...utils import OptionalDependencyNotAvailable, _LazyModule, is_tf_available, is_torch_available
+
+
+_import_structure = {
+    "configuration_esm": ["ESM_PRETRAINED_CONFIG_ARCHIVE_MAP", "EsmConfig"],
+    "tokenization_esm": ["EsmTokenizer"],
+}
+
+try:
+    if not is_torch_available():
+        raise OptionalDependencyNotAvailable()
+except OptionalDependencyNotAvailable:
+    pass
+else:
+    _import_structure["modeling_esm"] = [
+        "ESM_PRETRAINED_MODEL_ARCHIVE_LIST",
+        "EsmForMaskedLM",
+        "EsmForSequenceClassification",
+        "EsmForTokenClassification",
+        "EsmModel",
+        "EsmPreTrainedModel",
+    ]
+    _import_structure["modeling_esmfold"] = ["EsmForProteinFolding", "EsmFoldPreTrainedModel"]
+
+try:
+    if not is_tf_available():
+        raise OptionalDependencyNotAvailable()
+except OptionalDependencyNotAvailable:
+    pass
+else:
+    _import_structure["modeling_tf_esm"] = [
+        "TF_ESM_PRETRAINED_MODEL_ARCHIVE_LIST",
+        "TFEsmForMaskedLM",
+        "TFEsmForSequenceClassification",
+        "TFEsmForTokenClassification",
+        "TFEsmModel",
+        "TFEsmPreTrainedModel",
+    ]
+
+if TYPE_CHECKING:
+    from .configuration_esm import ESM_PRETRAINED_CONFIG_ARCHIVE_MAP, EsmConfig
+    from .tokenization_esm import EsmTokenizer
+
+    try:
+        if not is_torch_available():
+            raise OptionalDependencyNotAvailable()
+    except OptionalDependencyNotAvailable:
+        pass
+    else:
+        from .modeling_esm import (
+            ESM_PRETRAINED_MODEL_ARCHIVE_LIST,
+            EsmForMaskedLM,
+            EsmForSequenceClassification,
+            EsmForTokenClassification,
+            EsmModel,
+            EsmPreTrainedModel,
+        )
+        from .modeling_esmfold import EsmFoldPreTrainedModel, EsmForProteinFolding
+
+    try:
+        if not is_tf_available():
+            raise OptionalDependencyNotAvailable()
+    except OptionalDependencyNotAvailable:
+        pass
+    else:
+        from .modeling_tf_esm import (
+            TF_ESM_PRETRAINED_MODEL_ARCHIVE_LIST,
+            TFEsmForMaskedLM,
+            TFEsmForSequenceClassification,
+            TFEsmForTokenClassification,
+            TFEsmModel,
+            TFEsmPreTrainedModel,
+        )
+
+
+else:
+    import sys
+
+    sys.modules[__name__] = _LazyModule(__name__, globals()["__file__"], _import_structure)

llmeval-env/lib/python3.10/site-packages/transformers/models/esm/configuration_esm.py

@@ -0,0 +1,361 @@
+# coding=utf-8
+# Copyright 2022 Meta and The HuggingFace Inc. team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+""" ESM model configuration"""
+
+from dataclasses import asdict, dataclass
+from typing import Optional
+
+from ...configuration_utils import PretrainedConfig
+from ...utils import logging
+
+
+logger = logging.get_logger(__name__)
+
+# TODO Update this
+
+from ..deprecated._archive_maps import ESM_PRETRAINED_CONFIG_ARCHIVE_MAP  # noqa: F401, E402
+
+
+class EsmConfig(PretrainedConfig):
+    r"""
+    This is the configuration class to store the configuration of a [`ESMModel`]. It is used to instantiate a ESM model
+    according to the specified arguments, defining the model architecture. Instantiating a configuration with the
+    defaults will yield a similar configuration to that of the ESM
+    [facebook/esm-1b](https://huggingface.co/facebook/esm-1b) architecture.
+
+    Configuration objects inherit from [`PretrainedConfig`] and can be used to control the model outputs. Read the
+    documentation from [`PretrainedConfig`] for more information.
+
+
+    Args:
+        vocab_size (`int`, *optional*):
+            Vocabulary size of the ESM model. Defines the number of different tokens that can be represented by the
+            `inputs_ids` passed when calling [`ESMModel`].
+        mask_token_id (`int`, *optional*):
+            The index of the mask token in the vocabulary. This must be included in the config because of the
+            "mask-dropout" scaling trick, which will scale the inputs depending on the number of masked tokens.
+        pad_token_id (`int`, *optional*):
+            The index of the padding token in the vocabulary. This must be included in the config because certain parts
+            of the ESM code use this instead of the attention mask.
+        hidden_size (`int`, *optional*, defaults to 768):
+            Dimensionality of the encoder layers and the pooler layer.
+        num_hidden_layers (`int`, *optional*, defaults to 12):
+            Number of hidden layers in the Transformer encoder.
+        num_attention_heads (`int`, *optional*, defaults to 12):
+            Number of attention heads for each attention layer in the Transformer encoder.
+        intermediate_size (`int`, *optional*, defaults to 3072):
+            Dimensionality of the "intermediate" (often named feed-forward) layer in the Transformer encoder.
+        hidden_dropout_prob (`float`, *optional*, defaults to 0.1):
+            The dropout probability for all fully connected layers in the embeddings, encoder, and pooler.
+        attention_probs_dropout_prob (`float`, *optional*, defaults to 0.1):
+            The dropout ratio for the attention probabilities.
+        max_position_embeddings (`int`, *optional*, defaults to 1026):
+            The maximum sequence length that this model might ever be used with. Typically set this to something large
+            just in case (e.g., 512 or 1024 or 2048).
+        initializer_range (`float`, *optional*, defaults to 0.02):
+            The standard deviation of the truncated_normal_initializer for initializing all weight matrices.
+        layer_norm_eps (`float`, *optional*, defaults to 1e-12):
+            The epsilon used by the layer normalization layers.
+        position_embedding_type (`str`, *optional*, defaults to `"absolute"`):
+            Type of position embedding. Choose one of `"absolute"`, `"relative_key"`, `"relative_key_query", "rotary"`.
+            For positional embeddings use `"absolute"`. For more information on `"relative_key"`, please refer to
+            [Self-Attention with Relative Position Representations (Shaw et al.)](https://arxiv.org/abs/1803.02155).
+            For more information on `"relative_key_query"`, please refer to *Method 4* in [Improve Transformer Models
+            with Better Relative Position Embeddings (Huang et al.)](https://arxiv.org/abs/2009.13658).
+        is_decoder (`bool`, *optional*, defaults to `False`):
+            Whether the model is used as a decoder or not. If `False`, the model is used as an encoder.
+        use_cache (`bool`, *optional*, defaults to `True`):
+            Whether or not the model should return the last key/values attentions (not used by all models). Only
+            relevant if `config.is_decoder=True`.
+        emb_layer_norm_before (`bool`, *optional*):
+            Whether to apply layer normalization after embeddings but before the main stem of the network.
+        token_dropout (`bool`, defaults to `False`):
+            When this is enabled, masked tokens are treated as if they had been dropped out by input dropout.
+
+    Examples:
+
+    ```python
+    >>> from transformers import EsmModel, EsmConfig
+
+    >>> # Initializing a ESM facebook/esm-1b style configuration >>> configuration = EsmConfig()
+
+    >>> # Initializing a model from the configuration >>> model = ESMModel(configuration)
+
+    >>> # Accessing the model configuration >>> configuration = model.config
+    ```"""
+
+    model_type = "esm"
+
+    def __init__(
+        self,
+        vocab_size=None,
+        mask_token_id=None,
+        pad_token_id=None,
+        hidden_size=768,
+        num_hidden_layers=12,
+        num_attention_heads=12,
+        intermediate_size=3072,
+        hidden_dropout_prob=0.1,
+        attention_probs_dropout_prob=0.1,
+        max_position_embeddings=1026,
+        initializer_range=0.02,
+        layer_norm_eps=1e-12,
+        position_embedding_type="absolute",
+        use_cache=True,
+        emb_layer_norm_before=None,
+        token_dropout=False,
+        is_folding_model=False,
+        esmfold_config=None,
+        vocab_list=None,
+        **kwargs,
+    ):
+        super().__init__(pad_token_id=pad_token_id, mask_token_id=mask_token_id, **kwargs)
+
+        self.vocab_size = vocab_size
+        self.hidden_size = hidden_size
+        self.num_hidden_layers = num_hidden_layers
+        self.num_attention_heads = num_attention_heads
+        self.intermediate_size = intermediate_size
+        self.hidden_dropout_prob = hidden_dropout_prob
+        self.attention_probs_dropout_prob = attention_probs_dropout_prob
+        self.max_position_embeddings = max_position_embeddings
+        self.initializer_range = initializer_range
+        self.layer_norm_eps = layer_norm_eps
+        self.position_embedding_type = position_embedding_type
+        self.use_cache = use_cache
+        self.emb_layer_norm_before = emb_layer_norm_before
+        self.token_dropout = token_dropout
+        self.is_folding_model = is_folding_model
+        if is_folding_model:
+            if esmfold_config is None:
+                logger.info("No esmfold_config supplied for folding model, using default values.")
+                esmfold_config = EsmFoldConfig()
+            elif isinstance(esmfold_config, dict):
+                esmfold_config = EsmFoldConfig(**esmfold_config)
+            self.esmfold_config = esmfold_config
+            if vocab_list is None:
+                logger.warning("No vocab_list supplied for folding model, assuming the ESM-2 vocabulary!")
+                self.vocab_list = get_default_vocab_list()
+            else:
+                self.vocab_list = vocab_list
+        else:
+            self.esmfold_config = None
+            self.vocab_list = None
+        if self.esmfold_config is not None and getattr(self.esmfold_config, "use_esm_attn_map", False):
+            raise ValueError("The HuggingFace port of ESMFold does not support use_esm_attn_map at this time!")
+
+    def to_dict(self):
+        """
+        Serializes this instance to a Python dictionary. Override the default [`~PretrainedConfig.to_dict`].
+
+        Returns:
+            `Dict[str, any]`: Dictionary of all the attributes that make up this configuration instance,
+        """
+        output = super().to_dict()
+        if isinstance(self.esmfold_config, EsmFoldConfig):
+            output["esmfold_config"] = self.esmfold_config.to_dict()
+        return output
+
+
+@dataclass
+class EsmFoldConfig:
+    esm_type: str = None
+    fp16_esm: bool = True
+    use_esm_attn_map: bool = False
+    esm_ablate_pairwise: bool = False
+    esm_ablate_sequence: bool = False
+    esm_input_dropout: float = 0
+
+    embed_aa: bool = True
+    bypass_lm: bool = False
+
+    lddt_head_hid_dim: int = 128
+    trunk: "TrunkConfig" = None
+
+    def __post_init__(self):
+        if self.trunk is None:
+            self.trunk = TrunkConfig()
+        elif isinstance(self.trunk, dict):
+            self.trunk = TrunkConfig(**self.trunk)
+
+    def to_dict(self):
+        """
+        Serializes this instance to a Python dictionary. Override the default [`~PretrainedConfig.to_dict`].
+
+        Returns:
+            `Dict[str, any]`: Dictionary of all the attributes that make up this configuration instance,
+        """
+        output = asdict(self)
+        output["trunk"] = self.trunk.to_dict()
+        return output
+
+
+@dataclass
+class TrunkConfig:
+    num_blocks: int = 48
+    sequence_state_dim: int = 1024
+    pairwise_state_dim: int = 128
+    sequence_head_width: int = 32
+    pairwise_head_width: int = 32
+    position_bins: int = 32
+    dropout: float = 0
+    layer_drop: float = 0
+    cpu_grad_checkpoint: bool = False
+    max_recycles: int = 4
+    chunk_size: Optional[int] = 128
+    structure_module: "StructureModuleConfig" = None
+
+    def __post_init__(self):
+        if self.structure_module is None:
+            self.structure_module = StructureModuleConfig()
+        elif isinstance(self.structure_module, dict):
+            self.structure_module = StructureModuleConfig(**self.structure_module)
+
+        if self.max_recycles <= 0:
+            raise ValueError(f"`max_recycles` should be positive, got {self.max_recycles}.")
+        if self.sequence_state_dim % self.sequence_state_dim != 0:
+            raise ValueError(
+                "`sequence_state_dim` should be a round multiple of `sequence_state_dim`, got"
+                f" {self.sequence_state_dim} and {self.sequence_state_dim}."
+            )
+        if self.pairwise_state_dim % self.pairwise_state_dim != 0:
+            raise ValueError(
+                "`pairwise_state_dim` should be a round multiple of `pairwise_state_dim`, got"
+                f" {self.pairwise_state_dim} and {self.pairwise_state_dim}."
+            )
+
+        sequence_num_heads = self.sequence_state_dim // self.sequence_head_width
+        pairwise_num_heads = self.pairwise_state_dim // self.pairwise_head_width
+
+        if self.sequence_state_dim != sequence_num_heads * self.sequence_head_width:
+            raise ValueError(
+                "`sequence_state_dim` should be equal to `sequence_num_heads * sequence_head_width, got"
+                f" {self.sequence_state_dim} != {sequence_num_heads} * {self.sequence_head_width}."
+            )
+        if self.pairwise_state_dim != pairwise_num_heads * self.pairwise_head_width:
+            raise ValueError(
+                "`pairwise_state_dim` should be equal to `pairwise_num_heads * pairwise_head_width, got"
+                f" {self.pairwise_state_dim} != {pairwise_num_heads} * {self.pairwise_head_width}."
+            )
+        if self.pairwise_state_dim % 2 != 0:
+            raise ValueError(f"`pairwise_state_dim` should be even, got {self.pairwise_state_dim}.")
+
+        if self.dropout >= 0.4:
+            raise ValueError(f"`dropout` should not be greater than 0.4, got {self.dropout}.")
+
+    def to_dict(self):
+        """
+        Serializes this instance to a Python dictionary. Override the default [`~PretrainedConfig.to_dict`].
+
+        Returns:
+            `Dict[str, any]`: Dictionary of all the attributes that make up this configuration instance,
+        """
+        output = asdict(self)
+        output["structure_module"] = self.structure_module.to_dict()
+        return output
+
+
+@dataclass
+class StructureModuleConfig:
+    """
+    Args:
+        sequence_dim:
+            Single representation channel dimension
+        pairwise_dim:
+            Pair representation channel dimension
+        ipa_dim:
+            IPA hidden channel dimension
+        resnet_dim:
+            Angle resnet (Alg. 23 lines 11-14) hidden channel dimension
+        num_heads_ipa:
+            Number of IPA heads
+        num_qk_points:
+            Number of query/key points to generate during IPA
+        num_v_points:
+            Number of value points to generate during IPA
+        dropout_rate:
+            Dropout rate used throughout the layer
+        num_blocks:
+            Number of structure module blocks
+        num_transition_layers:
+            Number of layers in the single representation transition (Alg. 23 lines 8-9)
+        num_resnet_blocks:
+            Number of blocks in the angle resnet
+        num_angles:
+            Number of angles to generate in the angle resnet
+        trans_scale_factor:
+            Scale of single representation transition hidden dimension
+        epsilon:
+            Small number used in angle resnet normalization
+        inf:
+            Large number used for attention masking
+    """
+
+    sequence_dim: int = 384
+    pairwise_dim: int = 128
+    ipa_dim: int = 16
+    resnet_dim: int = 128
+    num_heads_ipa: int = 12
+    num_qk_points: int = 4
+    num_v_points: int = 8
+    dropout_rate: float = 0.1
+    num_blocks: int = 8
+    num_transition_layers: int = 1
+    num_resnet_blocks: int = 2
+    num_angles: int = 7
+    trans_scale_factor: int = 10
+    epsilon: float = 1e-8
+    inf: float = 1e5
+
+    def to_dict(self):
+        return asdict(self)
+
+
+def get_default_vocab_list():
+    return (
+        "<cls>",
+        "<pad>",
+        "<eos>",
+        "<unk>",
+        "L",
+        "A",
+        "G",
+        "V",
+        "S",
+        "E",
+        "R",
+        "T",
+        "I",
+        "D",
+        "P",
+        "K",
+        "Q",
+        "N",
+        "F",
+        "Y",
+        "M",
+        "H",
+        "W",
+        "C",
+        "X",
+        "B",
+        "U",
+        "Z",
+        "O",
+        ".",
+        "-",
+        "<null_1>",
+        "<mask>",
+    )

llmeval-env/lib/python3.10/site-packages/transformers/models/esm/convert_esm.py

@@ -0,0 +1,400 @@
+# coding=utf-8
+# Copyright 2022 The HuggingFace Inc. team.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Convert ESM checkpoint."""
+
+
+import argparse
+import pathlib
+from pathlib import Path
+from tempfile import TemporaryDirectory
+
+import esm as esm_module
+import torch
+from esm.esmfold.v1.misc import batch_encode_sequences as esmfold_encode_sequences
+from esm.esmfold.v1.pretrained import esmfold_v1
+
+from transformers.models.esm.configuration_esm import EsmConfig, EsmFoldConfig
+from transformers.models.esm.modeling_esm import (
+    EsmForMaskedLM,
+    EsmForSequenceClassification,
+    EsmIntermediate,
+    EsmLayer,
+    EsmOutput,
+    EsmSelfAttention,
+    EsmSelfOutput,
+)
+from transformers.models.esm.modeling_esmfold import EsmForProteinFolding
+from transformers.models.esm.tokenization_esm import EsmTokenizer
+from transformers.utils import logging
+
+
+logging.set_verbosity_info()
+logger = logging.get_logger(__name__)
+
+SAMPLE_DATA = [
+    (
+        "protein1",
+        "MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA",
+    ),
+    ("protein2", "MKTVRQERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVATPRGYVLA"),
+    ("protein3", "MKTVRQERLKSI<mask>RILERSKEPVSGAQLAEELS<mask>SRQVIVQDIAYLRSLGYN<mask>VATPRGYVLAGG"),
+    ("protein4", "MKTVRQERLKSI<mask>RILERSKEPVSGAQLAEELS<mask>SRQVIVQDIAYLRSLGYN<mask>VATPRGYVLA"),
+]
+
+MODEL_MAPPING = {
+    "esm1b_t33_650M_UR50S": esm_module.pretrained.esm1b_t33_650M_UR50S,
+    "esm1v_t33_650M_UR90S_1": esm_module.pretrained.esm1v_t33_650M_UR90S_1,
+    "esm1v_t33_650M_UR90S_2": esm_module.pretrained.esm1v_t33_650M_UR90S_2,
+    "esm1v_t33_650M_UR90S_3": esm_module.pretrained.esm1v_t33_650M_UR90S_3,
+    "esm1v_t33_650M_UR90S_4": esm_module.pretrained.esm1v_t33_650M_UR90S_4,
+    "esm1v_t33_650M_UR90S_5": esm_module.pretrained.esm1v_t33_650M_UR90S_5,
+    "esm2_t48_15B_UR50D": esm_module.pretrained.esm2_t48_15B_UR50D,
+    "esm2_t36_3B_UR50D": esm_module.pretrained.esm2_t36_3B_UR50D,
+    "esm2_t33_650M_UR50D": esm_module.pretrained.esm2_t33_650M_UR50D,
+    "esm2_t30_150M_UR50D": esm_module.pretrained.esm2_t30_150M_UR50D,
+    "esm2_t12_35M_UR50D": esm_module.pretrained.esm2_t12_35M_UR50D,
+    "esm2_t6_8M_UR50D": esm_module.pretrained.esm2_t6_8M_UR50D,
+    "esmfold_v1": esmfold_v1,
+}
+
+restypes = list("ARNDCQEGHILKMFPSTWYV")
+
+restypes_with_x = restypes + ["X"]
+restypes_with_extras = restypes_with_x + ["<pad>", "<mask>", "<cls>", "<sep>", "<eos>"]
+
+
+def get_esmfold_tokenizer():
+    with TemporaryDirectory() as tempdir:
+        vocab = "\n".join(restypes_with_extras)
+        vocab_file = Path(tempdir) / "vocab.txt"
+        vocab_file.write_text(vocab)
+        hf_tokenizer = EsmTokenizer(vocab_file=str(vocab_file))
+    hf_tokenizer.pad_token_id = 0  # Overlaps with 'A' but that seems to be what they want
+    return hf_tokenizer
+
+
+def transfer_and_check_weights(original_module, our_module):
+    status = our_module.load_state_dict(original_module.state_dict())
+    if status.missing_keys:
+        raise ValueError(f"Missing keys: {status.missing_keys}")
+    if status.unexpected_keys:
+        raise ValueError(f"Unexpected keys: {status.unexpected_keys}")
+
+
+def convert_esm_checkpoint_to_pytorch(
+    model: str, pytorch_dump_folder_path: str, classification_head: bool, push_to_repo: str, auth_token: str
+):
+    """
+    Copy/paste/tweak esm's weights to our BERT structure.
+    """
+    if model.startswith("esmfold"):
+        esm = MODEL_MAPPING[model]()
+    else:
+        esm, alphabet = MODEL_MAPPING[model]()
+    esm.eval()  # disable dropout
+
+    if model.startswith("esmfold"):
+        embed_dim = esm.esm.embed_dim
+        num_layers = esm.esm.num_layers
+        num_attention_heads = esm.esm.attention_heads
+        intermediate_size = 4 * embed_dim
+        token_dropout = esm.esm.token_dropout
+        emb_layer_norm_before = False  # This code path does not exist in ESM-2
+        position_embedding_type = "rotary"
+        is_folding_model = True
+        esmfold_config = EsmFoldConfig()
+        for key, val in esm.cfg.items():
+            if hasattr(esmfold_config, key) and key != "trunk":
+                setattr(esmfold_config, key, val)
+        for key, val in esm.cfg.trunk.items():
+            if hasattr(esmfold_config.trunk, key) and key != "structure_module":
+                setattr(esmfold_config.trunk, key, val)
+        for key, val in esm.cfg.trunk.structure_module.items():
+            if hasattr(esmfold_config.trunk.structure_module, key):
+                setattr(esmfold_config.trunk.structure_module, key, val)
+    elif hasattr(esm, "args"):
+        # Indicates an ESM-1b or ESM-1v model
+        embed_dim = esm.args.embed_dim
+        num_layers = esm.args.layers
+        num_attention_heads = esm.args.attention_heads
+        intermediate_size = esm.args.ffn_embed_dim
+        token_dropout = esm.args.token_dropout
+        emb_layer_norm_before = True if esm.emb_layer_norm_before else False
+        position_embedding_type = "absolute"
+        is_folding_model = False
+        esmfold_config = None
+    else:
+        # Indicates an ESM-2 model
+        embed_dim = esm.embed_dim
+        num_layers = esm.num_layers
+        num_attention_heads = esm.attention_heads
+        intermediate_size = 4 * embed_dim  # This is hardcoded in ESM-2
+        token_dropout = esm.token_dropout
+        emb_layer_norm_before = False  # This code path does not exist in ESM-2
+        position_embedding_type = "rotary"
+        is_folding_model = False
+        esmfold_config = None
+
+    if is_folding_model:
+        alphabet = esm.esm.alphabet
+    vocab_list = tuple(alphabet.all_toks)
+    mask_token_id = alphabet.mask_idx
+    pad_token_id = alphabet.padding_idx
+
+    if is_folding_model:
+        original_esm_model = esm.esm
+    else:
+        original_esm_model = esm
+
+    config = EsmConfig(
+        vocab_size=original_esm_model.embed_tokens.num_embeddings,
+        mask_token_id=mask_token_id,
+        hidden_size=embed_dim,
+        num_hidden_layers=num_layers,
+        num_attention_heads=num_attention_heads,
+        intermediate_size=intermediate_size,
+        max_position_embeddings=1026,
+        layer_norm_eps=1e-5,  # PyTorch default used in fairseq
+        attention_probs_dropout_prob=0.0,
+        hidden_dropout_prob=0.0,
+        pad_token_id=pad_token_id,
+        emb_layer_norm_before=emb_layer_norm_before,
+        token_dropout=token_dropout,
+        position_embedding_type=position_embedding_type,
+        is_folding_model=is_folding_model,
+        esmfold_config=esmfold_config,
+        vocab_list=vocab_list,
+    )
+    if classification_head:
+        config.num_labels = esm.classification_heads["mnli"].out_proj.weight.shape[0]
+    print("Our ESM config:", config)
+
+    if model.startswith("esmfold"):
+        model_class = EsmForProteinFolding
+    elif classification_head:
+        model_class = EsmForSequenceClassification
+    else:
+        model_class = EsmForMaskedLM
+    model = model_class(config)
+    model.eval()
+
+    # Now let's copy all the weights.
+    # Embeddings
+    model.esm.embeddings.word_embeddings.weight = original_esm_model.embed_tokens.weight
+    if position_embedding_type == "absolute":
+        model.esm.embeddings.position_embeddings.weight = original_esm_model.embed_positions.weight
+
+    if config.emb_layer_norm_before:
+        model.esm.embeddings.layer_norm.weight = original_esm_model.emb_layer_norm_before.weight
+        model.esm.embeddings.layer_norm.bias = original_esm_model.emb_layer_norm_before.bias
+
+    model.esm.encoder.emb_layer_norm_after.weight = original_esm_model.emb_layer_norm_after.weight
+    model.esm.encoder.emb_layer_norm_after.bias = original_esm_model.emb_layer_norm_after.bias
+
+    for i in range(config.num_hidden_layers):
+        # Encoder: start of layer
+        layer: EsmLayer = model.esm.encoder.layer[i]
+        # esm_layer: TransformerSentenceEncoderLayer = original_esm_model.layers[i]
+        esm_layer = original_esm_model.layers[i]
+
+        # self attention
+        self_attn: EsmSelfAttention = layer.attention.self
+        assert (
+            esm_layer.self_attn.k_proj.weight.data.shape
+            == esm_layer.self_attn.q_proj.weight.data.shape
+            == esm_layer.self_attn.v_proj.weight.data.shape
+            == torch.Size((config.hidden_size, config.hidden_size))
+        )
+
+        self_attn.query.weight.data = esm_layer.self_attn.q_proj.weight
+        self_attn.query.bias.data = esm_layer.self_attn.q_proj.bias
+        self_attn.key.weight.data = esm_layer.self_attn.k_proj.weight
+        self_attn.key.bias.data = esm_layer.self_attn.k_proj.bias
+        self_attn.value.weight.data = esm_layer.self_attn.v_proj.weight
+        self_attn.value.bias.data = esm_layer.self_attn.v_proj.bias
+
+        if getattr(esm_layer.self_attn, "rot_emb", None) is not None:
+            # Matt: Although inv_freq is not a trainable weight, it is computed at model init and cached.
+            # During the training of ESM-2 the model was converted to float16 precision, which also converts
+            # the inv_freq tensor, and the loss of precision remains even if the model is loaded later as float32.
+            # If we recompute inv_freq without this loss of precision then we will get subtly different rotary
+            # embeddings, which are enough to cause significant discrepancies in model outputs. To avoid this,
+            # we make sure the new model copies the data from the old inv_freq.
+            self_attn.rotary_embeddings.inv_freq.data = esm_layer.self_attn.rot_emb.inv_freq
+
+        # LayerNorm changes for pre-activation
+        layer.attention.LayerNorm.weight = esm_layer.self_attn_layer_norm.weight
+        layer.attention.LayerNorm.bias = esm_layer.self_attn_layer_norm.bias
+        layer.LayerNorm.weight = esm_layer.final_layer_norm.weight
+        layer.LayerNorm.bias = esm_layer.final_layer_norm.bias
+
+        # self-attention output
+        self_output: EsmSelfOutput = layer.attention.output
+        assert self_output.dense.weight.shape == esm_layer.self_attn.out_proj.weight.shape
+        self_output.dense.weight = esm_layer.self_attn.out_proj.weight
+        self_output.dense.bias = esm_layer.self_attn.out_proj.bias
+
+        # intermediate
+        intermediate: EsmIntermediate = layer.intermediate
+        assert intermediate.dense.weight.shape == esm_layer.fc1.weight.shape
+        intermediate.dense.weight = esm_layer.fc1.weight
+        intermediate.dense.bias = esm_layer.fc1.bias
+
+        # output
+        bert_output: EsmOutput = layer.output
+        assert bert_output.dense.weight.shape == esm_layer.fc2.weight.shape
+        bert_output.dense.weight = esm_layer.fc2.weight
+        bert_output.dense.bias = esm_layer.fc2.bias
+        # end of layer
+
+    if is_folding_model:
+        model.esm_s_combine.data = esm.esm_s_combine.data
+        model.af2_to_esm.data = esm.af2_to_esm.data
+        transfer_and_check_weights(esm.embedding, model.embedding)
+        transfer_and_check_weights(esm.esm_s_mlp, model.esm_s_mlp)
+        transfer_and_check_weights(esm.trunk, model.trunk)
+        transfer_and_check_weights(esm.distogram_head, model.distogram_head)
+        transfer_and_check_weights(esm.ptm_head, model.ptm_head)
+        transfer_and_check_weights(esm.lm_head, model.lm_head)
+        transfer_and_check_weights(esm.lddt_head, model.lddt_head)
+
+    elif classification_head:
+        model.classifier.dense.weight = esm.esm.classification_heads["mnli"].dense.weight
+        model.classifier.dense.bias = esm.classification_heads["mnli"].dense.bias
+        model.classifier.out_proj.weight = esm.classification_heads["mnli"].out_proj.weight
+        model.classifier.out_proj.bias = esm.classification_heads["mnli"].out_proj.bias
+    else:
+        # LM Head
+        model.lm_head.dense.weight = esm.lm_head.dense.weight
+        model.lm_head.dense.bias = esm.lm_head.dense.bias
+        model.lm_head.layer_norm.weight = esm.lm_head.layer_norm.weight
+        model.lm_head.layer_norm.bias = esm.lm_head.layer_norm.bias
+        model.lm_head.decoder.weight = esm.lm_head.weight
+        model.lm_head.bias = esm.lm_head.bias
+
+    # Contact prediction head
+    transfer_and_check_weights(esm.contact_head, model.esm.contact_head)
+
+    # Prepare data (first 2 sequences from ESMStructuralSplitDataset superfamily / 4)
+    if is_folding_model:
+        # Folding models aren't trained on masked inputs and don't like mask tokens.
+        sample_data = SAMPLE_DATA[:2]
+    else:
+        sample_data = SAMPLE_DATA
+
+    if is_folding_model:
+        hf_tokenizer = get_esmfold_tokenizer()
+        hf_tokens = hf_tokenizer(
+            [row[1] for row in sample_data], return_tensors="pt", padding=True, add_special_tokens=False
+        )
+        esmfold_aas, esmfold_mask, _, _, _ = esmfold_encode_sequences([row[1] for row in sample_data])
+        success = torch.all(hf_tokens["input_ids"] == esmfold_aas) and torch.all(
+            hf_tokens["attention_mask"] == esmfold_mask
+        )
+    else:
+        # Let's check that we get the same results.
+        batch_converter = alphabet.get_batch_converter()
+        batch_labels, batch_strs, batch_tokens = batch_converter(sample_data)
+        # Prepare tokenizer and make sure it matches
+        with TemporaryDirectory() as tempdir:
+            vocab = "\n".join(alphabet.all_toks)
+            vocab_file = Path(tempdir) / "vocab.txt"
+            vocab_file.write_text(vocab)
+            hf_tokenizer = EsmTokenizer(vocab_file=str(vocab_file))
+
+        hf_tokens = hf_tokenizer([row[1] for row in sample_data], return_tensors="pt", padding=True)
+        success = torch.all(hf_tokens["input_ids"] == batch_tokens)
+
+    print("Do both models tokenizers output the same tokens?", "🔥" if success else "💩")
+    if not success:
+        raise Exception("Tokenization does not match!")
+
+    with torch.no_grad():
+        if is_folding_model:
+            # Let's test the model in parts
+            # ESMFold always converts the ESM stem to float16, which requires float16 ops
+            # that don't exist on CPU. Therefore, to test it we need to run it on GPU. However,
+            # ESMFold is what we in the community call a "big boy" and so we desperately avoid putting both the
+            # original and the converted model on the GPU at the same time.
+            their_output = esm.cuda().infer([row[1] for row in sample_data])
+            our_output = model.cuda()(
+                input_ids=hf_tokens["input_ids"].cuda(), attention_mask=hf_tokens["attention_mask"].cuda()
+            )
+        else:
+            our_output = model(**hf_tokens, output_hidden_states=True)
+            our_output = our_output["logits"]
+            if classification_head:
+                their_output = esm.model.classification_heads["mnli"](esm.extract_features(batch_tokens))
+            else:
+                their_output = esm(hf_tokens["input_ids"], repr_layers=list(range(999)))
+                their_output = their_output["logits"]
+
+        if is_folding_model:
+            max_absolute_diff = torch.max(torch.abs(our_output["positions"] - their_output["positions"])).item()
+            success = torch.allclose(our_output["positions"], their_output["positions"], atol=1e-5)
+        else:
+            max_absolute_diff = torch.max(torch.abs(our_output - their_output)).item()
+            success = torch.allclose(our_output, their_output, atol=1e-5)
+
+        print(f"max_absolute_diff = {max_absolute_diff}")  # ~ 1e-5
+        print("Do both models output the same tensors?", "🔥" if success else "💩")
+
+        if not success:
+            raise Exception("Something went wRoNg")
+
+        if not is_folding_model:
+            # Let's check contact prediction too
+            our_output = model.predict_contacts(hf_tokens["input_ids"], hf_tokens["attention_mask"])
+            their_output = esm.predict_contacts(hf_tokens["input_ids"])
+            max_absolute_diff = torch.max(torch.abs(our_output - their_output)).item()
+            success = torch.allclose(our_output, their_output, atol=1e-5)
+
+            print("Contact prediction testing:")
+            print(f"max_absolute_diff = {max_absolute_diff}")  # ~ 1e-5
+            print("Do both models output the same tensors?", "🔥" if success else "💩")
+
+            if not success:
+                raise Exception("Something went wRoNg")
+
+        pathlib.Path(pytorch_dump_folder_path).mkdir(parents=True, exist_ok=True)
+        print(f"Saving model to {pytorch_dump_folder_path}")
+        model.save_pretrained(pytorch_dump_folder_path)
+
+        del esm  # Free up some memory before continuing
+
+    print(f"Saving tokenizer to {pytorch_dump_folder_path}")
+    hf_tokenizer.save_pretrained(pytorch_dump_folder_path)
+
+    if push_to_repo:
+        model.push_to_hub(repo_id=push_to_repo, token_token=auth_token)
+        hf_tokenizer.push_to_hub(repo_id=push_to_repo, token_token=auth_token)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    # Required parameters
+    parser.add_argument(
+        "--pytorch_dump_folder_path", type=str, required=True, help="Path to the output PyTorch model."
+    )
+    parser.add_argument(
+        "--classification_head", action="store_true", help="Whether to convert a final classification head."
+    )
+    parser.add_argument("--model", default=None, type=str, required=True, help="Name of model to convert.")
+    parser.add_argument("--push_to_repo", type=str, help="Repo to upload to (including username!).")
+    parser.add_argument("--auth_token", type=str, help="HuggingFace auth token.")
+    args = parser.parse_args()
+    convert_esm_checkpoint_to_pytorch(
+        args.model, args.pytorch_dump_folder_path, args.classification_head, args.push_to_repo, args.auth_token
+    )

llmeval-env/lib/python3.10/site-packages/transformers/models/esm/modeling_esm.py

@@ -0,0 +1,1265 @@
+# coding=utf-8
+# Copyright 2022 Meta and The HuggingFace Inc. team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+""" PyTorch ESM model."""
+
+import math
+from typing import List, Optional, Tuple, Union
+
+import torch
+import torch.utils.checkpoint
+from torch import nn
+from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss
+
+from ...file_utils import add_code_sample_docstrings, add_start_docstrings, add_start_docstrings_to_model_forward
+from ...modeling_outputs import (
+    BaseModelOutputWithPastAndCrossAttentions,
+    BaseModelOutputWithPoolingAndCrossAttentions,
+    MaskedLMOutput,
+    SequenceClassifierOutput,
+    TokenClassifierOutput,
+)
+from ...modeling_utils import PreTrainedModel, find_pruneable_heads_and_indices, prune_linear_layer
+from ...utils import logging
+from .configuration_esm import EsmConfig
+
+
+logger = logging.get_logger(__name__)
+
+_CHECKPOINT_FOR_DOC = "facebook/esm2_t6_8M_UR50D"
+_CONFIG_FOR_DOC = "EsmConfig"
+
+
+from ..deprecated._archive_maps import ESM_PRETRAINED_MODEL_ARCHIVE_LIST  # noqa: F401, E402
+
+
+def rotate_half(x):
+    x1, x2 = x.chunk(2, dim=-1)
+    return torch.cat((-x2, x1), dim=-1)
+
+
+def apply_rotary_pos_emb(x, cos, sin):
+    cos = cos[:, :, : x.shape[-2], :]
+    sin = sin[:, :, : x.shape[-2], :]
+
+    return (x * cos) + (rotate_half(x) * sin)
+
+
+def gelu(x):
+    """
+    This is the gelu implementation from the original ESM repo. Using F.gelu yields subtly wrong results.
+    """
+    return x * 0.5 * (1.0 + torch.erf(x / math.sqrt(2.0)))
+
+
+def symmetrize(x):
+    "Make layer symmetric in final two dimensions, used for contact prediction."
+    return x + x.transpose(-1, -2)
+
+
+def average_product_correct(x):
+    "Perform average product correct, used for contact prediction."
+    a1 = x.sum(-1, keepdims=True)
+    a2 = x.sum(-2, keepdims=True)
+    a12 = x.sum((-1, -2), keepdims=True)
+
+    avg = a1 * a2
+    avg.div_(a12)  # in-place to reduce memory
+    normalized = x - avg
+    return normalized
+
+
+class RotaryEmbedding(torch.nn.Module):
+    """
+    Rotary position embeddings based on those in
+    [RoFormer](https://huggingface.co/docs/transformers/model_doc/roformer). Query and keys are transformed by rotation
+    matrices which depend on their relative positions.
+    """
+
+    def __init__(self, dim: int):
+        super().__init__()
+        # Generate and save the inverse frequency buffer (non trainable)
+        inv_freq = 1.0 / (10000 ** (torch.arange(0, dim, 2, dtype=torch.int64).float() / dim))
+        inv_freq = inv_freq
+        self.register_buffer("inv_freq", inv_freq)
+
+        self._seq_len_cached = None
+        self._cos_cached = None
+        self._sin_cached = None
+
+    def _update_cos_sin_tables(self, x, seq_dimension=2):
+        seq_len = x.shape[seq_dimension]
+
+        # Reset the tables if the sequence length has changed,
+        # or if we're on a new device (possibly due to tracing for instance)
+        if seq_len != self._seq_len_cached or self._cos_cached.device != x.device:
+            self._seq_len_cached = seq_len
+            t = torch.arange(x.shape[seq_dimension], device=x.device).type_as(self.inv_freq)
+            freqs = torch.outer(t, self.inv_freq)
+            emb = torch.cat((freqs, freqs), dim=-1).to(x.device)
+
+            self._cos_cached = emb.cos()[None, None, :, :]
+            self._sin_cached = emb.sin()[None, None, :, :]
+
+        return self._cos_cached, self._sin_cached
+
+    def forward(self, q: torch.Tensor, k: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor]:
+        self._cos_cached, self._sin_cached = self._update_cos_sin_tables(k, seq_dimension=-2)
+
+        return (
+            apply_rotary_pos_emb(q, self._cos_cached, self._sin_cached),
+            apply_rotary_pos_emb(k, self._cos_cached, self._sin_cached),
+        )
+
+
+class EsmContactPredictionHead(nn.Module):
+    """Performs symmetrization, apc, and computes a logistic regression on the output features"""
+
+    def __init__(
+        self,
+        in_features: int,
+        bias=True,
+        eos_idx: int = 2,
+    ):
+        super().__init__()
+        self.in_features = in_features
+        self.eos_idx = eos_idx
+        self.regression = nn.Linear(in_features, 1, bias)
+        self.activation = nn.Sigmoid()
+
+    def forward(self, tokens, attentions):
+        # remove eos token attentions
+        eos_mask = tokens.ne(self.eos_idx).to(attentions)
+        eos_mask = eos_mask.unsqueeze(1) * eos_mask.unsqueeze(2)
+        attentions = attentions * eos_mask[:, None, None, :, :]
+        attentions = attentions[..., :-1, :-1]
+        # remove cls token attentions
+        attentions = attentions[..., 1:, 1:]
+        batch_size, layers, heads, seqlen, _ = attentions.size()
+        attentions = attentions.view(batch_size, layers * heads, seqlen, seqlen)
+
+        # features: batch x channels x tokens x tokens (symmetric)
+        attentions = attentions.to(
+            self.regression.weight.device
+        )  # attentions always float32, may need to convert to float16
+        attentions = average_product_correct(symmetrize(attentions))
+        attentions = attentions.permute(0, 2, 3, 1)
+        return self.activation(self.regression(attentions).squeeze(3))
+
+
+class EsmEmbeddings(nn.Module):
+    """
+    Same as BertEmbeddings with a tiny tweak for positional embeddings indexing.
+    """
+
+    def __init__(self, config):
+        super().__init__()
+        self.word_embeddings = nn.Embedding(config.vocab_size, config.hidden_size, padding_idx=config.pad_token_id)
+
+        if config.emb_layer_norm_before:
+            self.layer_norm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+        else:
+            self.layer_norm = None
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+        # position_ids (1, len position emb) is contiguous in memory and exported when serialized
+        self.position_embedding_type = getattr(config, "position_embedding_type", "absolute")
+        self.register_buffer(
+            "position_ids", torch.arange(config.max_position_embeddings).expand((1, -1)), persistent=False
+        )
+
+        self.padding_idx = config.pad_token_id
+        self.position_embeddings = nn.Embedding(
+            config.max_position_embeddings, config.hidden_size, padding_idx=self.padding_idx
+        )
+        self.token_dropout = config.token_dropout
+        self.mask_token_id = config.mask_token_id
+
+    def forward(
+        self, input_ids=None, attention_mask=None, position_ids=None, inputs_embeds=None, past_key_values_length=0
+    ):
+        if position_ids is None:
+            if input_ids is not None:
+                # Create the position ids from the input token ids. Any padded tokens remain padded.
+                position_ids = create_position_ids_from_input_ids(input_ids, self.padding_idx, past_key_values_length)
+            else:
+                position_ids = self.create_position_ids_from_inputs_embeds(inputs_embeds)
+
+        if inputs_embeds is None:
+            inputs_embeds = self.word_embeddings(input_ids)
+
+        # Note that if we want to support ESM-1 (not 1b!) in future then we need to support an
+        # embedding_scale factor here.
+        embeddings = inputs_embeds
+
+        # Matt: ESM has the option to handle masking in MLM in a slightly unusual way. If the token_dropout
+        # flag is False then it is handled in the same was as BERT/RoBERTa. If it is set to True, however,
+        # masked tokens are treated as if they were selected for input dropout and zeroed out.
+        # This "mask-dropout" is compensated for when masked tokens are not present, by scaling embeddings by
+        # a factor of (fraction of unmasked tokens during training) / (fraction of unmasked tokens in sample).
+        # This is analogous to the way that dropout layers scale down outputs during evaluation when not
+        # actually dropping out values (or, equivalently, scale up their un-dropped outputs in training).
+        if self.token_dropout:
+            embeddings = embeddings.masked_fill((input_ids == self.mask_token_id).unsqueeze(-1), 0.0)
+            mask_ratio_train = 0.15 * 0.8  # Hardcoded as the ratio used in all ESM model training runs
+            src_lengths = attention_mask.sum(-1)
+            mask_ratio_observed = (input_ids == self.mask_token_id).sum(-1).float() / src_lengths
+            embeddings = (embeddings * (1 - mask_ratio_train) / (1 - mask_ratio_observed)[:, None, None]).to(
+                embeddings.dtype
+            )
+
+        if self.position_embedding_type == "absolute":
+            position_embeddings = self.position_embeddings(position_ids)
+            embeddings = embeddings + position_embeddings
+
+        if self.layer_norm is not None:
+            embeddings = self.layer_norm(embeddings)
+        if attention_mask is not None:
+            embeddings = (embeddings * attention_mask.unsqueeze(-1)).to(embeddings.dtype)
+        # Matt: I think this line was copied incorrectly from BERT, disabling it for now.
+        # embeddings = self.dropout(embeddings)
+        return embeddings
+
+    def create_position_ids_from_inputs_embeds(self, inputs_embeds):
+        """
+        We are provided embeddings directly. We cannot infer which are padded so just generate sequential position ids.
+
+        Args:
+            inputs_embeds: torch.Tensor
+
+        Returns: torch.Tensor
+        """
+        input_shape = inputs_embeds.size()[:-1]
+        sequence_length = input_shape[1]
+
+        position_ids = torch.arange(
+            self.padding_idx + 1, sequence_length + self.padding_idx + 1, dtype=torch.long, device=inputs_embeds.device
+        )
+        return position_ids.unsqueeze(0).expand(input_shape)
+
+
+class EsmSelfAttention(nn.Module):
+    def __init__(self, config, position_embedding_type=None):
+        super().__init__()
+        if config.hidden_size % config.num_attention_heads != 0 and not hasattr(config, "embedding_size"):
+            raise ValueError(
+                f"The hidden size ({config.hidden_size}) is not a multiple of the number of attention "
+                f"heads ({config.num_attention_heads})"
+            )
+
+        self.num_attention_heads = config.num_attention_heads
+        self.attention_head_size = int(config.hidden_size / config.num_attention_heads)
+        self.all_head_size = self.num_attention_heads * self.attention_head_size
+
+        self.query = nn.Linear(config.hidden_size, self.all_head_size)
+        self.key = nn.Linear(config.hidden_size, self.all_head_size)
+        self.value = nn.Linear(config.hidden_size, self.all_head_size)
+
+        self.dropout = nn.Dropout(config.attention_probs_dropout_prob)
+        self.position_embedding_type = position_embedding_type or getattr(
+            config, "position_embedding_type", "absolute"
+        )
+        self.rotary_embeddings = None
+        if self.position_embedding_type == "relative_key" or self.position_embedding_type == "relative_key_query":
+            self.max_position_embeddings = config.max_position_embeddings
+            self.distance_embedding = nn.Embedding(2 * config.max_position_embeddings - 1, self.attention_head_size)
+        elif self.position_embedding_type == "rotary":
+            self.rotary_embeddings = RotaryEmbedding(dim=self.attention_head_size)
+
+        self.is_decoder = config.is_decoder
+
+    def transpose_for_scores(self, x: torch.Tensor) -> torch.Tensor:
+        new_x_shape = x.size()[:-1] + (self.num_attention_heads, self.attention_head_size)
+        x = x.view(new_x_shape)
+        return x.permute(0, 2, 1, 3)
+
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        encoder_hidden_states: Optional[torch.FloatTensor] = None,
+        encoder_attention_mask: Optional[torch.FloatTensor] = None,
+        past_key_value: Optional[Tuple[Tuple[torch.FloatTensor]]] = None,
+        output_attentions: Optional[bool] = False,
+    ) -> Tuple[torch.Tensor]:
+        mixed_query_layer = self.query(hidden_states)
+
+        # If this is instantiated as a cross-attention module, the keys
+        # and values come from an encoder; the attention mask needs to be
+        # such that the encoder's padding tokens are not attended to.
+        is_cross_attention = encoder_hidden_states is not None
+
+        if is_cross_attention and past_key_value is not None:
+            # reuse k,v, cross_attentions
+            key_layer = past_key_value[0]
+            value_layer = past_key_value[1]
+            attention_mask = encoder_attention_mask
+        elif is_cross_attention:
+            key_layer = self.transpose_for_scores(self.key(encoder_hidden_states))
+            value_layer = self.transpose_for_scores(self.value(encoder_hidden_states))
+            attention_mask = encoder_attention_mask
+        elif past_key_value is not None:
+            key_layer = self.transpose_for_scores(self.key(hidden_states))
+            value_layer = self.transpose_for_scores(self.value(hidden_states))
+            key_layer = torch.cat([past_key_value[0], key_layer], dim=2)
+            value_layer = torch.cat([past_key_value[1], value_layer], dim=2)
+        else:
+            key_layer = self.transpose_for_scores(self.key(hidden_states))
+            value_layer = self.transpose_for_scores(self.value(hidden_states))
+
+        query_layer = self.transpose_for_scores(mixed_query_layer)
+
+        # Matt: Our BERT model (which this code was derived from) scales attention logits down by sqrt(head_dim).
+        # ESM scales the query down by the same factor instead. Modulo numerical stability these are equivalent,
+        # but not when rotary embeddings get involved. Therefore, we scale the query here to match the original
+        # ESM code and fix rotary embeddings.
+        query_layer = query_layer * self.attention_head_size**-0.5
+
+        if self.is_decoder:
+            # if cross_attention save Tuple(torch.Tensor, torch.Tensor) of all cross attention key/value_states.
+            # Further calls to cross_attention layer can then reuse all cross-attention
+            # key/value_states (first "if" case)
+            # if uni-directional self-attention (decoder) save Tuple(torch.Tensor, torch.Tensor) of
+            # all previous decoder key/value_states. Further calls to uni-directional self-attention
+            # can concat previous decoder key/value_states to current projected key/value_states (third "elif" case)
+            # if encoder bi-directional self-attention `past_key_value` is always `None`
+            past_key_value = (key_layer, value_layer)
+
+        if self.position_embedding_type == "rotary":
+            query_layer, key_layer = self.rotary_embeddings(query_layer, key_layer)
+
+        # Take the dot product between "query" and "key" to get the raw attention scores.
+        attention_scores = torch.matmul(query_layer, key_layer.transpose(-1, -2))
+
+        if self.position_embedding_type == "relative_key" or self.position_embedding_type == "relative_key_query":
+            seq_length = hidden_states.size()[1]
+            position_ids_l = torch.arange(seq_length, dtype=torch.long, device=hidden_states.device).view(-1, 1)
+            position_ids_r = torch.arange(seq_length, dtype=torch.long, device=hidden_states.device).view(1, -1)
+            distance = position_ids_l - position_ids_r
+            positional_embedding = self.distance_embedding(distance + self.max_position_embeddings - 1)
+            positional_embedding = positional_embedding.to(dtype=query_layer.dtype)  # fp16 compatibility
+
+            if self.position_embedding_type == "relative_key":
+                relative_position_scores = torch.einsum("bhld,lrd->bhlr", query_layer, positional_embedding)
+                attention_scores = attention_scores + relative_position_scores
+            elif self.position_embedding_type == "relative_key_query":
+                relative_position_scores_query = torch.einsum("bhld,lrd->bhlr", query_layer, positional_embedding)
+                relative_position_scores_key = torch.einsum("bhrd,lrd->bhlr", key_layer, positional_embedding)
+                attention_scores = attention_scores + relative_position_scores_query + relative_position_scores_key
+
+        if attention_mask is not None:
+            # Apply the attention mask is (precomputed for all layers in EsmModel forward() function)
+            attention_scores = attention_scores + attention_mask
+
+        # Normalize the attention scores to probabilities.
+        attention_probs = nn.functional.softmax(attention_scores, dim=-1)
+
+        # This is actually dropping out entire tokens to attend to, which might
+        # seem a bit unusual, but is taken from the original Transformer paper.
+        attention_probs = self.dropout(attention_probs)
+
+        # Mask heads if we want to
+        if head_mask is not None:
+            attention_probs = attention_probs * head_mask
+
+        context_layer = torch.matmul(attention_probs.to(value_layer.dtype), value_layer)
+
+        context_layer = context_layer.permute(0, 2, 1, 3).contiguous()
+        new_context_layer_shape = context_layer.size()[:-2] + (self.all_head_size,)
+        context_layer = context_layer.view(new_context_layer_shape)
+
+        outputs = (context_layer, attention_probs) if output_attentions else (context_layer,)
+
+        if self.is_decoder:
+            outputs = outputs + (past_key_value,)
+        return outputs
+
+
+class EsmSelfOutput(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+
+    def forward(self, hidden_states, input_tensor):
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.dropout(hidden_states)
+        hidden_states = hidden_states + input_tensor
+        return hidden_states
+
+
+class EsmAttention(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.self = EsmSelfAttention(config)
+        self.output = EsmSelfOutput(config)
+        self.pruned_heads = set()
+        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+
+    def prune_heads(self, heads):
+        if len(heads) == 0:
+            return
+        heads, index = find_pruneable_heads_and_indices(
+            heads, self.self.num_attention_heads, self.self.attention_head_size, self.pruned_heads
+        )
+
+        # Prune linear layers
+        self.self.query = prune_linear_layer(self.self.query, index)
+        self.self.key = prune_linear_layer(self.self.key, index)
+        self.self.value = prune_linear_layer(self.self.value, index)
+        self.output.dense = prune_linear_layer(self.output.dense, index, dim=1)
+
+        # Update hyper params and store pruned heads
+        self.self.num_attention_heads = self.self.num_attention_heads - len(heads)
+        self.self.all_head_size = self.self.attention_head_size * self.self.num_attention_heads
+        self.pruned_heads = self.pruned_heads.union(heads)
+
+    def forward(
+        self,
+        hidden_states,
+        attention_mask=None,
+        head_mask=None,
+        encoder_hidden_states=None,
+        encoder_attention_mask=None,
+        past_key_value=None,
+        output_attentions=False,
+    ):
+        hidden_states_ln = self.LayerNorm(hidden_states)
+        self_outputs = self.self(
+            hidden_states_ln,
+            attention_mask,
+            head_mask,
+            encoder_hidden_states,
+            encoder_attention_mask,
+            past_key_value,
+            output_attentions,
+        )
+        attention_output = self.output(self_outputs[0], hidden_states)
+        outputs = (attention_output,) + self_outputs[1:]  # add attentions if we output them
+        return outputs
+
+
+class EsmIntermediate(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.intermediate_size)
+
+    def forward(self, hidden_states: torch.Tensor) -> torch.Tensor:
+        hidden_states = self.dense(hidden_states)
+        hidden_states = gelu(hidden_states)
+        return hidden_states
+
+
+class EsmOutput(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.intermediate_size, config.hidden_size)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+
+    def forward(self, hidden_states, input_tensor):
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.dropout(hidden_states)
+        hidden_states = hidden_states + input_tensor
+        return hidden_states
+
+
+class EsmLayer(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.chunk_size_feed_forward = config.chunk_size_feed_forward
+        self.seq_len_dim = 1
+        self.attention = EsmAttention(config)
+        self.is_decoder = config.is_decoder
+        self.add_cross_attention = config.add_cross_attention
+        if self.add_cross_attention:
+            if not self.is_decoder:
+                raise RuntimeError(f"{self} should be used as a decoder model if cross attention is added")
+            self.crossattention = EsmAttention(config)
+        self.intermediate = EsmIntermediate(config)
+        self.output = EsmOutput(config)
+        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+
+    def forward(
+        self,
+        hidden_states,
+        attention_mask=None,
+        head_mask=None,
+        encoder_hidden_states=None,
+        encoder_attention_mask=None,
+        past_key_value=None,
+        output_attentions=False,
+    ):
+        # decoder uni-directional self-attention cached key/values tuple is at positions 1,2
+        self_attn_past_key_value = past_key_value[:2] if past_key_value is not None else None
+        self_attention_outputs = self.attention(
+            hidden_states,
+            attention_mask,
+            head_mask,
+            output_attentions=output_attentions,
+            past_key_value=self_attn_past_key_value,
+        )
+        attention_output = self_attention_outputs[0]
+
+        # if decoder, the last output is tuple of self-attn cache
+        if self.is_decoder:
+            outputs = self_attention_outputs[1:-1]
+            present_key_value = self_attention_outputs[-1]
+        else:
+            outputs = self_attention_outputs[1:]  # add self attentions if we output attention weights
+
+        cross_attn_present_key_value = None
+        if self.is_decoder and encoder_hidden_states is not None:
+            if not hasattr(self, "crossattention"):
+                raise AttributeError(
+                    f"If `encoder_hidden_states` are passed, {self} has to be instantiated"
+                    " with cross-attention layers by setting `config.add_cross_attention=True`"
+                )
+
+            # cross_attn cached key/values tuple is at positions 3,4 of past_key_value tuple
+            cross_attn_past_key_value = past_key_value[-2:] if past_key_value is not None else None
+            cross_attention_outputs = self.crossattention(
+                attention_output,
+                attention_mask,
+                head_mask,
+                encoder_hidden_states,
+                encoder_attention_mask,
+                cross_attn_past_key_value,
+                output_attentions,
+            )
+            attention_output = cross_attention_outputs[0]
+            outputs = outputs + cross_attention_outputs[1:-1]  # add cross attentions if we output attention weights
+
+            # add cross-attn cache to positions 3,4 of present_key_value tuple
+            cross_attn_present_key_value = cross_attention_outputs[-1]
+            present_key_value = present_key_value + cross_attn_present_key_value
+
+        layer_output = self.feed_forward_chunk(attention_output)
+
+        outputs = (layer_output,) + outputs
+
+        # if decoder, return the attn key/values as the last output
+        if self.is_decoder:
+            outputs = outputs + (present_key_value,)
+        return outputs
+
+    def feed_forward_chunk(self, attention_output):
+        attention_output_ln = self.LayerNorm(attention_output)
+        intermediate_output = self.intermediate(attention_output_ln)
+        layer_output = self.output(intermediate_output, attention_output)
+        return layer_output
+
+
+class EsmEncoder(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.config = config
+        self.layer = nn.ModuleList([EsmLayer(config) for _ in range(config.num_hidden_layers)])
+        self.emb_layer_norm_after = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+        self.gradient_checkpointing = False
+
+    def forward(
+        self,
+        hidden_states,
+        attention_mask=None,
+        head_mask=None,
+        encoder_hidden_states=None,
+        encoder_attention_mask=None,
+        past_key_values=None,
+        use_cache=None,
+        output_attentions=False,
+        output_hidden_states=False,
+        return_dict=True,
+    ):
+        if self.gradient_checkpointing and self.training:
+            if use_cache:
+                logger.warning_once(
+                    "`use_cache=True` is incompatible with `config.gradient_checkpointing=True`. Setting "
+                    "`use_cache=False`..."
+                )
+                use_cache = False
+        all_hidden_states = () if output_hidden_states else None
+        all_self_attentions = () if output_attentions else None
+        all_cross_attentions = () if output_attentions and self.config.add_cross_attention else None
+
+        next_decoder_cache = () if use_cache else None
+        for i, layer_module in enumerate(self.layer):
+            if output_hidden_states:
+                all_hidden_states = all_hidden_states + (hidden_states,)
+
+            layer_head_mask = head_mask[i] if head_mask is not None else None
+            past_key_value = past_key_values[i] if past_key_values is not None else None
+
+            if self.gradient_checkpointing and self.training:
+                layer_outputs = self._gradient_checkpointing_func(
+                    layer_module.__call__,
+                    hidden_states,
+                    attention_mask,
+                    layer_head_mask,
+                    encoder_hidden_states,
+                    encoder_attention_mask,
+                    past_key_value,
+                    output_attentions,
+                )
+            else:
+                layer_outputs = layer_module(
+                    hidden_states,
+                    attention_mask,
+                    layer_head_mask,
+                    encoder_hidden_states,
+                    encoder_attention_mask,
+                    past_key_value,
+                    output_attentions,
+                )
+
+            hidden_states = layer_outputs[0]
+            if use_cache:
+                next_decoder_cache = next_decoder_cache + (layer_outputs[-1],)
+            if output_attentions:
+                all_self_attentions = all_self_attentions + (layer_outputs[1],)
+                if self.config.add_cross_attention:
+                    all_cross_attentions = all_cross_attentions + (layer_outputs[2],)
+
+        if self.emb_layer_norm_after:
+            hidden_states = self.emb_layer_norm_after(hidden_states)
+
+        if output_hidden_states:
+            all_hidden_states = all_hidden_states + (hidden_states,)
+
+        if not return_dict:
+            return tuple(
+                v
+                for v in [
+                    hidden_states,
+                    next_decoder_cache,
+                    all_hidden_states,
+                    all_self_attentions,
+                    all_cross_attentions,
+                ]
+                if v is not None
+            )
+        return BaseModelOutputWithPastAndCrossAttentions(
+            last_hidden_state=hidden_states,
+            past_key_values=next_decoder_cache,
+            hidden_states=all_hidden_states,
+            attentions=all_self_attentions,
+            cross_attentions=all_cross_attentions,
+        )
+
+
+# Copied from transformers.models.bert.modeling_bert.BertPooler
+class EsmPooler(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
+        self.activation = nn.Tanh()
+
+    def forward(self, hidden_states: torch.Tensor) -> torch.Tensor:
+        # We "pool" the model by simply taking the hidden state corresponding
+        # to the first token.
+        first_token_tensor = hidden_states[:, 0]
+        pooled_output = self.dense(first_token_tensor)
+        pooled_output = self.activation(pooled_output)
+        return pooled_output
+
+
+class EsmPreTrainedModel(PreTrainedModel):
+    """
+    An abstract class to handle weights initialization and a simple interface for downloading and loading pretrained
+    models.
+    """
+
+    config_class = EsmConfig
+    base_model_prefix = "esm"
+    supports_gradient_checkpointing = True
+    _no_split_modules = ["EsmLayer", "EsmFoldTriangularSelfAttentionBlock", "EsmEmbeddings"]
+
+    # Copied from transformers.models.bert.modeling_bert.BertPreTrainedModel._init_weights
+    def _init_weights(self, module):
+        """Initialize the weights"""
+        if isinstance(module, nn.Linear):
+            # Slightly different from the TF version which uses truncated_normal for initialization
+            # cf https://github.com/pytorch/pytorch/pull/5617
+            module.weight.data.normal_(mean=0.0, std=self.config.initializer_range)
+            if module.bias is not None:
+                module.bias.data.zero_()
+        elif isinstance(module, nn.Embedding):
+            module.weight.data.normal_(mean=0.0, std=self.config.initializer_range)
+            if module.padding_idx is not None:
+                module.weight.data[module.padding_idx].zero_()
+        elif isinstance(module, nn.LayerNorm):
+            module.bias.data.zero_()
+            module.weight.data.fill_(1.0)
+
+
+ESM_START_DOCSTRING = r"""
+
+    This model inherits from [`PreTrainedModel`]. Check the superclass documentation for the generic methods the
+    library implements for all its model (such as downloading or saving, resizing the input embeddings, pruning heads
+    etc.)
+
+    This model is also a PyTorch [torch.nn.Module](https://pytorch.org/docs/stable/nn.html#torch.nn.Module) subclass.
+    Use it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage
+    and behavior.
+
+    Parameters:
+        config ([`EsmConfig`]): Model configuration class with all the parameters of the
+            model. Initializing with a config file does not load the weights associated with the model, only the
+            configuration. Check out the [`~PreTrainedModel.from_pretrained`] method to load the model weights.
+"""
+
+ESM_INPUTS_DOCSTRING = r"""
+    Args:
+        input_ids (`torch.LongTensor` of shape `({0})`):
+            Indices of input sequence tokens in the vocabulary.
+
+            Indices can be obtained using [`AutoTokenizer`]. See [`PreTrainedTokenizer.encode`] and
+            [`PreTrainedTokenizer.__call__`] for details.
+
+            [What are input IDs?](../glossary#input-ids)
+        attention_mask (`torch.FloatTensor` of shape `({0})`, *optional*):
+            Mask to avoid performing attention on padding token indices. Mask values selected in `[0, 1]`:
+
+            - 1 for tokens that are **not masked**,
+            - 0 for tokens that are **masked**.
+
+            [What are attention masks?](../glossary#attention-mask)
+        position_ids (`torch.LongTensor` of shape `({0})`, *optional*):
+            Indices of positions of each input sequence tokens in the position embeddings. Selected in the range `[0,
+            config.max_position_embeddings - 1]`.
+
+            [What are position IDs?](../glossary#position-ids)
+        head_mask (`torch.FloatTensor` of shape `(num_heads,)` or `(num_layers, num_heads)`, *optional*):
+            Mask to nullify selected heads of the self-attention modules. Mask values selected in `[0, 1]`:
+
+            - 1 indicates the head is **not masked**,
+            - 0 indicates the head is **masked**.
+
+        inputs_embeds (`torch.FloatTensor` of shape `({0}, hidden_size)`, *optional*):
+            Optionally, instead of passing `input_ids` you can choose to directly pass an embedded representation. This
+            is useful if you want more control over how to convert `input_ids` indices into associated vectors than the
+            model's internal embedding lookup matrix.
+        output_attentions (`bool`, *optional*):
+            Whether or not to return the attentions tensors of all attention layers. See `attentions` under returned
+            tensors for more detail.
+        output_hidden_states (`bool`, *optional*):
+            Whether or not to return the hidden states of all layers. See `hidden_states` under returned tensors for
+            more detail.
+        return_dict (`bool`, *optional*):
+            Whether or not to return a [`~file_utils.ModelOutput`] instead of a plain tuple.
+"""
+
+
+@add_start_docstrings(
+    "The bare ESM Model transformer outputting raw hidden-states without any specific head on top.",
+    ESM_START_DOCSTRING,
+)
+class EsmModel(EsmPreTrainedModel):
+    """
+
+    The model can behave as an encoder (with only self-attention) as well as a decoder, in which case a layer of
+    cross-attention is added between the self-attention layers, following the architecture described in [Attention is
+    all you need](https://arxiv.org/abs/1706.03762) by Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit,
+    Llion Jones, Aidan N. Gomez, Lukasz Kaiser and Illia Polosukhin.
+
+    To behave as an decoder the model needs to be initialized with the `is_decoder` argument of the configuration set
+    to `True`. To be used in a Seq2Seq model, the model needs to initialized with both `is_decoder` argument and
+    `add_cross_attention` set to `True`; an `encoder_hidden_states` is then expected as an input to the forward pass.
+    """
+
+    def __init__(self, config, add_pooling_layer=True):
+        super().__init__(config)
+        self.config = config
+
+        self.embeddings = EsmEmbeddings(config)
+        self.encoder = EsmEncoder(config)
+
+        self.pooler = EsmPooler(config) if add_pooling_layer else None
+
+        self.contact_head = EsmContactPredictionHead(
+            in_features=config.num_hidden_layers * config.num_attention_heads, bias=True
+        )
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    def get_input_embeddings(self):
+        return self.embeddings.word_embeddings
+
+    def set_input_embeddings(self, value):
+        self.embeddings.word_embeddings = value
+
+    def _prune_heads(self, heads_to_prune):
+        """
+        Prunes heads of the model. heads_to_prune: dict of {layer_num: list of heads to prune in this layer} See base
+        class PreTrainedModel
+        """
+        for layer, heads in heads_to_prune.items():
+            self.encoder.layer[layer].attention.prune_heads(heads)
+
+    @add_start_docstrings_to_model_forward(ESM_INPUTS_DOCSTRING.format("(batch_size, sequence_length)"))
+    @add_code_sample_docstrings(
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=BaseModelOutputWithPoolingAndCrossAttentions,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def forward(
+        self,
+        input_ids: Optional[torch.Tensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.Tensor] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.Tensor] = None,
+        encoder_hidden_states: Optional[torch.Tensor] = None,
+        encoder_attention_mask: Optional[torch.Tensor] = None,
+        past_key_values: Optional[List[torch.FloatTensor]] = None,
+        use_cache: Optional[bool] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple[torch.Tensor], BaseModelOutputWithPoolingAndCrossAttentions]:
+        r"""
+        encoder_hidden_states  (`torch.FloatTensor` of shape `(batch_size, sequence_length, hidden_size)`, *optional*):
+            Sequence of hidden-states at the output of the last layer of the encoder. Used in the cross-attention if
+            the model is configured as a decoder.
+        encoder_attention_mask (`torch.FloatTensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Mask to avoid performing attention on the padding token indices of the encoder input. This mask is used in
+            the cross-attention if the model is configured as a decoder. Mask values selected in `[0, 1]`:
+
+            - 1 for tokens that are **not masked**,
+            - 0 for tokens that are **masked**.
+        past_key_values (`tuple(tuple(torch.FloatTensor))` of length `config.n_layers` with each tuple having 4 tensors of shape `(batch_size, num_heads, sequence_length - 1, embed_size_per_head)`):
+            Contains precomputed key and value hidden states of the attention blocks. Can be used to speed up decoding.
+
+            If `past_key_values` are used, the user can optionally input only the last `decoder_input_ids` (those that
+            don't have their past key value states given to this model) of shape `(batch_size, 1)` instead of all
+            `decoder_input_ids` of shape `(batch_size, sequence_length)`.
+        use_cache (`bool`, *optional*):
+            If set to `True`, `past_key_values` key value states are returned and can be used to speed up decoding (see
+            `past_key_values`).
+        """
+        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
+        output_hidden_states = (
+            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
+        )
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        if self.config.is_decoder:
+            use_cache = use_cache if use_cache is not None else self.config.use_cache
+        else:
+            use_cache = False
+
+        if input_ids is not None and inputs_embeds is not None:
+            raise ValueError("You cannot specify both input_ids and inputs_embeds at the same time")
+        elif input_ids is not None:
+            self.warn_if_padding_and_no_attention_mask(input_ids, attention_mask)
+            input_shape = input_ids.size()
+        elif inputs_embeds is not None:
+            input_shape = inputs_embeds.size()[:-1]
+        else:
+            raise ValueError("You have to specify either input_ids or inputs_embeds")
+
+        batch_size, seq_length = input_shape
+        device = input_ids.device if input_ids is not None else inputs_embeds.device
+
+        # past_key_values_length
+        past_key_values_length = past_key_values[0][0].shape[2] if past_key_values is not None else 0
+
+        if attention_mask is None:
+            attention_mask = torch.ones(((batch_size, seq_length + past_key_values_length)), device=device)
+
+        # We can provide a self-attention mask of dimensions [batch_size, from_seq_length, to_seq_length]
+        # ourselves in which case we just need to make it broadcastable to all heads.
+        extended_attention_mask: torch.Tensor = self.get_extended_attention_mask(attention_mask, input_shape)
+
+        # If a 2D or 3D attention mask is provided for the cross-attention
+        # we need to make broadcastable to [batch_size, num_heads, seq_length, seq_length]
+        if self.config.is_decoder and encoder_hidden_states is not None:
+            encoder_batch_size, encoder_sequence_length, _ = encoder_hidden_states.size()
+            encoder_hidden_shape = (encoder_batch_size, encoder_sequence_length)
+            if encoder_attention_mask is None:
+                encoder_attention_mask = torch.ones(encoder_hidden_shape, device=device)
+            encoder_extended_attention_mask = self.invert_attention_mask(encoder_attention_mask)
+        else:
+            encoder_extended_attention_mask = None
+
+        # Prepare head mask if needed
+        # 1.0 in head_mask indicate we keep the head
+        # attention_probs has shape bsz x n_heads x N x N
+        # input head_mask has shape [num_heads] or [num_hidden_layers x num_heads]
+        # and head_mask is converted to shape [num_hidden_layers x batch x num_heads x seq_length x seq_length]
+        head_mask = self.get_head_mask(head_mask, self.config.num_hidden_layers)
+
+        embedding_output = self.embeddings(
+            input_ids=input_ids,
+            position_ids=position_ids,
+            attention_mask=attention_mask,
+            inputs_embeds=inputs_embeds,
+            past_key_values_length=past_key_values_length,
+        )
+        encoder_outputs = self.encoder(
+            embedding_output,
+            attention_mask=extended_attention_mask,
+            head_mask=head_mask,
+            encoder_hidden_states=encoder_hidden_states,
+            encoder_attention_mask=encoder_extended_attention_mask,
+            past_key_values=past_key_values,
+            use_cache=use_cache,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+        sequence_output = encoder_outputs[0]
+        pooled_output = self.pooler(sequence_output) if self.pooler is not None else None
+
+        if not return_dict:
+            return (sequence_output, pooled_output) + encoder_outputs[1:]
+
+        return BaseModelOutputWithPoolingAndCrossAttentions(
+            last_hidden_state=sequence_output,
+            pooler_output=pooled_output,
+            past_key_values=encoder_outputs.past_key_values,
+            hidden_states=encoder_outputs.hidden_states,
+            attentions=encoder_outputs.attentions,
+            cross_attentions=encoder_outputs.cross_attentions,
+        )
+
+    def predict_contacts(self, tokens, attention_mask):
+        attns = self(tokens, attention_mask=attention_mask, return_dict=True, output_attentions=True).attentions
+        attns = torch.stack(attns, dim=1)  # Matches the original model layout
+        # In the original model, attentions for padding tokens are completely zeroed out.
+        # This makes no difference most of the time because the other tokens won't attend to them,
+        # but it does for the contact prediction task, which takes attentions as input,
+        # so we have to mimic that here.
+        attns *= attention_mask.unsqueeze(1).unsqueeze(2).unsqueeze(3)
+        attns *= attention_mask.unsqueeze(1).unsqueeze(2).unsqueeze(4)
+        return self.contact_head(tokens, attns)
+
+
+@add_start_docstrings("""ESM Model with a `language modeling` head on top.""", ESM_START_DOCSTRING)
+class EsmForMaskedLM(EsmPreTrainedModel):
+    _tied_weights_keys = ["lm_head.decoder.weight"]
+
+    def __init__(self, config):
+        super().__init__(config)
+
+        if config.is_decoder:
+            logger.warning(
+                "If you want to use `EsmForMaskedLM` make sure `config.is_decoder=False` for "
+                "bi-directional self-attention."
+            )
+
+        self.esm = EsmModel(config, add_pooling_layer=False)
+        self.lm_head = EsmLMHead(config)
+
+        self.init_weights()
+
+    def get_output_embeddings(self):
+        return self.lm_head.decoder
+
+    def set_output_embeddings(self, new_embeddings):
+        self.lm_head.decoder = new_embeddings
+
+    @add_start_docstrings_to_model_forward(ESM_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @add_code_sample_docstrings(
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=MaskedLMOutput,
+        config_class=_CONFIG_FOR_DOC,
+        mask="<mask>",
+    )
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        encoder_hidden_states: Optional[torch.FloatTensor] = None,
+        encoder_attention_mask: Optional[torch.Tensor] = None,
+        labels: Optional[torch.LongTensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple, MaskedLMOutput]:
+        r"""
+        labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Labels for computing the masked language modeling loss. Indices should be in `[-100, 0, ...,
+            config.vocab_size]` (see `input_ids` docstring) Tokens with indices set to `-100` are ignored (masked), the
+            loss is only computed for the tokens with labels in `[0, ..., config.vocab_size]`
+        kwargs (`Dict[str, any]`, optional, defaults to *{}*):
+            Used to hide legacy arguments that have been deprecated.
+        """
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.esm(
+            input_ids,
+            attention_mask=attention_mask,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            encoder_hidden_states=encoder_hidden_states,
+            encoder_attention_mask=encoder_attention_mask,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+        sequence_output = outputs[0]
+        prediction_scores = self.lm_head(sequence_output)
+
+        masked_lm_loss = None
+        if labels is not None:
+            loss_fct = CrossEntropyLoss()
+
+            labels = labels.to(prediction_scores.device)
+            masked_lm_loss = loss_fct(prediction_scores.view(-1, self.config.vocab_size), labels.view(-1))
+
+        if not return_dict:
+            output = (prediction_scores,) + outputs[2:]
+            return ((masked_lm_loss,) + output) if masked_lm_loss is not None else output
+
+        return MaskedLMOutput(
+            loss=masked_lm_loss,
+            logits=prediction_scores,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+    def predict_contacts(self, tokens, attention_mask):
+        return self.esm.predict_contacts(tokens, attention_mask=attention_mask)
+
+
+class EsmLMHead(nn.Module):
+    """ESM Head for masked language modeling."""
+
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
+        self.layer_norm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+
+        self.decoder = nn.Linear(config.hidden_size, config.vocab_size, bias=False)
+        self.bias = nn.Parameter(torch.zeros(config.vocab_size))
+
+    def forward(self, features, **kwargs):
+        x = self.dense(features)
+        x = gelu(x)
+        x = self.layer_norm(x)
+
+        # project back to size of vocabulary with bias
+        x = self.decoder(x) + self.bias
+        return x
+
+
+@add_start_docstrings(
+    """
+    ESM Model transformer with a sequence classification/regression head on top (a linear layer on top of the pooled
+    output) e.g. for GLUE tasks.
+    """,
+    ESM_START_DOCSTRING,
+)
+class EsmForSequenceClassification(EsmPreTrainedModel):
+    def __init__(self, config):
+        super().__init__(config)
+        self.num_labels = config.num_labels
+        self.config = config
+
+        self.esm = EsmModel(config, add_pooling_layer=False)
+        self.classifier = EsmClassificationHead(config)
+
+        self.init_weights()
+
+    @add_start_docstrings_to_model_forward(ESM_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @add_code_sample_docstrings(
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=SequenceClassifierOutput,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        labels: Optional[torch.LongTensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple, SequenceClassifierOutput]:
+        r"""
+        labels (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
+            Labels for computing the sequence classification/regression loss. Indices should be in `[0, ...,
+            config.num_labels - 1]`. If `config.num_labels == 1` a regression loss is computed (Mean-Square loss), If
+            `config.num_labels > 1` a classification loss is computed (Cross-Entropy).
+        """
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.esm(
+            input_ids,
+            attention_mask=attention_mask,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+        sequence_output = outputs[0]
+        logits = self.classifier(sequence_output)
+
+        loss = None
+        if labels is not None:
+            labels = labels.to(logits.device)
+
+            if self.config.problem_type is None:
+                if self.num_labels == 1:
+                    self.config.problem_type = "regression"
+                elif self.num_labels > 1 and (labels.dtype == torch.long or labels.dtype == torch.int):
+                    self.config.problem_type = "single_label_classification"
+                else:
+                    self.config.problem_type = "multi_label_classification"
+
+            if self.config.problem_type == "regression":
+                loss_fct = MSELoss()
+                if self.num_labels == 1:
+                    loss = loss_fct(logits.squeeze(), labels.squeeze())
+                else:
+                    loss = loss_fct(logits, labels)
+            elif self.config.problem_type == "single_label_classification":
+                loss_fct = CrossEntropyLoss()
+                loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1))
+            elif self.config.problem_type == "multi_label_classification":
+                loss_fct = BCEWithLogitsLoss()
+                loss = loss_fct(logits, labels)
+
+        if not return_dict:
+            output = (logits,) + outputs[2:]
+            return ((loss,) + output) if loss is not None else output
+
+        return SequenceClassifierOutput(
+            loss=loss,
+            logits=logits,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+
+@add_start_docstrings(
+    """
+    ESM Model with a token classification head on top (a linear layer on top of the hidden-states output) e.g. for
+    Named-Entity-Recognition (NER) tasks.
+    """,
+    ESM_START_DOCSTRING,
+)
+class EsmForTokenClassification(EsmPreTrainedModel):
+    def __init__(self, config):
+        super().__init__(config)
+        self.num_labels = config.num_labels
+
+        self.esm = EsmModel(config, add_pooling_layer=False)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+        self.classifier = nn.Linear(config.hidden_size, config.num_labels)
+
+        self.init_weights()
+
+    @add_start_docstrings_to_model_forward(ESM_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @add_code_sample_docstrings(
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=TokenClassifierOutput,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        labels: Optional[torch.LongTensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple, TokenClassifierOutput]:
+        r"""
+        labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Labels for computing the token classification loss. Indices should be in `[0, ..., config.num_labels - 1]`.
+        """
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.esm(
+            input_ids,
+            attention_mask=attention_mask,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        sequence_output = outputs[0]
+
+        sequence_output = self.dropout(sequence_output)
+        logits = self.classifier(sequence_output)
+
+        loss = None
+        if labels is not None:
+            loss_fct = CrossEntropyLoss()
+
+            labels = labels.to(logits.device)
+            loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1))
+
+        if not return_dict:
+            output = (logits,) + outputs[2:]
+            return ((loss,) + output) if loss is not None else output
+
+        return TokenClassifierOutput(
+            loss=loss,
+            logits=logits,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+
+class EsmClassificationHead(nn.Module):
+    """Head for sentence-level classification tasks."""
+
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+        self.out_proj = nn.Linear(config.hidden_size, config.num_labels)
+
+    def forward(self, features, **kwargs):
+        x = features[:, 0, :]  # take <s> token (equiv. to [CLS])
+        x = self.dropout(x)
+        x = self.dense(x)
+        x = torch.tanh(x)
+        x = self.dropout(x)
+        x = self.out_proj(x)
+        return x
+
+
+def create_position_ids_from_input_ids(input_ids, padding_idx, past_key_values_length=0):
+    """
+    Replace non-padding symbols with their position numbers. Position numbers begin at padding_idx+1. Padding symbols
+    are ignored. This is modified from fairseq's `utils.make_positions`.
+
+    Args:
+        x: torch.Tensor x:
+
+    Returns: torch.Tensor
+    """
+    # The series of casts and type-conversions here are carefully balanced to both work with ONNX export and XLA.
+    mask = input_ids.ne(padding_idx).int()
+    incremental_indices = (torch.cumsum(mask, dim=1).type_as(mask) + past_key_values_length) * mask
+    return incremental_indices.long() + padding_idx

llmeval-env/lib/python3.10/site-packages/transformers/models/esm/modeling_esmfold.py

@@ -0,0 +1,2322 @@
+# coding=utf-8
+# Copyright 2022 Meta and The HuggingFace Inc. team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+import math
+import sys
+from dataclasses import dataclass
+from functools import partial
+from typing import Callable, Dict, List, Optional, Sequence, Tuple, Union
+
+import numpy as np
+import torch
+import torch.nn as nn
+from torch.nn import LayerNorm
+
+from ...integrations.deepspeed import is_deepspeed_available
+from ...modeling_outputs import ModelOutput
+from ...utils import (
+    ContextManagers,
+    add_start_docstrings,
+    add_start_docstrings_to_model_forward,
+    is_scipy_available,
+    logging,
+    replace_return_docstrings,
+)
+from .configuration_esm import EsmConfig
+from .modeling_esm import ESM_START_DOCSTRING, EsmModel, EsmPreTrainedModel
+from .openfold_utils import (
+    OFProtein,
+    Rigid,
+    Rotation,
+    atom14_to_atom37,
+    chunk_layer,
+    compute_predicted_aligned_error,
+    compute_tm,
+    frames_and_literature_positions_to_atom14_pos,
+    make_atom14_masks,
+    residue_constants,
+    to_pdb,
+    torsion_angles_to_frames,
+)
+
+
+logger = logging.get_logger(__name__)
+_CHECKPOINT_FOR_DOC = "facebook/esmfold_v1"
+_CONFIG_FOR_DOC = "EsmConfig"
+
+
+@dataclass
+class EsmForProteinFoldingOutput(ModelOutput):
+    """
+    Output type of [`EsmForProteinFoldingOutput`].
+
+    Args:
+        frames (`torch.FloatTensor`):
+            Output frames.
+        sidechain_frames (`torch.FloatTensor`):
+            Output sidechain frames.
+        unnormalized_angles (`torch.FloatTensor`):
+            Predicted unnormalized backbone and side chain torsion angles.
+        angles (`torch.FloatTensor`):
+            Predicted backbone and side chain torsion angles.
+        positions (`torch.FloatTensor`):
+            Predicted positions of the backbone and side chain atoms.
+        states (`torch.FloatTensor`):
+            Hidden states from the protein folding trunk.
+        s_s (`torch.FloatTensor`):
+            Per-residue embeddings derived by concatenating the hidden states of each layer of the ESM-2 LM stem.
+        s_z (`torch.FloatTensor`):
+            Pairwise residue embeddings.
+        distogram_logits (`torch.FloatTensor`):
+            Input logits to the distogram used to compute residue distances.
+        lm_logits (`torch.FloatTensor`):
+            Logits output by the ESM-2 protein language model stem.
+        aatype (`torch.FloatTensor`):
+            Input amino acids (AlphaFold2 indices).
+        atom14_atom_exists (`torch.FloatTensor`):
+            Whether each atom exists in the atom14 representation.
+        residx_atom14_to_atom37 (`torch.FloatTensor`):
+            Mapping between atoms in the atom14 and atom37 representations.
+        residx_atom37_to_atom14 (`torch.FloatTensor`):
+            Mapping between atoms in the atom37 and atom14 representations.
+        atom37_atom_exists (`torch.FloatTensor`):
+            Whether each atom exists in the atom37 representation.
+        residue_index (`torch.FloatTensor`):
+            The index of each residue in the protein chain. Unless internal padding tokens are used, this will just be
+            a sequence of integers from 0 to `sequence_length`.
+        lddt_head (`torch.FloatTensor`):
+            Raw outputs from the lddt head used to compute plddt.
+        plddt (`torch.FloatTensor`):
+            Per-residue confidence scores. Regions of low confidence may indicate areas where the model's prediction is
+            uncertain, or where the protein structure is disordered.
+        ptm_logits (`torch.FloatTensor`):
+            Raw logits used for computing ptm.
+        ptm (`torch.FloatTensor`):
+            TM-score output representing the model's high-level confidence in the overall structure.
+        aligned_confidence_probs (`torch.FloatTensor`):
+            Per-residue confidence scores for the aligned structure.
+        predicted_aligned_error (`torch.FloatTensor`):
+            Predicted error between the model's prediction and the ground truth.
+        max_predicted_aligned_error (`torch.FloatTensor`):
+            Per-sample maximum predicted error.
+    """
+
+    frames: torch.FloatTensor = None
+    sidechain_frames: torch.FloatTensor = None
+    unnormalized_angles: torch.FloatTensor = None
+    angles: torch.FloatTensor = None
+    positions: torch.FloatTensor = None
+    states: torch.FloatTensor = None
+    s_s: torch.FloatTensor = None
+    s_z: torch.FloatTensor = None
+    distogram_logits: torch.FloatTensor = None
+    lm_logits: torch.FloatTensor = None
+    aatype: torch.FloatTensor = None
+    atom14_atom_exists: torch.FloatTensor = None
+    residx_atom14_to_atom37: torch.FloatTensor = None
+    residx_atom37_to_atom14: torch.FloatTensor = None
+    atom37_atom_exists: torch.FloatTensor = None
+    residue_index: torch.FloatTensor = None
+    lddt_head: torch.FloatTensor = None
+    plddt: torch.FloatTensor = None
+    ptm_logits: torch.FloatTensor = None
+    ptm: torch.FloatTensor = None
+    aligned_confidence_probs: torch.FloatTensor = None
+    predicted_aligned_error: torch.FloatTensor = None
+    max_predicted_aligned_error: torch.FloatTensor = None
+
+
+ESMFOLD_INPUTS_DOCSTRING = r"""
+    Args:
+        input_ids (`torch.LongTensor` of shape `({0})`):
+            Indices of input sequence tokens in the vocabulary.
+
+            Indices can be obtained using [`AutoTokenizer`]. See [`PreTrainedTokenizer.encode`] and
+            [`PreTrainedTokenizer.__call__`] for details.
+
+            [What are input IDs?](../glossary#input-ids)
+        attention_mask (`torch.FloatTensor` of shape `({0})`, *optional*):
+            Mask to avoid performing attention on padding token indices. Mask values selected in `[0, 1]`:
+
+            - 1 for tokens that are **not masked**,
+            - 0 for tokens that are **masked**.
+
+            [What are attention masks?](../glossary#attention-mask)
+        position_ids (`torch.LongTensor` of shape `({0})`, *optional*):
+            Indices of positions of each input sequence tokens in the position embeddings. Selected in the range `[0,
+            config.max_position_embeddings - 1]`.
+
+            [What are position IDs?](../glossary#position-ids)
+        masking_pattern (`torch.LongTensor` of shape `({0})`, *optional*):
+            Locations of tokens to mask during training as a form of regularization. Mask values selected in `[0, 1]`.
+        num_recycles (`int`, *optional*, defaults to `None`):
+            Number of times to recycle the input sequence. If `None`, defaults to `config.num_recycles`. "Recycling"
+            consists of passing the output of the folding trunk back in as input to the trunk. During training, the
+            number of recycles should vary with each batch, to ensure that the model learns to output valid predictions
+            after each recycle. During inference, num_recycles should be set to the highest value that the model was
+            trained with for maximum accuracy. Accordingly, when this value is set to `None`, config.max_recycles is
+            used.
+"""
+
+
+def is_fp16_enabled():
+    # Autocast world
+    fp16_enabled = torch.get_autocast_gpu_dtype() == torch.float16
+    fp16_enabled = fp16_enabled and torch.is_autocast_enabled()
+
+    return fp16_enabled
+
+
+def is_deepspeed_initialized():
+    if is_deepspeed_available():
+        return False
+    else:
+        try:
+            import deepspeed
+
+            # This is not available in all DeepSpeed versions.
+            return deepspeed.utils.is_initialized()
+        except Exception:
+            return False
+
+
+def collate_dense_tensors(samples: List[torch.Tensor], pad_v: float = 0) -> torch.Tensor:
+    """
+    Takes a list of tensors with the following dimensions:
+        [(d_11, ..., d_1K),
+         (d_21, ..., d_2K), ..., (d_N1, ..., d_NK)]
+    and stack + pads them into a single tensor of:
+    (N, max_i=1,N { d_i1 }, ..., max_i=1,N {diK})
+    """
+    if len(samples) == 0:
+        return torch.Tensor()
+    if len({x.dim() for x in samples}) != 1:
+        raise RuntimeError(f"Samples has varying dimensions: {[x.dim() for x in samples]}")
+    (device,) = tuple({x.device for x in samples})  # assumes all on same device
+    max_shape = [max(lst) for lst in zip(*[x.shape for x in samples])]
+    result = torch.empty(len(samples), *max_shape, dtype=samples[0].dtype, device=device)
+    result.fill_(pad_v)
+    for i in range(len(samples)):
+        result_i = result[i]
+        t = samples[i]
+        result_i[tuple(slice(0, k) for k in t.shape)] = t
+    return result
+
+
+def flatten_final_dims(t: torch.Tensor, no_dims: int):
+    return t.reshape(t.shape[:-no_dims] + (-1,))
+
+
+def permute_final_dims(tensor: torch.Tensor, inds: List[int]):
+    zero_index = -1 * len(inds)
+    first_inds = list(range(len(tensor.shape[:zero_index])))
+    return tensor.permute(first_inds + [zero_index + i for i in inds])
+
+
+def dict_multimap(fn, dicts):
+    first = dicts[0]
+    new_dict = {}
+    for k, v in first.items():
+        all_v = [d[k] for d in dicts]
+        if isinstance(v, dict):
+            new_dict[k] = dict_multimap(fn, all_v)
+        else:
+            new_dict[k] = fn(all_v)
+
+    return new_dict
+
+
+def trunc_normal_init_(weights, scale=1.0, fan="fan_in"):
+    shape = weights.shape
+    scale = scale / max(1, shape[1])
+
+    if not is_scipy_available():
+        logger.warning(
+            "This init requires scipy, but scipy was not found, default to an approximation that might not be"
+            " equivalent."
+        )
+        std = math.sqrt(scale)
+        torch.nn.init.normal_(weights, std=std).clamp(min=0.0, max=2.0 * std)
+
+    else:
+        from scipy.stats import truncnorm
+
+        std = math.sqrt(scale) / truncnorm.std(a=-2, b=2, loc=0, scale=1)
+        samples = truncnorm.rvs(a=-2, b=2, loc=0, scale=std, size=weights.numel())
+        samples = np.reshape(samples, shape)
+        weights.copy_(torch.tensor(samples, device=weights.device))
+
+
+def ipa_point_weights_init_(weights):
+    with torch.no_grad():
+        softplus_inverse_1 = 0.541324854612918
+        weights.fill_(softplus_inverse_1)
+
+
+class EsmFoldLinear(nn.Linear):
+    """
+    A Linear layer with built-in nonstandard initializations. Called just like torch.nn.Linear.
+
+    Implements the initializers in 1.11.4, plus some additional ones found in the code.
+    """
+
+    def __init__(
+        self,
+        in_dim: int,
+        out_dim: int,
+        bias: bool = True,
+        init: str = "default",
+        init_fn: Optional[Callable[[torch.Tensor, torch.Tensor], None]] = None,
+    ):
+        """
+        Args:
+            in_dim:
+                The final dimension of inputs to the layer
+            out_dim:
+                The final dimension of layer outputs
+            bias:
+                Whether to learn an additive bias. True by default
+            init:
+                The initializer to use. Choose from:
+
+                "default": LeCun fan-in truncated normal initialization "relu": He initialization w/ truncated normal
+                distribution "glorot": Fan-average Glorot uniform initialization "gating": Weights=0, Bias=1 "normal":
+                Normal initialization with std=1/sqrt(fan_in) "final": Weights=0, Bias=0
+
+                Overridden by init_fn if the latter is not None.
+            init_fn:
+                A custom initializer taking weight and bias as inputs. Overrides init if not None.
+        """
+        super().__init__(in_dim, out_dim, bias=bias)
+
+        if bias:
+            with torch.no_grad():
+                self.bias.fill_(0)
+        self.init = init
+        self.init_fn = init_fn
+
+        if init not in ["default", "relu", "glorot", "gating", "normal", "final"]:
+            raise ValueError("Invalid init string.")
+
+
+class EsmFoldLayerNorm(nn.Module):
+    def __init__(self, c_in, eps=1e-5):
+        super().__init__()
+
+        self.c_in = (c_in,)
+        self.eps = eps
+
+        self.weight = nn.Parameter(torch.ones(c_in))
+        self.bias = nn.Parameter(torch.zeros(c_in))
+
+    def forward(self, x):
+        d = x.dtype
+        if d is torch.bfloat16 and not is_deepspeed_initialized():
+            with torch.cuda.amp.autocast(enabled=False):
+                out = nn.functional.layer_norm(x, self.c_in, self.weight.to(dtype=d), self.bias.to(dtype=d), self.eps)
+        else:
+            out = nn.functional.layer_norm(x, self.c_in, self.weight, self.bias, self.eps)
+
+        return out
+
+
+@torch.jit.ignore
+def softmax_no_cast(t: torch.Tensor, dim: int = -1) -> torch.Tensor:
+    """
+    Softmax, but without automatic casting to fp32 when the input is of type bfloat16
+    """
+    d = t.dtype
+    if d is torch.bfloat16 and not is_deepspeed_initialized():
+        with torch.cuda.amp.autocast(enabled=False):
+            s = torch.nn.functional.softmax(t, dim=dim)
+    else:
+        s = torch.nn.functional.softmax(t, dim=dim)
+
+    return s
+
+
+class EsmFoldAttention(nn.Module):
+    """
+    Standard multi-head attention using AlphaFold's default layer initialization. Allows multiple bias vectors.
+    """
+
+    def __init__(
+        self,
+        c_q: int,
+        c_k: int,
+        c_v: int,
+        c_hidden: int,
+        no_heads: int,
+        gating: bool = True,
+    ):
+        """
+        Args:
+            c_q:
+                Input dimension of query data
+            c_k:
+                Input dimension of key data
+            c_v:
+                Input dimension of value data
+            c_hidden:
+                Per-head hidden dimension
+            no_heads:
+                Number of attention heads
+            gating:
+                Whether the output should be gated using query data
+        """
+        super().__init__()
+
+        self.c_q = c_q
+        self.c_k = c_k
+        self.c_v = c_v
+        self.c_hidden = c_hidden
+        self.no_heads = no_heads
+        self.gating = gating
+
+        # DISCREPANCY: c_hidden is not the per-head channel dimension, as
+        # stated in the supplement, but the overall channel dimension.
+
+        self.linear_q = EsmFoldLinear(self.c_q, self.c_hidden * self.no_heads, bias=False, init="glorot")
+        self.linear_k = EsmFoldLinear(self.c_k, self.c_hidden * self.no_heads, bias=False, init="glorot")
+        self.linear_v = EsmFoldLinear(self.c_v, self.c_hidden * self.no_heads, bias=False, init="glorot")
+        self.linear_o = EsmFoldLinear(self.c_hidden * self.no_heads, self.c_q, init="final")
+
+        self.linear_g = None
+        if self.gating:
+            self.linear_g = EsmFoldLinear(self.c_q, self.c_hidden * self.no_heads, init="gating")
+
+        self.sigmoid = nn.Sigmoid()
+
+    def _prep_qkv(self, q_x: torch.Tensor, kv_x: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]:
+        # [*, Q/K/V, H * C_hidden]
+        q = self.linear_q(q_x)
+        k = self.linear_k(kv_x)
+        v = self.linear_v(kv_x)
+
+        # [*, Q/K, H, C_hidden]
+        q = q.view(q.shape[:-1] + (self.no_heads, -1))
+        k = k.view(k.shape[:-1] + (self.no_heads, -1))
+        v = v.view(v.shape[:-1] + (self.no_heads, -1))
+
+        # [*, H, Q/K, C_hidden]
+        q = q.transpose(-2, -3)
+        k = k.transpose(-2, -3)
+        v = v.transpose(-2, -3)
+
+        q /= math.sqrt(self.c_hidden)
+
+        return q, k, v
+
+    def _wrap_up(self, o: torch.Tensor, q_x: torch.Tensor) -> torch.Tensor:
+        if self.linear_g is not None:
+            g = self.sigmoid(self.linear_g(q_x))
+
+            # [*, Q, H, C_hidden]
+            g = g.view(g.shape[:-1] + (self.no_heads, -1))
+            o = o * g
+
+        # [*, Q, H * C_hidden]
+        o = flatten_final_dims(o, 2)
+
+        # [*, Q, C_q]
+        o = self.linear_o(o)
+
+        return o
+
+    def forward(
+        self,
+        q_x: torch.Tensor,
+        kv_x: torch.Tensor,
+        biases: Optional[List[torch.Tensor]] = None,
+        use_memory_efficient_kernel: bool = False,
+        use_lma: bool = False,
+        lma_q_chunk_size: int = 1024,
+        lma_kv_chunk_size: int = 4096,
+        use_flash: bool = False,
+        flash_mask: Optional[torch.Tensor] = None,
+    ) -> torch.Tensor:
+        """
+        Args:
+            q_x:
+                [*, Q, C_q] query data
+            kv_x:
+                [*, K, C_k] key data
+            biases:
+                List of biases that broadcast to [*, H, Q, K]
+            use_memory_efficient_kernel:
+                Whether to use a custom memory-efficient attention kernel. This should be the default choice for most.
+                If none of the "use_<...>" flags are True, a stock PyTorch implementation is used instead
+            use_lma:
+                Whether to use low-memory attention (Staats & Rabe 2021). If none of the "use_<...>" flags are True, a
+                stock PyTorch implementation is used instead
+            lma_q_chunk_size:
+                Query chunk size (for LMA)
+            lma_kv_chunk_size:
+                Key/Value chunk size (for LMA)
+        Returns
+            [*, Q, C_q] attention update
+        """
+        if use_lma and (lma_q_chunk_size is None or lma_kv_chunk_size is None):
+            raise ValueError("If use_lma is specified, lma_q_chunk_size and lma_kv_chunk_size must be provided")
+
+        if use_flash and biases is not None:
+            raise ValueError("use_flash is incompatible with the bias option. For masking, use flash_mask instead")
+
+        attn_options = [use_memory_efficient_kernel, use_lma, use_flash]
+        if sum(attn_options) > 1:
+            raise ValueError("Choose at most one alternative attention algorithm")
+
+        if biases is None:
+            biases = []
+
+        # [*, H, Q/K, C_hidden]
+        query, key, value = self._prep_qkv(q_x, kv_x)
+        key = permute_final_dims(key, (1, 0))
+
+        # [*, H, Q, K]
+        output = torch.matmul(query, key)
+        for b in biases:
+            output += b
+        output = softmax_no_cast(output, -1)
+
+        # [*, H, Q, C_hidden]
+        output = torch.matmul(output, value)
+        output = output.transpose(-2, -3)
+        output = self._wrap_up(output, q_x)
+
+        return output
+
+
+class EsmFoldTriangleAttention(nn.Module):
+    def __init__(self, c_in, c_hidden, no_heads, starting=True, inf=1e9):
+        """
+        Args:
+            c_in:
+                Input channel dimension
+            c_hidden:
+                Overall hidden channel dimension (not per-head)
+            no_heads:
+                Number of attention heads
+        """
+        super().__init__()
+
+        self.c_in = c_in
+        self.c_hidden = c_hidden
+        self.no_heads = no_heads
+        self.starting = starting
+        self.inf = inf
+
+        self.layer_norm = LayerNorm(self.c_in)
+
+        self.linear = EsmFoldLinear(c_in, self.no_heads, bias=False, init="normal")
+
+        self.mha = EsmFoldAttention(self.c_in, self.c_in, self.c_in, self.c_hidden, self.no_heads)
+
+    @torch.jit.ignore
+    def _chunk(
+        self,
+        x: torch.Tensor,
+        biases: List[torch.Tensor],
+        chunk_size: int,
+        use_memory_efficient_kernel: bool = False,
+        use_lma: bool = False,
+        inplace_safe: bool = False,
+    ) -> torch.Tensor:
+        "triangle! triangle!"
+        mha_inputs = {
+            "q_x": x,
+            "kv_x": x,
+            "biases": biases,
+        }
+
+        return chunk_layer(
+            partial(self.mha, use_memory_efficient_kernel=use_memory_efficient_kernel, use_lma=use_lma),
+            mha_inputs,
+            chunk_size=chunk_size,
+            no_batch_dims=len(x.shape[:-2]),
+            _out=x if inplace_safe else None,
+        )
+
+    def forward(
+        self,
+        x: torch.Tensor,
+        mask: Optional[torch.Tensor] = None,
+        chunk_size: Optional[int] = None,
+        use_memory_efficient_kernel: bool = False,
+        use_lma: bool = False,
+        inplace_safe: bool = False,
+    ) -> torch.Tensor:
+        """
+        Args:
+            x:
+                [*, I, J, C_in] input tensor (e.g. the pair representation)
+        Returns:
+            [*, I, J, C_in] output tensor
+        """
+        if mask is None:
+            # [*, I, J]
+            mask = x.new_ones(
+                x.shape[:-1],
+            )
+
+        if not self.starting:
+            x = x.transpose(-2, -3)
+            mask = mask.transpose(-1, -2)
+
+        # [*, I, J, C_in]
+        x = self.layer_norm(x)
+
+        # [*, I, 1, 1, J]
+        mask_bias = (self.inf * (mask - 1))[..., :, None, None, :]
+
+        # [*, H, I, J]
+        triangle_bias = permute_final_dims(self.linear(x), (2, 0, 1))
+
+        # [*, 1, H, I, J]
+        triangle_bias = triangle_bias.unsqueeze(-4)
+
+        biases = [mask_bias, triangle_bias]
+
+        if chunk_size is not None:
+            x = self._chunk(
+                x,
+                biases,
+                chunk_size,
+                use_memory_efficient_kernel=use_memory_efficient_kernel,
+                use_lma=use_lma,
+                inplace_safe=inplace_safe,
+            )
+        else:
+            x = self.mha(
+                q_x=x, kv_x=x, biases=biases, use_memory_efficient_kernel=use_memory_efficient_kernel, use_lma=use_lma
+            )
+
+        if not self.starting:
+            x = x.transpose(-2, -3)
+
+        return x
+
+
+class EsmFoldTriangleMultiplicativeUpdate(nn.Module):
+    """
+    Implements Algorithms 11 and 12.
+    """
+
+    def __init__(self, config, _outgoing=True):
+        super().__init__()
+        c_hidden = config.pairwise_state_dim
+        self._outgoing = _outgoing
+
+        self.linear_a_p = EsmFoldLinear(c_hidden, c_hidden)
+        self.linear_a_g = EsmFoldLinear(c_hidden, c_hidden, init="gating")
+        self.linear_b_p = EsmFoldLinear(c_hidden, c_hidden)
+        self.linear_b_g = EsmFoldLinear(c_hidden, c_hidden, init="gating")
+        self.linear_g = EsmFoldLinear(c_hidden, c_hidden, init="gating")
+        self.linear_z = EsmFoldLinear(c_hidden, c_hidden, init="final")
+
+        self.layer_norm_in = LayerNorm(c_hidden)
+        self.layer_norm_out = LayerNorm(c_hidden)
+
+        self.sigmoid = nn.Sigmoid()
+
+    def _combine_projections(
+        self, a: torch.Tensor, b: torch.Tensor, _inplace_chunk_size: Optional[int] = None
+    ) -> torch.Tensor:
+        if self._outgoing:
+            a = permute_final_dims(a, (2, 0, 1))
+            b = permute_final_dims(b, (2, 1, 0))
+        else:
+            a = permute_final_dims(a, (2, 1, 0))
+            b = permute_final_dims(b, (2, 0, 1))
+
+        if _inplace_chunk_size is not None:
+            # To be replaced by torch vmap
+            for i in range(0, a.shape[-3], _inplace_chunk_size):
+                a_chunk = a[..., i : i + _inplace_chunk_size, :, :]
+                b_chunk = b[..., i : i + _inplace_chunk_size, :, :]
+                a[..., i : i + _inplace_chunk_size, :, :] = torch.matmul(
+                    a_chunk,
+                    b_chunk,
+                )
+
+            p = a
+        else:
+            p = torch.matmul(a, b)
+
+        return permute_final_dims(p, (1, 2, 0))
+
+    def _inference_forward(
+        self,
+        z: torch.Tensor,
+        mask: Optional[torch.Tensor] = None,
+        inplace_chunk_size: Optional[int] = None,
+        with_add: bool = True,
+    ):
+        """
+        Args:
+            z:
+                A [*, N, N, C_z] pair representation
+            mask:
+                A [*, N, N] pair mask
+            inplace_chunk_size:
+                Size of chunks used in the main computation. Increase to trade memory for speed.
+            with_add:
+                If True, z is overwritten with (z + update). Otherwise, it is overwritten with (update).
+        Returns:
+            A reference to the overwritten z
+
+        More memory-efficient, inference-only version of the forward function. Uses in-place operations, fusion of the
+        addition that happens after this module in the Evoformer, a smidge of recomputation, and a cache of overwritten
+        values to lower peak memory consumption of this module from 5x the size of the input tensor z to 2.5x its size.
+        Useful for inference on extremely long sequences.
+
+        It works as follows. We will make reference to variables used in the default forward implementation below.
+        Naively, triangle multiplication attention requires the manifestation of 5 tensors the size of z: 1) z, the
+        "square" input tensor, 2) a, the first projection of z, 3) b, the second projection of b, 4) g, a z-sized mask,
+        and 5) a z-sized tensor for intermediate computations. For large N, this is prohibitively expensive; for
+        N=4000, for example, z is more than 8GB alone. To avoid this problem, we compute b, g, and all intermediate
+        tensors in small chunks, noting that the chunks required to compute a chunk of the output depend only on the
+        tensor a and corresponding vertical and horizontal chunks of z. This suggests an algorithm that loops over
+        pairs of chunks of z: hereafter "columns" and "rows" of z, even though each "column" and "row" in fact contains
+        inplace_chunk_size contiguous true columns and rows of z. Writing output chunks to a new tensor would bring
+        total memory consumption down to 3x the size of z. However, more memory can be saved by writing output chunks
+        directly to z in-place. WLOG, we choose to write output chunks vertically, overwriting the ith "column" of z at
+        the end of the ith iteration of the main loop. Despite this overwriting, the ith column is always one column
+        ahead of previously overwritten columns and can be recovered directly from z. After the first iteration,
+        however, the ith row of z is always at least partially overwritten. For this reason, we introduce the z-cache,
+        a tensor one-half the size of z. The z-cache initially contains the left half (2nd and 3rd quadrants) of z. For
+        0 < i < N/2, the missing left part of the ith row of z is recovered from this cache at the beginning of the ith
+        iteration. Once i exceeds n/2, the cache is "reoriented" to encompass the 3rd and 4th quadrants of z instead.
+        Though the 3rd quadrant of the original z is entirely overwritten at this point, it can be recovered from the
+        z-cache itself. Thereafter, the ith row of z can be recovered in its entirety from the reoriented z-cache.
+        After the final iteration, z has been completely overwritten and contains the triangular multiplicative update.
+        If with_add is True, it instead contains the sum of z and the triangular multiplicative update. In either case,
+        peak memory consumption is just 2.5x the size of z, disregarding memory used for chunks and other small
+        variables.
+        """
+        if mask is None:
+            mask = z.new_ones(z.shape[:-1])
+
+        mask = mask.unsqueeze(-1)
+
+        def compute_projection_helper(pair, mask, a=True):
+            if a:
+                linear_g = self.linear_a_g
+                linear_p = self.linear_a_p
+            else:
+                linear_g = self.linear_b_g
+                linear_p = self.linear_b_p
+
+            pair = self.layer_norm_in(pair)
+            p = linear_g(pair)
+            p.sigmoid_()
+            p *= linear_p(pair)
+            p *= mask
+            p = permute_final_dims(p, (2, 0, 1))
+            return p
+
+        def compute_projection(pair, mask, a=True, chunked=True):
+            need_transpose = self._outgoing ^ a
+            if not chunked:
+                p = compute_projection_helper(pair, mask, a)
+                if need_transpose:
+                    p = p.transpose(-1, -2)
+            else:
+                # This computation is chunked so as not to exceed our 2.5x
+                # budget with a large intermediate tensor
+                linear_g = self.linear_a_g if a else self.linear_b_g
+                c = linear_g.bias.shape[-1]
+                out_shape = pair.shape[:-3] + (c,) + pair.shape[-3:-1]
+                p = pair.new_zeros(out_shape)
+                for i in range(0, pair.shape[-3], inplace_chunk_size):
+                    pair_chunk = pair[..., i : i + inplace_chunk_size, :, :]
+                    pair_chunk = compute_projection_helper(
+                        pair[..., i : i + inplace_chunk_size, :, :],
+                        mask[..., i : i + inplace_chunk_size, :, :],
+                        a,
+                    )
+                    if need_transpose:
+                        pair_chunk = pair_chunk.transpose(-1, -2)
+                        p[..., i : i + inplace_chunk_size] = pair_chunk
+                    else:
+                        p[..., i : i + inplace_chunk_size, :] = pair_chunk
+
+                    del pair_chunk
+
+            return p
+
+        # We start by fully manifesting a. In addition to the input, this
+        # brings total memory consumption to 2x z (disregarding size of chunks)
+        # [*, N, N, c]
+        a = compute_projection(z, mask, True, chunked=True)
+
+        if inplace_chunk_size is not None:
+            n = a.shape[-1]
+            half_n = n // 2 + n % 2
+            row_dim = -3
+            col_dim = -2
+            b_chunk_dim = row_dim if self._outgoing else col_dim
+
+            def empty_slicer(t):
+                return [slice(None) for _ in t.shape]
+
+            def slice_tensor(t, start, end, dim):
+                # Slices start:end from the dim dimension of t
+                s = empty_slicer(t)
+                s[dim] = slice(start, end)
+                return t[s]
+
+            def flip_z_cache_(z_cache, z):
+                # "Reorient" the z_cache (see below), filling it with quadrants
+                # 3---recovered from the z_cache---and 4---recovered from z---
+                # of the input tensor z.
+                quadrant_3 = slice_tensor(z_cache, half_n, None, row_dim)
+                z_cache = z_cache.transpose(row_dim, col_dim)
+
+                # If n is odd, we need to shrink the z_cache by one row
+                z_cache = z_cache[..., : (n // 2), :, :]
+
+                # Move the 3rd quadrant of z into the
+                first_half_slicer = empty_slicer(z_cache)
+                first_half_slicer[col_dim] = slice(0, half_n)
+                z_cache[first_half_slicer] = quadrant_3
+
+                # Get the fourth quadrant of z
+                quadrant_4 = slice_tensor(z, half_n, None, row_dim)
+                quadrant_4 = slice_tensor(quadrant_4, half_n, None, col_dim)
+
+                # Insert said quadrant into the rotated z-cache
+                quadrant_3_slicer = empty_slicer(z_cache)
+                quadrant_3_slicer[col_dim] = slice(half_n, None)
+
+                z_cache[quadrant_3_slicer] = quadrant_4
+
+                return z_cache
+
+            # Initialize the z cache to the left half of z.
+            z_cache_shape = list(z.shape)
+            z_cache_shape[col_dim] = half_n
+            z_cache = z.new_zeros(z_cache_shape)
+            z_cache_slicer = empty_slicer(z_cache)
+            z_cache_slicer[col_dim] = slice(0, half_n)
+            z_cache.copy_(z[z_cache_slicer])
+            z_cache_rotated = False
+
+            # We need to reorient the z-cache at the halfway point, and we
+            # don't want a single chunk to straddle that point. We contract one
+            # of the chunks in the middle to address that problem.
+            i_range = list(range(0, half_n, inplace_chunk_size))
+            initial_offsets = [i_2 - i_1 for i_1, i_2 in zip(i_range, i_range[1:] + [half_n])]
+            after_half = list(range(half_n, n, inplace_chunk_size))
+            after_half_offsets = [inplace_chunk_size for _ in after_half]
+            combined_range_with_offsets = zip(i_range + after_half, initial_offsets + after_half_offsets)
+            for i, offset in combined_range_with_offsets:
+                if not z_cache_rotated and i >= half_n:
+                    z_cache = flip_z_cache_(z_cache, z)
+                    z_cache_rotated = True
+
+                z_chunk_b = slice_tensor(z, i, i + offset, b_chunk_dim)
+                mask_chunk = slice_tensor(mask, i, i + offset, b_chunk_dim)
+
+                z_chunk_b = z_chunk_b.clone()
+                if b_chunk_dim == col_dim:
+                    z_chunk_b = slice_tensor(z, i, i + offset, col_dim)
+                else:  # b_chunk_dim == row_dim
+                    # In this case, the b-dimension (b_chunk_dim) is partially
+                    # overwritten at the end of each iteration. We need to
+                    # restore the missing component from the z-cache.
+                    if not z_cache_rotated:
+                        z_chunk_slicer = empty_slicer(z_chunk_b)
+                        z_chunk_slicer[col_dim] = slice(0, half_n)
+                        z_chunk_b[z_chunk_slicer] = slice_tensor(z_cache, i, i + offset, row_dim)
+                    else:
+                        z_cache_offset = i - half_n
+                        z_chunk_b = slice_tensor(z_cache, z_cache_offset, z_cache_offset + offset, row_dim)
+
+                b_chunk = compute_projection(z_chunk_b, mask_chunk, a=False, chunked=False)
+                del z_chunk_b
+
+                x_chunk = torch.matmul(a, b_chunk)
+                x_chunk = permute_final_dims(x_chunk, (1, 2, 0))
+                x_chunk = self.layer_norm_out(x_chunk)
+                x_chunk = self.linear_z(x_chunk)
+
+                # The g dimension (col_dim) is parallel to and ahead of the
+                # overwrites in z. We can extract the g chunk normally.
+                z_chunk_g = slice_tensor(z, i, i + offset, col_dim)
+                g_chunk = self.linear_g(self.layer_norm_in(z_chunk_g))
+                g_chunk.sigmoid_()
+                del z_chunk_g
+
+                x_chunk *= g_chunk
+
+                # Write the columns into z in-place
+                z_slicer = empty_slicer(z)
+                z_slicer[col_dim] = slice(i, i + offset)
+                if with_add:
+                    z[z_slicer] += x_chunk
+                else:
+                    z[z_slicer] = x_chunk
+        else:
+            b = compute_projection(z, mask, False, False)
+            x = torch.matmul(a, b)
+            x = self.layer_norm_out(x)
+            x = self.linear_z(x)
+            g = self.linear_g(z)
+            g.sigmoid_()
+            x *= g
+            if with_add:
+                z += x
+            else:
+                z = x
+
+        return z
+
+    def forward(
+        self,
+        z: torch.Tensor,
+        mask: Optional[torch.Tensor] = None,
+        inplace_safe: bool = False,
+        _add_with_inplace: bool = False,
+        _inplace_chunk_size: Optional[int] = 256,
+    ) -> torch.Tensor:
+        """
+        Args:
+            x:
+                [*, N_res, N_res, C_z] input tensor
+            mask:
+                [*, N_res, N_res] input mask
+        Returns:
+            [*, N_res, N_res, C_z] output tensor
+        """
+        if inplace_safe:
+            x = self._inference_forward(
+                z,
+                mask,
+                inplace_chunk_size=_inplace_chunk_size,
+                with_add=_add_with_inplace,
+            )
+            return x
+
+        if mask is None:
+            mask = z.new_ones(z.shape[:-1])
+
+        mask = mask.unsqueeze(-1)
+
+        z = self.layer_norm_in(z)
+        a = mask
+        a = a * self.sigmoid(self.linear_a_g(z))
+        a = a * self.linear_a_p(z)
+        b = mask
+        b = b * self.sigmoid(self.linear_b_g(z))
+        b = b * self.linear_b_p(z)
+
+        if is_fp16_enabled():
+            with torch.cuda.amp.autocast(enabled=False):
+                x = self._combine_projections(a.float(), b.float())
+        else:
+            x = self._combine_projections(a, b)
+
+        del a, b
+        x = self.layer_norm_out(x)
+        x = self.linear_z(x)
+        g = self.sigmoid(self.linear_g(z))
+        x = x * g
+
+        return x
+
+
+class EsmFoldPreTrainedModel(EsmPreTrainedModel):
+    """
+    An abstract class to handle weights initialization and a simple interface for downloading and loading pretrained
+    models.
+    """
+
+    # Subclass `EsMPreTrainedModel` to deal with special init
+    def _init_weights(self, module):
+        """Initialize the weights"""
+        if isinstance(module, EsmFoldLinear):
+            with torch.no_grad():
+                if module.init_fn is not None:
+                    module.init_fn(module.weight, module.bias)
+                elif module.init == "default":
+                    trunc_normal_init_(module.weight, scale=1.0)
+                elif module.init == "relu":
+                    trunc_normal_init_(module.weight, scale=2.0)
+                elif module.init == "glorot":
+                    nn.init.xavier_uniform_(module.weight, gain=1)
+                elif module.init == "gating":
+                    module.weight.fill_(0.0)
+                    if module.bias:
+                        module.bias.fill_(1.0)
+                elif module.init == "normal":
+                    torch.nn.init.kaiming_normal_(module.weight, nonlinearity="linear")
+                elif module.init == "final":
+                    module.weight.fill_(0.0)
+        elif isinstance(module, EsmFoldInvariantPointAttention):
+            ipa_point_weights_init_(module.head_weights)
+        elif isinstance(module, EsmFoldTriangularSelfAttentionBlock):
+            torch.nn.init.zeros_(module.tri_mul_in.linear_z.weight)
+            torch.nn.init.zeros_(module.tri_mul_in.linear_z.bias)
+            torch.nn.init.zeros_(module.tri_mul_out.linear_z.weight)
+            torch.nn.init.zeros_(module.tri_mul_out.linear_z.bias)
+            torch.nn.init.zeros_(module.tri_att_start.mha.linear_o.weight)
+            torch.nn.init.zeros_(module.tri_att_start.mha.linear_o.bias)
+            torch.nn.init.zeros_(module.tri_att_end.mha.linear_o.weight)
+            torch.nn.init.zeros_(module.tri_att_end.mha.linear_o.bias)
+
+            torch.nn.init.zeros_(module.sequence_to_pair.o_proj.weight)
+            torch.nn.init.zeros_(module.sequence_to_pair.o_proj.bias)
+            torch.nn.init.zeros_(module.pair_to_sequence.linear.weight)
+            torch.nn.init.zeros_(module.seq_attention.o_proj.weight)
+            torch.nn.init.zeros_(module.seq_attention.o_proj.bias)
+            torch.nn.init.zeros_(module.mlp_seq.mlp[-2].weight)
+            torch.nn.init.zeros_(module.mlp_seq.mlp[-2].bias)
+            torch.nn.init.zeros_(module.mlp_pair.mlp[-2].weight)
+            torch.nn.init.zeros_(module.mlp_pair.mlp[-2].bias)
+        else:
+            super()._init_weights(module)
+
+
+class EsmFoldSelfAttention(nn.Module):
+    def __init__(self, embed_dim, num_heads, head_width, gated=False):
+        super().__init__()
+        assert embed_dim == num_heads * head_width
+
+        self.embed_dim = embed_dim
+        self.num_heads = num_heads
+        self.head_width = head_width
+
+        self.proj = nn.Linear(embed_dim, embed_dim * 3, bias=False)
+        self.o_proj = nn.Linear(embed_dim, embed_dim, bias=True)
+        self.gated = gated
+        if gated:
+            self.g_proj = nn.Linear(embed_dim, embed_dim)
+            torch.nn.init.zeros_(self.g_proj.weight)
+            torch.nn.init.ones_(self.g_proj.bias)
+
+        self.rescale_factor = self.head_width**-0.5
+
+        torch.nn.init.zeros_(self.o_proj.bias)
+
+    def forward(self, x, mask=None, bias=None, indices=None):
+        """
+        Basic self attention with optional mask and external pairwise bias. To handle sequences of different lengths,
+        use mask.
+
+        Inputs:
+            x: batch of input sequneces (.. x L x C) mask: batch of boolean masks where 1=valid, 0=padding position (..
+            x L_k) bias: batch of scalar pairwise attention biases (.. x Lq x Lk x num_heads)
+
+        Outputs:
+          sequence projection (B x L x embed_dim), attention maps (B x L x L x num_heads)
+        """
+
+        t = self.proj(x).view(*x.shape[:2], self.num_heads, -1)
+        t = t.permute(0, 2, 1, 3)
+        q, k, v = t.chunk(3, dim=-1)
+
+        q = self.rescale_factor * q
+        a = torch.einsum("...qc,...kc->...qk", q, k)
+
+        # Add external attention bias.
+        if bias is not None:
+            a = a + bias.permute(0, 3, 1, 2)
+
+        # Do not attend to padding tokens.
+        if mask is not None:
+            mask = mask[:, None, None]
+            a = a.masked_fill(mask == False, -np.inf)  # noqa: E712
+
+        a = nn.functional.softmax(a, dim=-1)
+
+        y = torch.einsum("...hqk,...hkc->...qhc", a, v)
+        y = y.reshape(*y.shape[:2], -1)
+
+        if self.gated:
+            y = self.g_proj(x).sigmoid() * y
+        y = self.o_proj(y)
+
+        return y, a.permute(0, 3, 1, 2)
+
+
+class EsmFoldDropout(nn.Module):
+    """
+    Implementation of dropout with the ability to share the dropout mask along a particular dimension.
+    """
+
+    def __init__(self, r: float, batch_dim: Union[int, List[int]]):
+        super().__init__()
+
+        self.r = r
+        if isinstance(batch_dim, int):
+            batch_dim = [batch_dim]
+        self.batch_dim = batch_dim
+        self.dropout = nn.Dropout(self.r)
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        shape = list(x.shape)
+        if self.batch_dim is not None:
+            for bd in self.batch_dim:
+                shape[bd] = 1
+        return x * self.dropout(x.new_ones(shape))
+
+
+class EsmFoldSequenceToPair(nn.Module):
+    def __init__(self, sequence_state_dim, inner_dim, pairwise_state_dim):
+        super().__init__()
+
+        self.layernorm = nn.LayerNorm(sequence_state_dim)
+        self.proj = nn.Linear(sequence_state_dim, inner_dim * 2, bias=True)
+        self.o_proj = nn.Linear(2 * inner_dim, pairwise_state_dim, bias=True)
+
+        torch.nn.init.zeros_(self.proj.bias)
+        torch.nn.init.zeros_(self.o_proj.bias)
+
+    def forward(self, sequence_state):
+        """
+        Inputs:
+          sequence_state: B x L x sequence_state_dim
+
+        Output:
+          pairwise_state: B x L x L x pairwise_state_dim
+
+        Intermediate state:
+          B x L x L x 2*inner_dim
+        """
+
+        assert len(sequence_state.shape) == 3
+
+        s = self.layernorm(sequence_state)
+        s = self.proj(s)
+        q, k = s.chunk(2, dim=-1)
+
+        prod = q[:, None, :, :] * k[:, :, None, :]
+        diff = q[:, None, :, :] - k[:, :, None, :]
+
+        x = torch.cat([prod, diff], dim=-1)
+        x = self.o_proj(x)
+
+        return x
+
+
+class EsmFoldPairToSequence(nn.Module):
+    def __init__(self, pairwise_state_dim, num_heads):
+        super().__init__()
+
+        self.layernorm = nn.LayerNorm(pairwise_state_dim)
+        self.linear = nn.Linear(pairwise_state_dim, num_heads, bias=False)
+
+    def forward(self, pairwise_state):
+        """
+        Inputs:
+          pairwise_state: B x L x L x pairwise_state_dim
+
+        Output:
+          pairwise_bias: B x L x L x num_heads
+        """
+        assert len(pairwise_state.shape) == 4
+        z = self.layernorm(pairwise_state)
+        pairwise_bias = self.linear(z)
+        return pairwise_bias
+
+
+class EsmFoldResidueMLP(nn.Module):
+    def __init__(self, embed_dim, inner_dim, dropout=0):
+        super().__init__()
+
+        self.mlp = nn.Sequential(
+            nn.LayerNorm(embed_dim),
+            nn.Linear(embed_dim, inner_dim),
+            nn.ReLU(),
+            nn.Linear(inner_dim, embed_dim),
+            nn.Dropout(dropout),
+        )
+
+    def forward(self, x):
+        return x + self.mlp(x)
+
+
+class EsmFoldTriangularSelfAttentionBlock(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.config = config
+
+        sequence_state_dim = config.sequence_state_dim
+        pairwise_state_dim = config.pairwise_state_dim
+        sequence_num_heads = sequence_state_dim // config.sequence_head_width
+        pairwise_num_heads = pairwise_state_dim // config.pairwise_head_width
+
+        self.layernorm_1 = nn.LayerNorm(sequence_state_dim)
+
+        self.sequence_to_pair = EsmFoldSequenceToPair(sequence_state_dim, pairwise_state_dim // 2, pairwise_state_dim)
+        self.pair_to_sequence = EsmFoldPairToSequence(pairwise_state_dim, sequence_num_heads)
+
+        self.seq_attention = EsmFoldSelfAttention(
+            sequence_state_dim, sequence_num_heads, config.sequence_head_width, gated=True
+        )
+        self.tri_mul_out = EsmFoldTriangleMultiplicativeUpdate(config, _outgoing=True)
+        self.tri_mul_in = EsmFoldTriangleMultiplicativeUpdate(config, _outgoing=False)
+
+        self.tri_att_start = EsmFoldTriangleAttention(
+            pairwise_state_dim, config.pairwise_head_width, pairwise_num_heads, inf=1e9, starting=True
+        )
+        self.tri_att_end = EsmFoldTriangleAttention(
+            pairwise_state_dim, config.pairwise_head_width, pairwise_num_heads, inf=1e9, starting=False
+        )
+
+        self.mlp_seq = EsmFoldResidueMLP(sequence_state_dim, 4 * sequence_state_dim, dropout=config.dropout)
+        self.mlp_pair = EsmFoldResidueMLP(pairwise_state_dim, 4 * pairwise_state_dim, dropout=config.dropout)
+
+        self.drop = nn.Dropout(config.dropout)
+        self.row_drop = EsmFoldDropout(config.dropout * 2, 2)
+        self.col_drop = EsmFoldDropout(config.dropout * 2, 1)
+
+    def forward(self, sequence_state, pairwise_state, mask=None, chunk_size=None, **__kwargs):
+        """
+        Inputs:
+          sequence_state: B x L x sequence_state_dim pairwise_state: B x L x L x pairwise_state_dim mask: B x L boolean
+          tensor of valid positions
+
+        Output:
+          sequence_state: B x L x sequence_state_dim pairwise_state: B x L x L x pairwise_state_dim
+        """
+        if len(sequence_state.shape) != 3:
+            raise ValueError(f"`sequence_state` should be a 3d-tensor, got {len(sequence_state.shape)} dims.")
+        if len(pairwise_state.shape) != 4:
+            raise ValueError(f"`pairwise_state` should be a 4d-tensor, got {len(pairwise_state.shape)} dims.")
+        if mask is not None and len(mask.shape) != 2:
+            raise ValueError(f"`mask` should be a 2d-tensor, got {len(mask.shape)} dims.")
+
+        batch_dim, seq_dim, sequence_state_dim = sequence_state.shape
+        pairwise_state_dim = pairwise_state.shape[3]
+
+        if sequence_state_dim != self.config.sequence_state_dim:
+            raise ValueError(
+                "`sequence_state` last dimension should be equal to `self.sequence_state_dim`. Got "
+                f"{sequence_state_dim} != {self.config.sequence_state_dim}."
+            )
+        if pairwise_state_dim != self.config.pairwise_state_dim:
+            raise ValueError(
+                "`pairwise_state` last dimension should be equal to `self.pairwise_state_dim`. Got "
+                f"{pairwise_state_dim} != {self.config.pairwise_state_dim}."
+            )
+        if batch_dim != pairwise_state.shape[0]:
+            raise ValueError(
+                f"`sequence_state` and `pairwise_state` have inconsistent batch size: {batch_dim} != "
+                f"{pairwise_state.shape[0]}."
+            )
+        if seq_dim != pairwise_state.shape[1] or seq_dim != pairwise_state.shape[2]:
+            raise ValueError(
+                f"`sequence_state` and `pairwise_state` have inconsistent sequence length: {seq_dim} != "
+                f"{pairwise_state.shape[1]} or {pairwise_state.shape[2]}."
+            )
+
+        # Update sequence state
+        bias = self.pair_to_sequence(pairwise_state)
+
+        # Self attention with bias + mlp.
+        y = self.layernorm_1(sequence_state)
+        y, _ = self.seq_attention(y, mask=mask, bias=bias)
+        sequence_state = sequence_state + self.drop(y)
+        sequence_state = self.mlp_seq(sequence_state)
+
+        # Update pairwise state
+        pairwise_state = pairwise_state + self.sequence_to_pair(sequence_state)
+
+        # Axial attention with triangular bias.
+        tri_mask = mask.unsqueeze(2) * mask.unsqueeze(1) if mask is not None else None
+        pairwise_state = pairwise_state + self.row_drop(self.tri_mul_out(pairwise_state, mask=tri_mask))
+        pairwise_state = pairwise_state + self.col_drop(self.tri_mul_in(pairwise_state, mask=tri_mask))
+        pairwise_state = pairwise_state + self.row_drop(
+            self.tri_att_start(pairwise_state, mask=tri_mask, chunk_size=chunk_size)
+        )
+        pairwise_state = pairwise_state + self.col_drop(
+            self.tri_att_end(pairwise_state, mask=tri_mask, chunk_size=chunk_size)
+        )
+
+        # MLP over pairs.
+        pairwise_state = self.mlp_pair(pairwise_state)
+
+        return sequence_state, pairwise_state
+
+
+class EsmCategoricalMixture:
+    def __init__(self, param, bins=50, start=0, end=1):
+        # All tensors are of shape ..., bins.
+        self.logits = param
+        bins = torch.linspace(start, end, bins + 1, device=self.logits.device, dtype=self.logits.dtype)
+        self.v_bins = (bins[:-1] + bins[1:]) / 2
+
+    def log_prob(self, true):
+        # Shapes are:
+        #     self.probs: ... x bins
+        #     true      : ...
+        true_index = (true.unsqueeze(-1) - self.v_bins[[None] * true.ndim]).abs().argmin(-1)
+        nll = self.logits.log_softmax(-1)
+        return torch.take_along_dim(nll, true_index.unsqueeze(-1), dim=-1).squeeze(-1)
+
+    def mean(self):
+        return (self.logits.softmax(-1) @ self.v_bins.unsqueeze(1)).squeeze(-1)
+
+
+def categorical_lddt(logits, bins=50):
+    # Logits are ..., 37, bins.
+    return EsmCategoricalMixture(logits, bins=bins).mean()
+
+
+def get_axial_mask(mask):
+    """
+    Helper to convert B x L mask of valid positions to axial mask used in row column attentions.
+
+    Input:
+      mask: B x L tensor of booleans
+
+    Output:
+      mask: B x L x L tensor of booleans
+    """
+
+    if mask is None:
+        return None
+
+    if len(mask.shape) != 2:
+        raise ValueError(f"`mask` should be a 2d-tensor, got {len(mask.shape)} dims.")
+    batch_dim, seq_dim = mask.shape
+    m = mask.unsqueeze(1).expand(batch_dim, seq_dim, seq_dim)
+    m = m.reshape(batch_dim * seq_dim, seq_dim)
+    return m
+
+
+class EsmFoldRelativePosition(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.bins = config.position_bins
+
+        # Note an additional offset is used so that the 0th position
+        # is reserved for masked pairs.
+        self.embedding = torch.nn.Embedding(2 * self.bins + 2, config.pairwise_state_dim)
+
+    def forward(self, residue_index, mask=None):
+        """
+        Input:
+          residue_index: B x L tensor of indices (dytpe=torch.long) mask: B x L tensor of booleans
+
+        Output:
+          pairwise_state: B x L x L x pairwise_state_dim tensor of embeddings
+        """
+        if residue_index.dtype != torch.long:
+            raise ValueError(f"`residue_index` has dtype {residue_index.dtype}, it should be `torch.long`.")
+        if mask is not None and residue_index.shape != mask.shape:
+            raise ValueError(
+                f"`residue_index` and `mask` have inconsistent shapes: {residue_index.shape} != {mask.shape}."
+            )
+
+        diff = residue_index[:, None, :] - residue_index[:, :, None]
+        diff = diff.clamp(-self.bins, self.bins)
+        diff = diff + self.bins + 1  # Add 1 to adjust for padding index.
+
+        if mask is not None:
+            mask = mask[:, None, :] * mask[:, :, None]
+            diff[mask == False] = 0  # noqa: E712
+
+        output = self.embedding(diff)
+        return output
+
+
+class EsmFoldAngleResnetBlock(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+
+        self.linear_1 = EsmFoldLinear(config.resnet_dim, config.resnet_dim, init="relu")
+        self.linear_2 = EsmFoldLinear(config.resnet_dim, config.resnet_dim, init="final")
+
+        self.relu = nn.ReLU()
+
+    def forward(self, a: torch.Tensor) -> torch.Tensor:
+        s_initial = a
+
+        a = self.relu(a)
+        a = self.linear_1(a)
+        a = self.relu(a)
+        a = self.linear_2(a)
+
+        return a + s_initial
+
+
+class EsmFoldAngleResnet(nn.Module):
+    """
+    Implements Algorithm 20, lines 11-14
+    """
+
+    def __init__(self, config):
+        super().__init__()
+        self.config = config
+
+        self.linear_in = EsmFoldLinear(config.sequence_dim, config.resnet_dim)
+        self.linear_initial = EsmFoldLinear(config.sequence_dim, config.resnet_dim)
+
+        self.layers = nn.ModuleList()
+        for _ in range(config.num_resnet_blocks):
+            layer = EsmFoldAngleResnetBlock(config)
+            self.layers.append(layer)
+
+        self.linear_out = EsmFoldLinear(config.resnet_dim, config.num_angles * 2)
+
+        self.relu = nn.ReLU()
+
+    def forward(self, s: torch.Tensor, s_initial: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor]:
+        """
+        Args:
+            s:
+                [*, C_hidden] single embedding
+            s_initial:
+                [*, C_hidden] single embedding as of the start of the StructureModule
+        Returns:
+            [*, no_angles, 2] predicted angles
+        """
+        # NOTE: The ReLU's applied to the inputs are absent from the supplement
+        # pseudocode but present in the source. For maximal compatibility with
+        # the pretrained weights, I'm going with the source.
+
+        # [*, C_hidden]
+        s_initial = self.relu(s_initial)
+        s_initial = self.linear_initial(s_initial)
+        s = self.relu(s)
+        s = self.linear_in(s)
+        s = s + s_initial
+
+        for l in self.layers:
+            s = l(s)
+
+        s = self.relu(s)
+
+        # [*, no_angles * 2]
+        s = self.linear_out(s)
+
+        # [*, no_angles, 2]
+        s = s.view(s.shape[:-1] + (-1, 2))
+
+        unnormalized_s = s
+        norm_denom = torch.sqrt(
+            torch.clamp(
+                torch.sum(s**2, dim=-1, keepdim=True),
+                min=self.config.epsilon,
+            )
+        )
+        s = s / norm_denom
+
+        return unnormalized_s, s
+
+
+class EsmFoldInvariantPointAttention(nn.Module):
+    """
+    Implements Algorithm 22.
+    """
+
+    def __init__(self, config):
+        super().__init__()
+        self.config = config
+
+        c_s = config.sequence_dim
+        c_z = config.pairwise_dim
+        self.hidden_dim = config.ipa_dim
+        self.num_heads = config.num_heads_ipa
+        self.num_qk_points = config.num_qk_points
+        self.num_v_points = config.num_v_points
+
+        # These linear layers differ from their specifications in the
+        # supplement. There, they lack bias and use Glorot initialization.
+        # Here as in the official source, they have bias and use the default
+        # Lecun initialization.
+        hc = config.ipa_dim * config.num_heads_ipa
+        self.linear_q = EsmFoldLinear(c_s, hc)
+        self.linear_kv = EsmFoldLinear(c_s, 2 * hc)
+
+        hpq = config.num_heads_ipa * config.num_qk_points * 3
+        self.linear_q_points = EsmFoldLinear(c_s, hpq)
+
+        hpkv = config.num_heads_ipa * (config.num_qk_points + config.num_v_points) * 3
+        self.linear_kv_points = EsmFoldLinear(c_s, hpkv)
+
+        self.linear_b = EsmFoldLinear(c_z, config.num_heads_ipa)
+
+        self.head_weights = nn.Parameter(torch.zeros((config.num_heads_ipa)))
+
+        concat_out_dim = config.num_heads_ipa * (c_z + config.ipa_dim + config.num_v_points * 4)
+        self.linear_out = EsmFoldLinear(concat_out_dim, c_s, init="final")
+
+        self.softmax = nn.Softmax(dim=-1)
+        self.softplus = nn.Softplus()
+
+    def forward(
+        self,
+        s: torch.Tensor,
+        z: Optional[torch.Tensor],
+        r: Rigid,
+        mask: torch.Tensor,
+        _offload_inference: bool = False,
+        _z_reference_list: Optional[Sequence[torch.Tensor]] = None,
+    ) -> torch.Tensor:
+        """
+        Args:
+            s:
+                [*, N_res, C_s] single representation
+            z:
+                [*, N_res, N_res, C_z] pair representation
+            r:
+                [*, N_res] transformation object
+            mask:
+                [*, N_res] mask
+        Returns:
+            [*, N_res, C_s] single representation update
+        """
+        z = [z]
+
+        #######################################
+        # Generate scalar and point activations
+        #######################################
+        # [*, N_res, H * C_hidden]
+        q = self.linear_q(s)
+        kv = self.linear_kv(s)
+
+        # [*, N_res, H, C_hidden]
+        q = q.view(q.shape[:-1] + (self.num_heads, -1))
+
+        # [*, N_res, H, 2 * C_hidden]
+        kv = kv.view(kv.shape[:-1] + (self.num_heads, -1))
+
+        # [*, N_res, H, C_hidden]
+        k, v = torch.split(kv, self.hidden_dim, dim=-1)
+
+        # [*, N_res, H * P_q * 3]
+        q_pts = self.linear_q_points(s)
+
+        # This is kind of clunky, but it's how the original does it
+        # [*, N_res, H * P_q, 3]
+        q_pts = torch.split(q_pts, q_pts.shape[-1] // 3, dim=-1)
+        q_pts = torch.stack(q_pts, dim=-1)
+        q_pts = r[..., None].apply(q_pts)
+
+        # [*, N_res, H, P_q, 3]
+        q_pts = q_pts.view(q_pts.shape[:-2] + (self.num_heads, self.num_qk_points, 3))
+
+        # [*, N_res, H * (P_q + P_v) * 3]
+        kv_pts = self.linear_kv_points(s)
+
+        # [*, N_res, H * (P_q + P_v), 3]
+        kv_pts = torch.split(kv_pts, kv_pts.shape[-1] // 3, dim=-1)
+        kv_pts = torch.stack(kv_pts, dim=-1)
+        kv_pts = r[..., None].apply(kv_pts)
+
+        # [*, N_res, H, (P_q + P_v), 3]
+        kv_pts = kv_pts.view(kv_pts.shape[:-2] + (self.num_heads, -1, 3))
+
+        # [*, N_res, H, P_q/P_v, 3]
+        k_pts, v_pts = torch.split(kv_pts, [self.num_qk_points, self.num_v_points], dim=-2)
+
+        ##########################
+        # Compute attention scores
+        ##########################
+        # [*, N_res, N_res, H]
+        b = self.linear_b(z[0])
+
+        if _offload_inference:
+            assert sys.getrefcount(z[0]) == 2
+            z[0] = z[0].cpu()
+
+        # [*, H, N_res, N_res]
+        if is_fp16_enabled():
+            with torch.cuda.amp.autocast(enabled=False):
+                a = torch.matmul(
+                    permute_final_dims(q.float(), (1, 0, 2)),  # [*, H, N_res, C_hidden]
+                    permute_final_dims(k.float(), (1, 2, 0)),  # [*, H, C_hidden, N_res]
+                )
+        else:
+            a = torch.matmul(
+                permute_final_dims(q, (1, 0, 2)),  # [*, H, N_res, C_hidden]
+                permute_final_dims(k, (1, 2, 0)),  # [*, H, C_hidden, N_res]
+            )
+
+        a *= math.sqrt(1.0 / (3 * self.hidden_dim))
+        a += math.sqrt(1.0 / 3) * permute_final_dims(b, (2, 0, 1))
+
+        # [*, N_res, N_res, H, P_q, 3]
+        pt_att = q_pts.unsqueeze(-4) - k_pts.unsqueeze(-5)
+        pt_att = pt_att**2
+
+        # [*, N_res, N_res, H, P_q]
+        pt_att = sum(torch.unbind(pt_att, dim=-1))
+        head_weights = self.softplus(self.head_weights).view(*((1,) * len(pt_att.shape[:-2]) + (-1, 1)))
+        head_weights = head_weights * math.sqrt(1.0 / (3 * (self.num_qk_points * 9.0 / 2)))
+        pt_att = pt_att * head_weights
+
+        # [*, N_res, N_res, H]
+        pt_att = torch.sum(pt_att, dim=-1) * (-0.5)
+        # [*, N_res, N_res]
+        square_mask = mask.unsqueeze(-1) * mask.unsqueeze(-2)
+        square_mask = self.config.inf * (square_mask - 1)
+
+        # [*, H, N_res, N_res]
+        pt_att = permute_final_dims(pt_att, (2, 0, 1))
+
+        a = a + pt_att
+        a = a + square_mask.unsqueeze(-3)
+        a = self.softmax(a)
+
+        ################
+        # Compute output
+        ################
+        # [*, N_res, H, C_hidden]
+        o = torch.matmul(a, v.transpose(-2, -3).to(dtype=a.dtype)).transpose(-2, -3)
+
+        # [*, N_res, H * C_hidden]
+        o = flatten_final_dims(o, 2)
+
+        # [*, H, 3, N_res, P_v]
+        o_pt = torch.sum(
+            (a[..., None, :, :, None] * permute_final_dims(v_pts, (1, 3, 0, 2))[..., None, :, :]),
+            dim=-2,
+        )
+
+        # [*, N_res, H, P_v, 3]
+        o_pt = permute_final_dims(o_pt, (2, 0, 3, 1))
+        o_pt = r[..., None, None].invert_apply(o_pt)
+
+        # [*, N_res, H * P_v]
+        o_pt_norm = flatten_final_dims(torch.sqrt(torch.sum(o_pt**2, dim=-1) + self.config.epsilon), 2)
+
+        # [*, N_res, H * P_v, 3]
+        o_pt = o_pt.reshape(*o_pt.shape[:-3], -1, 3)
+
+        if _offload_inference:
+            z[0] = z[0].to(o_pt.device)
+
+        # [*, N_res, H, C_z]
+        o_pair = torch.matmul(a.transpose(-2, -3), z[0].to(dtype=a.dtype))
+
+        # [*, N_res, H * C_z]
+        o_pair = flatten_final_dims(o_pair, 2)
+
+        # [*, N_res, C_s]
+        s = self.linear_out(
+            torch.cat((o, *torch.unbind(o_pt, dim=-1), o_pt_norm, o_pair), dim=-1).to(dtype=z[0].dtype)
+        )
+
+        return s
+
+
+class EsmFoldBackboneUpdate(nn.Module):
+    """
+    Implements part of Algorithm 23.
+    """
+
+    def __init__(self, config):
+        super().__init__()
+
+        self.linear = EsmFoldLinear(config.sequence_dim, 6, init="final")
+
+    def forward(self, s: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor]:
+        """
+        Args:
+            [*, N_res, C_s] single representation
+        Returns:
+            [*, N_res, 6] update vector
+        """
+        # [*, 6]
+        update = self.linear(s)
+
+        return update
+
+
+class EsmFoldStructureModuleTransitionLayer(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+
+        self.linear_1 = EsmFoldLinear(config.sequence_dim, config.sequence_dim, init="relu")
+        self.linear_2 = EsmFoldLinear(config.sequence_dim, config.sequence_dim, init="relu")
+        self.linear_3 = EsmFoldLinear(config.sequence_dim, config.sequence_dim, init="final")
+
+        self.relu = nn.ReLU()
+
+    def forward(self, s):
+        s_initial = s
+        s = self.linear_1(s)
+        s = self.relu(s)
+        s = self.linear_2(s)
+        s = self.relu(s)
+        s = self.linear_3(s)
+
+        s = s + s_initial
+
+        return s
+
+
+class EsmFoldStructureModuleTransition(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.config = config
+
+        self.layers = nn.ModuleList()
+        for _ in range(config.num_transition_layers):
+            l = EsmFoldStructureModuleTransitionLayer(config)
+            self.layers.append(l)
+
+        self.dropout = nn.Dropout(config.dropout_rate)
+        self.layer_norm = LayerNorm(config.sequence_dim)
+
+    def forward(self, s):
+        for l in self.layers:
+            s = l(s)
+
+        s = self.dropout(s)
+        s = self.layer_norm(s)
+
+        return s
+
+
+class EsmFoldStructureModule(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.config = config
+
+        # Buffers to be lazily initialized later
+        # self.default_frames
+        # self.group_idx
+        # self.atom_mask
+        # self.lit_positions
+
+        self.layer_norm_s = LayerNorm(config.sequence_dim)
+        self.layer_norm_z = LayerNorm(config.pairwise_dim)
+
+        self.linear_in = EsmFoldLinear(config.sequence_dim, config.sequence_dim)
+
+        self.ipa = EsmFoldInvariantPointAttention(config)
+
+        self.ipa_dropout = nn.Dropout(config.dropout_rate)
+        self.layer_norm_ipa = LayerNorm(config.sequence_dim)
+
+        self.transition = EsmFoldStructureModuleTransition(config)
+        self.bb_update = EsmFoldBackboneUpdate(config)
+        self.angle_resnet = EsmFoldAngleResnet(config)
+
+    def forward(
+        self,
+        evoformer_output_dict,
+        aatype,
+        mask=None,
+        _offload_inference=False,
+    ):
+        """
+        Args:
+            evoformer_output_dict:
+                Dictionary containing:
+                    "single":
+                        [*, N_res, C_s] single representation
+                    "pair":
+                        [*, N_res, N_res, C_z] pair representation
+            aatype:
+                [*, N_res] amino acid indices
+            mask:
+                Optional [*, N_res] sequence mask
+        Returns:
+            A dictionary of outputs
+        """
+        s = evoformer_output_dict["single"]
+
+        if mask is None:
+            # [*, N]
+            mask = s.new_ones(s.shape[:-1])
+
+        # [*, N, C_s]
+        s = self.layer_norm_s(s)
+
+        # [*, N, N, C_z]
+        z = self.layer_norm_z(evoformer_output_dict["pair"])
+
+        z_reference_list = None
+        if _offload_inference:
+            assert sys.getrefcount(evoformer_output_dict["pair"]) == 2
+            evoformer_output_dict["pair"] = evoformer_output_dict["pair"].cpu()
+            z_reference_list = [z]
+            z = None
+
+        # [*, N, C_s]
+        s_initial = s
+        s = self.linear_in(s)
+
+        # [*, N]
+        rigids = Rigid.identity(
+            s.shape[:-1],
+            s.dtype,
+            s.device,
+            self.training,
+            fmt="quat",
+        )
+        outputs = []
+        for i in range(self.config.num_blocks):
+            # [*, N, C_s]
+            s = s + self.ipa(
+                s,
+                z,
+                rigids,
+                mask,
+                _offload_inference=_offload_inference,
+                _z_reference_list=z_reference_list,
+            )
+            s = self.ipa_dropout(s)
+            s = self.layer_norm_ipa(s)
+            s = self.transition(s)
+
+            # [*, N]
+            rigids = rigids.compose_q_update_vec(self.bb_update(s))
+
+            # To hew as closely as possible to AlphaFold, we convert our
+            # quaternion-based transformations to rotation-matrix ones
+            # here
+            backb_to_global = Rigid(
+                Rotation(rot_mats=rigids.get_rots().get_rot_mats(), quats=None),
+                rigids.get_trans(),
+            )
+
+            backb_to_global = backb_to_global.scale_translation(self.config.trans_scale_factor)
+
+            # [*, N, 7, 2]
+            unnormalized_angles, angles = self.angle_resnet(s, s_initial)
+
+            all_frames_to_global = self.torsion_angles_to_frames(backb_to_global, angles, aatype)
+
+            pred_xyz = self.frames_and_literature_positions_to_atom14_pos(all_frames_to_global, aatype)
+
+            scaled_rigids = rigids.scale_translation(self.config.trans_scale_factor)
+
+            preds = {
+                "frames": scaled_rigids.to_tensor_7(),
+                "sidechain_frames": all_frames_to_global.to_tensor_4x4(),
+                "unnormalized_angles": unnormalized_angles,
+                "angles": angles,
+                "positions": pred_xyz,
+                "states": s,
+            }
+
+            outputs.append(preds)
+
+            rigids = rigids.stop_rot_gradient()
+
+        del z, z_reference_list
+
+        if _offload_inference:
+            evoformer_output_dict["pair"] = evoformer_output_dict["pair"].to(s.device)
+
+        outputs = dict_multimap(torch.stack, outputs)
+        outputs["single"] = s
+
+        return outputs
+
+    def _init_residue_constants(self, float_dtype, device):
+        if not hasattr(self, "default_frames"):
+            self.register_buffer(
+                "default_frames",
+                torch.tensor(
+                    residue_constants.restype_rigid_group_default_frame,
+                    dtype=float_dtype,
+                    device=device,
+                    requires_grad=False,
+                ),
+                persistent=False,
+            )
+        if not hasattr(self, "group_idx"):
+            self.register_buffer(
+                "group_idx",
+                torch.tensor(
+                    residue_constants.restype_atom14_to_rigid_group,
+                    device=device,
+                    requires_grad=False,
+                ),
+                persistent=False,
+            )
+        if not hasattr(self, "atom_mask"):
+            self.register_buffer(
+                "atom_mask",
+                torch.tensor(
+                    residue_constants.restype_atom14_mask,
+                    dtype=float_dtype,
+                    device=device,
+                    requires_grad=False,
+                ),
+                persistent=False,
+            )
+        if not hasattr(self, "lit_positions"):
+            self.register_buffer(
+                "lit_positions",
+                torch.tensor(
+                    residue_constants.restype_atom14_rigid_group_positions,
+                    dtype=float_dtype,
+                    device=device,
+                    requires_grad=False,
+                ),
+                persistent=False,
+            )
+
+    def torsion_angles_to_frames(self, r, alpha, f):
+        # Lazily initialize the residue constants on the correct device
+        self._init_residue_constants(alpha.dtype, alpha.device)
+        # Separated purely to make testing less annoying
+        return torsion_angles_to_frames(r, alpha, f, self.default_frames)
+
+    def frames_and_literature_positions_to_atom14_pos(self, r, f):  # [*, N, 8]  # [*, N]
+        # Lazily initialize the residue constants on the correct device
+        self._init_residue_constants(r.get_rots().dtype, r.get_rots().device)
+        return frames_and_literature_positions_to_atom14_pos(
+            r,
+            f,
+            self.default_frames,
+            self.group_idx,
+            self.atom_mask,
+            self.lit_positions,
+        )
+
+
+class EsmFoldingTrunk(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.config = config
+
+        c_s = config.sequence_state_dim
+        c_z = config.pairwise_state_dim
+
+        self.pairwise_positional_embedding = EsmFoldRelativePosition(config)
+
+        self.blocks = nn.ModuleList([EsmFoldTriangularSelfAttentionBlock(config) for _ in range(config.num_blocks)])
+
+        self.recycle_bins = 15
+        self.recycle_s_norm = nn.LayerNorm(c_s)
+        self.recycle_z_norm = nn.LayerNorm(c_z)
+        self.recycle_disto = nn.Embedding(self.recycle_bins, c_z)
+        self.recycle_disto.weight[0].detach().zero_()
+
+        self.structure_module = EsmFoldStructureModule(config.structure_module)
+        self.trunk2sm_s = nn.Linear(c_s, config.structure_module.sequence_dim)
+        self.trunk2sm_z = nn.Linear(c_z, config.structure_module.pairwise_dim)
+
+        self.chunk_size = config.chunk_size
+
+    def set_chunk_size(self, chunk_size):
+        # This parameter means the axial attention will be computed
+        # in a chunked manner. This should make the memory used more or less O(L) instead of O(L^2).
+        # It's equivalent to running a for loop over chunks of the dimension we're iterative over,
+        # where the chunk_size is the size of the chunks, so 128 would mean to parse 128-length chunks.
+        self.chunk_size = chunk_size
+
+    def forward(self, seq_feats, pair_feats, true_aa, residx, mask, no_recycles):
+        """
+        Inputs:
+          seq_feats: B x L x C tensor of sequence features pair_feats: B x L x L x C tensor of pair features residx: B
+          x L long tensor giving the position in the sequence mask: B x L boolean tensor indicating valid residues
+
+        Output:
+          predicted_structure: B x L x (num_atoms_per_residue * 3) tensor wrapped in a Coordinates object
+        """
+
+        device = seq_feats.device
+        s_s_0 = seq_feats
+        s_z_0 = pair_feats
+
+        if no_recycles is None:
+            no_recycles = self.config.max_recycles
+        else:
+            if no_recycles < 0:
+                raise ValueError("Number of recycles must not be negative.")
+            no_recycles += 1  # First 'recycle' is just the standard forward pass through the model.
+
+        def trunk_iter(s, z, residx, mask):
+            z = z + self.pairwise_positional_embedding(residx, mask=mask)
+
+            for block in self.blocks:
+                s, z = block(s, z, mask=mask, residue_index=residx, chunk_size=self.chunk_size)
+            return s, z
+
+        s_s = s_s_0
+        s_z = s_z_0
+        recycle_s = torch.zeros_like(s_s)
+        recycle_z = torch.zeros_like(s_z)
+        recycle_bins = torch.zeros(*s_z.shape[:-1], device=device, dtype=torch.int64)
+
+        for recycle_idx in range(no_recycles):
+            with ContextManagers([] if recycle_idx == no_recycles - 1 else [torch.no_grad()]):
+                # === Recycling ===
+                recycle_s = self.recycle_s_norm(recycle_s.detach()).to(device)
+                recycle_z = self.recycle_z_norm(recycle_z.detach()).to(device)
+                recycle_z += self.recycle_disto(recycle_bins.detach()).to(device)
+
+                s_s, s_z = trunk_iter(s_s_0 + recycle_s, s_z_0 + recycle_z, residx, mask)
+
+                # === Structure module ===
+                structure = self.structure_module(
+                    {"single": self.trunk2sm_s(s_s), "pair": self.trunk2sm_z(s_z)},
+                    true_aa,
+                    mask.float(),
+                )
+
+                recycle_s = s_s
+                recycle_z = s_z
+                # Distogram needs the N, CA, C coordinates, and bin constants same as alphafold.
+                recycle_bins = EsmFoldingTrunk.distogram(
+                    structure["positions"][-1][:, :, :3],
+                    3.375,
+                    21.375,
+                    self.recycle_bins,
+                )
+
+        structure["s_s"] = s_s
+        structure["s_z"] = s_z
+
+        return structure
+
+    @staticmethod
+    def distogram(coords, min_bin, max_bin, num_bins):
+        # Coords are [... L x 3 x 3], where it's [N, CA, C] x 3 coordinates.
+        boundaries = torch.linspace(
+            min_bin,
+            max_bin,
+            num_bins - 1,
+            device=coords.device,
+        )
+        boundaries = boundaries**2
+        N, CA, C = [x.squeeze(-2) for x in coords.chunk(3, dim=-2)]
+        # Infer CB coordinates.
+        b = CA - N
+        c = C - CA
+        a = b.cross(c, dim=-1)
+        CB = -0.58273431 * a + 0.56802827 * b - 0.54067466 * c + CA
+        dists = (CB[..., None, :, :] - CB[..., :, None, :]).pow(2).sum(dim=-1, keepdims=True)
+        bins = torch.sum(dists > boundaries, dim=-1)  # [..., L, L]
+        return bins
+
+
+# TODO Add information to the docstring about any methods that convert to PDB format, or otherwise prepare
+#      the outputs for downstream use.
+
+
+@add_start_docstrings(
+    """
+    ESMForProteinFolding is the HuggingFace port of the original ESMFold model. It consists of an ESM-2 "stem" followed
+    by a protein folding "head", although unlike most other output heads, this "head" is similar in size and runtime to
+    the rest of the model combined! It outputs a dictionary containing predicted structural information about the input
+    protein(s).
+    """,
+    ESM_START_DOCSTRING,
+)
+class EsmForProteinFolding(EsmPreTrainedModel):
+    _no_split_modules = ["EsmFoldStructureModule", "EsmFoldTriangularSelfAttentionBlock"]
+
+    def __init__(self, config):
+        super().__init__(config)
+
+        self.config = config
+
+        self.distogram_bins = 64
+
+        self.esm = EsmModel(config, add_pooling_layer=False)
+
+        self.esm.requires_grad_(False)
+        if self.config.esmfold_config.fp16_esm:
+            self.esm.half()
+
+        self.esm_feats = self.config.hidden_size
+        self.esm_attns = self.config.num_hidden_layers * self.config.num_attention_heads
+        self.esm_layers = self.config.num_hidden_layers
+        self.register_buffer("af2_to_esm", self._af2_to_esm_from_vocab_list(config.vocab_list))
+        self.esm_s_combine = nn.Parameter(torch.zeros(self.esm_layers + 1))
+
+        trunk_config = self.config.esmfold_config.trunk
+        c_s = trunk_config.sequence_state_dim
+        c_z = trunk_config.pairwise_state_dim
+        self.esm_s_mlp = nn.Sequential(
+            LayerNorm(self.esm_feats),
+            nn.Linear(self.esm_feats, c_s),
+            nn.ReLU(),
+            nn.Linear(c_s, c_s),
+        )
+
+        # 0 is padding, N is unknown residues, N + 1 is mask.
+        self.n_tokens_embed = residue_constants.restype_num + 3
+        self.pad_idx = 0
+        self.unk_idx = self.n_tokens_embed - 2
+        self.mask_idx = self.n_tokens_embed - 1
+        self.esm_dict_cls_idx = self.config.vocab_list.index("<cls>")
+        self.esm_dict_mask_idx = self.config.vocab_list.index("<mask>")
+        self.esm_dict_eos_idx = self.config.vocab_list.index("<eos>")
+        self.esm_dict_padding_idx = self.config.vocab_list.index("<pad>")
+        if self.config.esmfold_config.embed_aa:
+            self.embedding = nn.Embedding(self.n_tokens_embed, c_s, padding_idx=0)
+
+        self.trunk = EsmFoldingTrunk(trunk_config)
+
+        self.distogram_head = nn.Linear(c_z, self.distogram_bins)
+        self.ptm_head = nn.Linear(c_z, self.distogram_bins)
+        self.lm_head = nn.Linear(c_s, self.n_tokens_embed)
+        self.lddt_bins = 50
+        structure_module_config = trunk_config.structure_module
+        self.lddt_head = nn.Sequential(
+            nn.LayerNorm(structure_module_config.sequence_dim),
+            nn.Linear(structure_module_config.sequence_dim, self.config.esmfold_config.lddt_head_hid_dim),
+            nn.Linear(self.config.esmfold_config.lddt_head_hid_dim, self.config.esmfold_config.lddt_head_hid_dim),
+            nn.Linear(self.config.esmfold_config.lddt_head_hid_dim, 37 * self.lddt_bins),
+        )
+
+    @staticmethod
+    def _af2_to_esm_from_vocab_list(vocab_list: List[str]) -> torch.Tensor:
+        # Remember that t is shifted from residue_constants by 1 (0 is padding).
+        esm_reorder = [vocab_list.index("<pad>")] + [vocab_list.index(v) for v in residue_constants.restypes_with_x]
+        return torch.tensor(esm_reorder)
+
+    @add_start_docstrings_to_model_forward(ESMFOLD_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @replace_return_docstrings(output_type=EsmForProteinFoldingOutput, config_class=EsmConfig)
+    def forward(
+        self,
+        input_ids: torch.Tensor,
+        attention_mask: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.Tensor] = None,
+        masking_pattern: Optional[torch.Tensor] = None,
+        num_recycles: Optional[int] = None,
+    ) -> EsmForProteinFoldingOutput:
+        r"""
+        Returns:
+
+        Example:
+
+        ```python
+        >>> from transformers import AutoTokenizer, EsmForProteinFolding
+
+        >>> model = EsmForProteinFolding.from_pretrained("facebook/esmfold_v1")
+        >>> tokenizer = AutoTokenizer.from_pretrained("facebook/esmfold_v1")
+        >>> inputs = tokenizer(["MLKNVQVQLV"], return_tensors="pt", add_special_tokens=False)  # A tiny random peptide
+        >>> outputs = model(**inputs)
+        >>> folded_positions = outputs.positions
+        ```
+
+        """
+        cfg = self.config.esmfold_config
+
+        aa = input_ids  # B x L
+        B = aa.shape[0]
+        L = aa.shape[1]
+        device = input_ids.device
+        if attention_mask is None:
+            attention_mask = torch.ones_like(aa, device=device)
+        if position_ids is None:
+            position_ids = torch.arange(L, device=device).expand_as(input_ids)
+
+        # === ESM ===
+        esmaa = self.af2_idx_to_esm_idx(aa, attention_mask)
+
+        if masking_pattern is not None:
+            masked_aa, esmaa, mlm_targets = self.bert_mask(aa, esmaa, attention_mask, masking_pattern)
+        else:
+            masked_aa = aa
+            mlm_targets = None
+
+        # We get sequence and pair representations from whatever version of ESM /
+        # configuration we are using. The sequence representation esm_s is always
+        # present. The pair embedding esm_z may be present depending on the
+        # configuration of the model. If esm_z is not used by the model then it
+        # is returned as None here.
+        esm_s = self.compute_language_model_representations(esmaa)
+
+        # Convert esm_s and esm_z, if present, to the precision used by the trunk and
+        # the structure module. These tensors may be a lower precision if, for example,
+        # we're running the language model in fp16 precision.
+        esm_s = esm_s.to(self.esm_s_combine.dtype)
+
+        if cfg.esm_ablate_sequence:
+            esm_s = esm_s * 0
+
+        esm_s = esm_s.detach()
+
+        # === preprocessing ===
+        esm_s = (self.esm_s_combine.softmax(0).unsqueeze(0) @ esm_s).squeeze(2)
+        s_s_0 = self.esm_s_mlp(esm_s)
+
+        s_z_0 = s_s_0.new_zeros(B, L, L, cfg.trunk.pairwise_state_dim)
+
+        if self.config.esmfold_config.embed_aa:
+            s_s_0 += self.embedding(masked_aa)
+
+        structure: dict = self.trunk(s_s_0, s_z_0, aa, position_ids, attention_mask, no_recycles=num_recycles)
+        # Documenting what we expect:
+        structure = {
+            k: v
+            for k, v in structure.items()
+            if k
+            in [
+                "s_z",
+                "s_s",
+                "frames",
+                "sidechain_frames",
+                "unnormalized_angles",
+                "angles",
+                "positions",
+                "states",
+            ]
+        }
+
+        # Add BERT mask for the loss to use, if available.
+        if mlm_targets:
+            structure["mlm_targets"] = mlm_targets
+
+        disto_logits = self.distogram_head(structure["s_z"])
+        disto_logits = (disto_logits + disto_logits.transpose(1, 2)) / 2
+        structure["distogram_logits"] = disto_logits
+
+        lm_logits = self.lm_head(structure["s_s"])
+        structure["lm_logits"] = lm_logits
+
+        structure["aatype"] = aa
+        make_atom14_masks(structure)
+        # Of course, this doesn't respect the true mask because it doesn't know about it...
+        # We're not going to properly mask change of index tensors:
+        #    "residx_atom14_to_atom37",
+        #    "residx_atom37_to_atom14",
+        for k in [
+            "atom14_atom_exists",
+            "atom37_atom_exists",
+        ]:
+            structure[k] *= attention_mask.unsqueeze(-1)
+        structure["residue_index"] = position_ids
+
+        lddt_head = self.lddt_head(structure["states"]).reshape(structure["states"].shape[0], B, L, -1, self.lddt_bins)
+        structure["lddt_head"] = lddt_head
+        plddt = categorical_lddt(lddt_head[-1], bins=self.lddt_bins)
+        structure["plddt"] = plddt
+
+        ptm_logits = self.ptm_head(structure["s_z"])
+        structure["ptm_logits"] = ptm_logits
+        structure["ptm"] = compute_tm(ptm_logits, max_bin=31, no_bins=self.distogram_bins)
+        structure.update(compute_predicted_aligned_error(ptm_logits, max_bin=31, no_bins=self.distogram_bins))
+
+        return EsmForProteinFoldingOutput(**structure)
+
+    def af2_idx_to_esm_idx(self, aa, mask):
+        # avoid indexing on different devices
+        if self.af2_to_esm.device != aa.device:
+            self.af2_to_esm = self.af2_to_esm.to(aa.device)
+        aa = (aa + 1).masked_fill(mask != 1, 0)
+        return self.af2_to_esm[aa]
+
+    def compute_language_model_representations(self, esmaa: torch.Tensor) -> torch.Tensor:
+        device = next(self.parameters()).device
+        B, L = esmaa.shape  # B = batch size, L = sequence length.
+
+        if self.config.esmfold_config.bypass_lm:
+            esm_s = torch.zeros(B, L, self.esm_s_combine.size[0], -1, self.esm_feats, device=device)
+            return esm_s
+
+        bosi, eosi = self.esm_dict_cls_idx, self.esm_dict_eos_idx
+        bos = esmaa.new_full((B, 1), bosi)
+        eos = esmaa.new_full((B, 1), self.esm_dict_padding_idx)
+        esmaa = torch.cat([bos, esmaa, eos], dim=1)
+        # Use the first padding index as eos during inference.
+        esmaa[range(B), (esmaa != 1).sum(1)] = eosi
+
+        # _, esm_z, esm_s = self.esm(esmaa, return_pairs=self.config.esmfold_config.use_esm_attn_map)
+        # Because we do not support use_esm_attn_map in the HF port as it is not used in any public models,
+        # esm_z is always None
+        esm_hidden_states = self.esm(esmaa, attention_mask=esmaa != 1, output_hidden_states=True)["hidden_states"]
+        esm_s = torch.stack(esm_hidden_states, dim=2)
+
+        esm_s = esm_s[:, 1:-1]  # B, L, nLayers, C
+
+        return esm_s
+
+    def bert_mask(self, aa, esmaa, mask, pattern):
+        new_aa = aa.clone()
+        target = aa.clone()
+        new_esmaa = esmaa.clone()
+        new_aa[pattern == 1] = self.mask_idx
+        target[pattern != 1] = 0
+        new_esmaa[pattern == 1] = self.esm_dict_mask_idx
+        return new_aa, new_esmaa, target
+
+    @torch.no_grad()
+    def infer(
+        self,
+        seqs: Union[str, List[str]],
+        position_ids=None,
+    ):
+        if isinstance(seqs, str):
+            lst = [seqs]
+        else:
+            lst = seqs
+        # Returns the raw outputs of the model given an input sequence.
+        device = next(self.parameters()).device
+        aatype = collate_dense_tensors(
+            [
+                torch.from_numpy(
+                    residue_constants.sequence_to_onehot(
+                        sequence=seq,
+                        mapping=residue_constants.restype_order_with_x,
+                        map_unknown_to_x=True,
+                    )
+                )
+                .to(device)
+                .argmax(dim=1)
+                for seq in lst
+            ]
+        )  # B=1 x L
+        mask = collate_dense_tensors([aatype.new_ones(len(seq)) for seq in lst])
+        position_ids = (
+            torch.arange(aatype.shape[1], device=device).expand(len(lst), -1)
+            if position_ids is None
+            else position_ids.to(device)
+        )
+        if position_ids.ndim == 1:
+            position_ids = position_ids.unsqueeze(0)
+        return self.forward(
+            aatype,
+            mask,
+            position_ids=position_ids,
+        )
+
+    @staticmethod
+    def output_to_pdb(output: Dict) -> List[str]:
+        """Returns the pbd (file) string from the model given the model output."""
+        output = {k: v.to("cpu").numpy() for k, v in output.items()}
+        pdbs = []
+        final_atom_positions = atom14_to_atom37(output["positions"][-1], output)
+        final_atom_mask = output["atom37_atom_exists"]
+        for i in range(output["aatype"].shape[0]):
+            aa = output["aatype"][i]
+            pred_pos = final_atom_positions[i]
+            mask = final_atom_mask[i]
+            resid = output["residue_index"][i] + 1
+            pred = OFProtein(
+                aatype=aa,
+                atom_positions=pred_pos,
+                atom_mask=mask,
+                residue_index=resid,
+                b_factors=output["plddt"][i],
+            )
+            pdbs.append(to_pdb(pred))
+        return pdbs
+
+    def infer_pdb(self, seqs, *args, **kwargs) -> str:
+        """Returns the pdb (file) string from the model given an input sequence."""
+        assert isinstance(seqs, str)
+        output = self.infer(seqs, *args, **kwargs)
+        return self.output_to_pdb(output)[0]
+
+    def infer_pdbs(self, seqs: List[str], *args, **kwargs) -> List[str]:
+        """Returns the pdb (file) string from the model given an input sequence."""
+        output = self.infer(seqs, *args, **kwargs)
+        return self.output_to_pdb(output)

llmeval-env/lib/python3.10/site-packages/transformers/models/esm/modeling_tf_esm.py

@@ -0,0 +1,1567 @@
+# coding=utf-8
+# Copyright 2022 Meta and The HuggingFace Inc. team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+""" PyTorch ESM model."""
+
+
+from __future__ import annotations
+
+import os
+from typing import Optional, Tuple, Union
+
+import numpy as np
+import tensorflow as tf
+
+from ...file_utils import add_code_sample_docstrings, add_start_docstrings, add_start_docstrings_to_model_forward
+from ...modeling_tf_outputs import (
+    TFBaseModelOutputWithPastAndCrossAttentions,
+    TFBaseModelOutputWithPoolingAndCrossAttentions,
+    TFMaskedLMOutput,
+    TFSequenceClassifierOutput,
+    TFTokenClassifierOutput,
+)
+from ...modeling_tf_utils import (
+    TFMaskedLanguageModelingLoss,
+    TFModelInputType,
+    TFPreTrainedModel,
+    TFSequenceClassificationLoss,
+    TFTokenClassificationLoss,
+    get_initializer,
+    keras,
+    shape_list,
+    unpack_inputs,
+)
+from ...tf_utils import check_embeddings_within_bounds, stable_softmax
+from ...utils import logging
+from .configuration_esm import EsmConfig
+
+
+logger = logging.get_logger(__name__)
+
+_CHECKPOINT_FOR_DOC = "facebook/esm2_t6_8M_UR50D"
+_CONFIG_FOR_DOC = "EsmConfig"
+
+
+def rotate_half(x):
+    x1, x2 = tf.split(x, 2, axis=-1)
+    return tf.concat((-x2, x1), axis=-1)
+
+
+def apply_rotary_pos_emb(x, cos, sin):
+    cos = cos[:, :, : tf.shape(x)[-2], :]
+    sin = sin[:, :, : tf.shape(x)[-2], :]
+
+    return (x * cos) + (rotate_half(x) * sin)
+
+
+def symmetrize(x):
+    "Make layer symmetric in final two dimensions, used for contact prediction."
+    return x + tf.linalg.matrix_transpose(x)  # Transposes last two dimensions only
+
+
+def average_product_correct(x):
+    "Perform average product correct, used for contact prediction."
+    a1 = tf.reduce_sum(x, -1, keepdims=True)
+    a2 = tf.reduce_sum(x, -2, keepdims=True)
+    a12 = tf.reduce_sum(x, (-1, -2), keepdims=True)
+
+    avg = a1 * a2
+    avg = avg / a12
+    normalized = x - avg
+    return normalized
+
+
+class TFRotaryEmbedding(keras.layers.Layer):
+    """
+    Rotary position embeddings based on those in
+    [RoFormer](https://huggingface.co/docs/transformers/model_doc/roformer). Query and keys are transformed by rotation
+    matrices which depend on their relative positions.
+    """
+
+    def __init__(self, dim: int, name=None):
+        super().__init__(name=name)
+        # Matt: The PyTorch version of this layer does a lot of work to cache values, but we just rely on TF compilation
+        # and/or XLA to sort out constants like that. It actually may not seem like this layer needs to be stateful at
+        # all when we benefit from TF compilation, but it does. The reason is that self.inv_freq is a buffer in the
+        # original implementation, but all the shared ESM checkpoints were trained with fp16 params. This means that
+        # the inv_freq tensor was stored as a float16, and we need to replicate those lower-precision values or our
+        # models give different outputs from the original.
+        self.dim = dim
+
+    def build(self, input_shape):
+        super().build(input_shape)
+        self.inv_freq = self.add_weight(
+            "inv_freq", shape=(self.dim // 2,), dtype=tf.float32, initializer=get_initializer(1.0), trainable=False
+        )
+        self.inv_freq.assign(
+            1.0 / (10000 ** (tf.range(start=0, limit=self.dim, delta=2, dtype=tf.float32) / self.dim))
+        )
+
+    def _compute_cos_sin(self, x, seq_dimension=2):
+        seq_len = tf.shape(x)[seq_dimension]
+
+        t = tf.range(seq_len, dtype=self.inv_freq.dtype)
+        freqs = tf.einsum("i, j -> ij", t, self.inv_freq)  # Outer multiplication
+        emb = tf.concat((freqs, freqs), axis=-1)[None, None, :, :]
+
+        return tf.cos(emb), tf.sin(emb)
+
+    def call(self, q: tf.Tensor, k: tf.Tensor) -> Tuple[tf.Tensor, tf.Tensor]:
+        cos_emb, sin_emb = self._compute_cos_sin(k, seq_dimension=-2)
+
+        return (
+            apply_rotary_pos_emb(q, cos_emb, sin_emb),
+            apply_rotary_pos_emb(k, cos_emb, sin_emb),
+        )
+
+
+class TFEsmContactPredictionHead(keras.layers.Layer):
+    """Performs symmetrization, apc, and computes a logistic regression on the output features"""
+
+    def __init__(
+        self,
+        in_features: int,
+        bias=True,
+        eos_idx: int = 2,
+        name=None,
+    ):
+        super().__init__(name=name)
+        self.eos_idx = eos_idx
+        self.in_features = in_features
+        self.regression = keras.layers.Dense(1, use_bias=bias, activation="sigmoid", name="regression")
+
+    def build(self, input_shape=None):
+        if self.built:
+            return
+        self.built = True
+        if getattr(self, "regression", None) is not None:
+            with tf.name_scope(self.regression.name):
+                self.regression.build((None, self.in_features))
+
+    def call(self, tokens, attentions):
+        # remove eos token attentions
+        eos_mask = tf.cast(tokens != self.eos_idx, attentions.dtype)
+        eos_mask = tf.expand_dims(eos_mask, 1) * tf.expand_dims(eos_mask, 2)
+        attentions = attentions * eos_mask[:, None, None, :, :]
+        attentions = attentions[..., :-1, :-1]
+        # remove cls token attentions
+        attentions = attentions[..., 1:, 1:]
+        batch_size, layers, heads, seqlen, _ = shape_list(attentions)
+        attentions = tf.reshape(attentions, (batch_size, layers * heads, seqlen, seqlen))
+
+        # features: batch x channels x tokens x tokens (symmetric)
+        attentions = average_product_correct(symmetrize(attentions))
+        attentions = tf.transpose(attentions, perm=(0, 2, 3, 1))
+        return tf.squeeze(self.regression(attentions), 3)
+
+
+class TFEsmEmbeddings(keras.layers.Layer):
+    """
+    Same as BertEmbeddings with a tiny tweak for positional embeddings indexing.
+    """
+
+    def __init__(self, config, name=None):
+        super().__init__(name=name)
+        self.word_embeddings = keras.layers.Embedding(
+            config.vocab_size,
+            config.hidden_size,
+            embeddings_initializer=get_initializer(config.initializer_range),
+            name="word_embeddings",
+        )
+        self.position_embeddings = keras.layers.Embedding(
+            config.max_position_embeddings,
+            config.hidden_size,
+            embeddings_initializer=get_initializer(config.initializer_range),
+            name="position_embeddings",
+        )
+
+        if config.emb_layer_norm_before:
+            self.layer_norm = keras.layers.LayerNormalization(epsilon=config.layer_norm_eps, name="layer_norm")
+        else:
+            self.layer_norm = None
+        # Matt: I think this line was copied incorrectly from BERT, disabling for now
+        # self.dropout = Dropout(config.hidden_dropout_prob)
+        self.position_embedding_type = getattr(config, "position_embedding_type", "absolute")
+
+        self.position_ids = tf.range(config.max_position_embeddings)[None, :]
+
+        self.padding_idx = config.pad_token_id
+        self.token_dropout = config.token_dropout
+        self.mask_token_id = config.mask_token_id
+        self.config = config
+
+    def call(
+        self, input_ids=None, attention_mask=None, position_ids=None, inputs_embeds=None, past_key_values_length=0
+    ):
+        if position_ids is None:
+            if input_ids is not None:
+                # Create the position ids from the input token ids. Any padded tokens remain padded.
+                position_ids = create_position_ids_from_input_ids(input_ids, self.padding_idx, past_key_values_length)
+            else:
+                position_ids = self.create_position_ids_from_inputs_embeds(inputs_embeds)
+
+        if inputs_embeds is None:
+            check_embeddings_within_bounds(input_ids, self.config.vocab_size)
+            inputs_embeds = self.word_embeddings(input_ids)
+
+        # Note that if we want to support ESM-1 (not 1b!) in future then we need to support an
+        # embedding_scale factor here.
+        embeddings = inputs_embeds
+
+        # Matt: ESM has the option to handle masking in MLM in a slightly unusual way. If the token_dropout
+        # flag is False then it is handled in the same was as BERT/RoBERTa. If it is set to True, however,
+        # masked tokens are treated as if they were selected for input dropout and zeroed out.
+        # This "mask-dropout" is compensated for when masked tokens are not present, by scaling embeddings by
+        # a factor of (fraction of unmasked tokens during training) / (fraction of unmasked tokens in sample).
+        # This is analogous to the way that dropout layers scale down outputs during evaluation when not
+        # actually dropping out values (or, equivalently, scale up their un-dropped outputs in training).
+        if self.token_dropout:
+            embeddings = tf.where((input_ids == self.mask_token_id)[:, :, None], 0.0, embeddings)
+            mask_ratio_train = 0.15 * 0.8  # Hardcoded as the ratio used in all ESM model training runs
+            src_lengths = tf.cast(tf.reduce_sum(attention_mask, axis=-1), tf.float32)
+            masked_tokens = input_ids == self.mask_token_id
+            mask_ratio_observed = tf.math.count_nonzero(masked_tokens, dtype=tf.float32, axis=-1) / src_lengths
+            embeddings = embeddings * (1 - mask_ratio_train) / (1 - mask_ratio_observed)[:, None, None]
+
+        if self.position_embedding_type == "absolute":
+            position_embeddings = self.position_embeddings(position_ids)
+            embeddings += position_embeddings
+
+        if self.layer_norm is not None:
+            embeddings = self.layer_norm(embeddings)
+        if attention_mask is not None:
+            embeddings = embeddings * tf.cast(tf.expand_dims(attention_mask, -1), embeddings.dtype)
+        # Matt: I think this line was copied incorrectly from BERT, disabling it for now.
+        # embeddings = self.dropout(embeddings)
+        return embeddings
+
+    def create_position_ids_from_inputs_embeds(self, inputs_embeds):
+        """
+        We are provided embeddings directly. We cannot infer which are padded so just generate sequential position ids.
+
+        Args:
+            inputs_embeds: tf.Tensor
+
+        Returns: tf.Tensor
+        """
+        input_shape = shape_list(inputs_embeds)[:-1]
+        sequence_length = input_shape[1]
+
+        position_ids = tf.range(
+            start=self.padding_idx + 1, limit=sequence_length + self.padding_idx + 1, dtype=tf.int64
+        )
+        return tf.broadcast_to(tf.expand_dims(position_ids, 0), input_shape)
+
+    def build(self, input_shape=None):
+        if self.built:
+            return
+        self.built = True
+        if getattr(self, "word_embeddings", None) is not None:
+            with tf.name_scope(self.word_embeddings.name):
+                self.word_embeddings.build(None)
+        if getattr(self, "position_embeddings", None) is not None:
+            with tf.name_scope(self.position_embeddings.name):
+                self.position_embeddings.build(None)
+        if getattr(self, "layer_norm", None) is not None:
+            with tf.name_scope(self.layer_norm.name):
+                self.layer_norm.build([None, None, self.config.hidden_size])
+
+
+class TFEsmSelfAttention(keras.layers.Layer):
+    def __init__(self, config, position_embedding_type=None, name=None):
+        super().__init__(name=name)
+        if config.hidden_size % config.num_attention_heads != 0 and not hasattr(config, "embedding_size"):
+            raise ValueError(
+                f"The hidden size ({config.hidden_size}) is not a multiple of the number of attention "
+                f"heads ({config.num_attention_heads})"
+            )
+
+        self.num_attention_heads = config.num_attention_heads
+        self.attention_head_size = int(config.hidden_size / config.num_attention_heads)
+        self.all_head_size = self.num_attention_heads * self.attention_head_size
+
+        self.query = keras.layers.Dense(
+            self.all_head_size, kernel_initializer=get_initializer(config.initializer_range), name="query"
+        )
+        self.key = keras.layers.Dense(
+            self.all_head_size, kernel_initializer=get_initializer(config.initializer_range), name="key"
+        )
+        self.value = keras.layers.Dense(
+            self.all_head_size, kernel_initializer=get_initializer(config.initializer_range), name="value"
+        )
+
+        self.dropout = keras.layers.Dropout(config.attention_probs_dropout_prob)
+        self.position_embedding_type = position_embedding_type or getattr(
+            config, "position_embedding_type", "absolute"
+        )
+        self.rotary_embeddings = None
+        if self.position_embedding_type == "relative_key" or self.position_embedding_type == "relative_key_query":
+            self.max_position_embeddings = config.max_position_embeddings
+            self.distance_embedding = keras.layers.Embedding(
+                2 * config.max_position_embeddings - 1,
+                self.attention_head_size,
+                embeddings_initializer=get_initializer(config.initializer_range),
+            )
+        elif self.position_embedding_type == "rotary":
+            self.rotary_embeddings = TFRotaryEmbedding(dim=self.attention_head_size, name="rotary_embeddings")
+
+        self.is_decoder = config.is_decoder
+        self.config = config
+
+    def transpose_for_scores(self, x: tf.Tensor) -> tf.Tensor:
+        new_x_shape = shape_list(x)[:-1] + [self.num_attention_heads, self.attention_head_size]
+        x = tf.reshape(x, new_x_shape)
+        return tf.transpose(x, perm=(0, 2, 1, 3))
+
+    def call(
+        self,
+        hidden_states: tf.Tensor,
+        attention_mask: tf.Tensor | None = None,
+        head_mask: tf.Tensor | None = None,
+        encoder_hidden_states: tf.Tensor | None = None,
+        encoder_attention_mask: tf.Tensor | None = None,
+        past_key_value: Tuple[Tuple[tf.Tensor]] | None = None,
+        output_attentions: Optional[bool] = False,
+        training: bool = False,
+    ) -> Tuple[tf.Tensor]:
+        mixed_query_layer = self.query(hidden_states)
+
+        # If this is instantiated as a cross-attention module, the keys
+        # and values come from an encoder; the attention mask needs to be
+        # such that the encoder's padding tokens are not attended to.
+        is_cross_attention = encoder_hidden_states is not None
+
+        if is_cross_attention and past_key_value is not None:
+            # reuse k,v, cross_attentions
+            key_layer = past_key_value[0]
+            value_layer = past_key_value[1]
+            attention_mask = encoder_attention_mask
+        elif is_cross_attention:
+            key_layer = self.transpose_for_scores(self.key(encoder_hidden_states))
+            value_layer = self.transpose_for_scores(self.value(encoder_hidden_states))
+            attention_mask = encoder_attention_mask
+        elif past_key_value is not None:
+            key_layer = self.transpose_for_scores(self.key(hidden_states))
+            value_layer = self.transpose_for_scores(self.value(hidden_states))
+            key_layer = tf.concat([past_key_value[0], key_layer], axis=2)
+            value_layer = tf.concat([past_key_value[1], value_layer], axis=2)
+        else:
+            key_layer = self.transpose_for_scores(self.key(hidden_states))
+            value_layer = self.transpose_for_scores(self.value(hidden_states))
+
+        query_layer = self.transpose_for_scores(mixed_query_layer)
+
+        # Matt: Our BERT model (which this code was derived from) scales attention logits down by sqrt(head_dim).
+        # ESM scales the query down by the same factor instead. Modulo numerical stability these are equivalent,
+        # but not when rotary embeddings get involved. Therefore, we scale the query here to match the original
+        # ESM code and fix rotary embeddings.
+        query_layer = query_layer * self.attention_head_size**-0.5
+
+        if self.is_decoder:
+            # if cross_attention save Tuple(tf.Tensor, tf.Tensor) of all cross attention key/value_states.
+            # Further calls to cross_attention layer can then reuse all cross-attention
+            # key/value_states (first "if" case)
+            # if uni-directional self-attention (decoder) save Tuple(tf.Tensor, tf.Tensor) of
+            # all previous decoder key/value_states. Further calls to uni-directional self-attention
+            # can concat previous decoder key/value_states to current projected key/value_states (third "elif" case)
+            # if encoder bi-directional self-attention `past_key_value` is always `None`
+            past_key_value = (key_layer, value_layer)
+
+        if self.position_embedding_type == "rotary":
+            query_layer, key_layer = self.rotary_embeddings(query_layer, key_layer)
+
+        # Take the dot product between "query" and "key" to get the raw attention scores.
+        attention_scores = tf.matmul(query_layer, key_layer, transpose_b=True)
+
+        if self.position_embedding_type == "relative_key" or self.position_embedding_type == "relative_key_query":
+            seq_length = shape_list(hidden_states)[1]
+            position_ids_l = tf.expand_dims(tf.range(seq_length, dtype=tf.int64), -1)
+            position_ids_r = tf.expand_dims(tf.range(seq_length, dtype=tf.int64), 0)
+            distance = position_ids_l - position_ids_r
+            positional_embedding = self.distance_embedding(distance + self.max_position_embeddings - 1)
+            positional_embedding = tf.cast(positional_embedding, query_layer.dtype)  # fp16 compatibility
+
+            if self.position_embedding_type == "relative_key":
+                relative_position_scores = tf.einsum("bhld,lrd->bhlr", query_layer, positional_embedding)
+                attention_scores = attention_scores + relative_position_scores
+            elif self.position_embedding_type == "relative_key_query":
+                relative_position_scores_query = tf.einsum("bhld,lrd->bhlr", query_layer, positional_embedding)
+                relative_position_scores_key = tf.einsum("bhrd,lrd->bhlr", key_layer, positional_embedding)
+                attention_scores = attention_scores + relative_position_scores_query + relative_position_scores_key
+
+        if attention_mask is not None:
+            # Apply the attention mask is (precomputed for all layers in EsmModel forward() function)
+            attention_scores = attention_scores + attention_mask
+
+        # Normalize the attention scores to probabilities.
+        attention_probs = stable_softmax(attention_scores, axis=-1)
+
+        # This is actually dropping out entire tokens to attend to, which might
+        # seem a bit unusual, but is taken from the original Transformer paper.
+        attention_probs = self.dropout(attention_probs, training=training)
+
+        # Mask heads if we want to
+        if head_mask is not None:
+            attention_probs = attention_probs * head_mask
+
+        context_layer = attention_probs @ value_layer
+
+        context_layer = tf.transpose(context_layer, perm=(0, 2, 1, 3))
+        new_context_layer_shape = shape_list(context_layer)[:-2] + [self.all_head_size]
+        context_layer = tf.reshape(context_layer, new_context_layer_shape)
+
+        outputs = (context_layer, attention_probs) if output_attentions else (context_layer,)
+
+        if self.is_decoder:
+            outputs = outputs + (past_key_value,)
+        return outputs
+
+    def build(self, input_shape=None):
+        if self.built:
+            return
+        self.built = True
+        if getattr(self, "query", None) is not None:
+            with tf.name_scope(self.query.name):
+                self.query.build([None, None, self.config.hidden_size])
+        if getattr(self, "key", None) is not None:
+            with tf.name_scope(self.key.name):
+                self.key.build([None, None, self.config.hidden_size])
+        if getattr(self, "value", None) is not None:
+            with tf.name_scope(self.value.name):
+                self.value.build([None, None, self.config.hidden_size])
+        if getattr(self, "rotary_embeddings", None) is not None:
+            with tf.name_scope(self.rotary_embeddings.name):
+                self.rotary_embeddings.build(None)
+
+
+class TFEsmSelfOutput(keras.layers.Layer):
+    def __init__(self, config, name=None):
+        super().__init__(name=name)
+        self.dense = keras.layers.Dense(
+            config.hidden_size, kernel_initializer=get_initializer(config.initializer_range), name="dense"
+        )
+        self.dropout = keras.layers.Dropout(config.hidden_dropout_prob)
+        self.config = config
+
+    def call(self, hidden_states, input_tensor, training=False):
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.dropout(hidden_states, training=training)
+        hidden_states += input_tensor
+        return hidden_states
+
+    def build(self, input_shape=None):
+        if self.built:
+            return
+        self.built = True
+        if getattr(self, "dense", None) is not None:
+            with tf.name_scope(self.dense.name):
+                self.dense.build([None, None, self.config.hidden_size])
+
+
+class TFEsmAttention(keras.layers.Layer):
+    def __init__(self, config, name=None):
+        super().__init__(name=name)
+        self.self = TFEsmSelfAttention(config, name="self")
+        self.output_layer = TFEsmSelfOutput(config, name="output")
+        self.pruned_heads = set()
+        self.LayerNorm = keras.layers.LayerNormalization(epsilon=config.layer_norm_eps, name="LayerNorm")
+        self.config = config
+
+    def prune_heads(self, heads):
+        raise NotImplementedError
+
+    def call(
+        self,
+        hidden_states,
+        attention_mask=None,
+        head_mask=None,
+        encoder_hidden_states=None,
+        encoder_attention_mask=None,
+        past_key_value=None,
+        output_attentions=False,
+        training=False,
+    ):
+        hidden_states_ln = self.LayerNorm(hidden_states)
+        self_outputs = self.self(
+            hidden_states_ln,
+            attention_mask,
+            head_mask,
+            encoder_hidden_states,
+            encoder_attention_mask,
+            past_key_value,
+            output_attentions,
+            training,
+        )
+        attention_output = self.output_layer(self_outputs[0], hidden_states)
+        outputs = (attention_output,) + self_outputs[1:]  # add attentions if we output them
+        return outputs
+
+    def build(self, input_shape=None):
+        if self.built:
+            return
+        self.built = True
+        if getattr(self, "self", None) is not None:
+            with tf.name_scope(self.self.name):
+                self.self.build(None)
+        if getattr(self, "output_layer", None) is not None:
+            with tf.name_scope(self.output_layer.name):
+                self.output_layer.build(None)
+        if getattr(self, "LayerNorm", None) is not None:
+            with tf.name_scope(self.LayerNorm.name):
+                self.LayerNorm.build([None, None, self.config.hidden_size])
+
+
+class TFEsmIntermediate(keras.layers.Layer):
+    def __init__(self, config: EsmConfig, **kwargs):
+        super().__init__(**kwargs)
+
+        self.dense = keras.layers.Dense(
+            units=config.intermediate_size,
+            kernel_initializer=get_initializer(config.initializer_range),
+            name="dense",
+        )
+        self.config = config
+
+    def call(self, hidden_states: tf.Tensor) -> tf.Tensor:
+        hidden_states = self.dense(inputs=hidden_states)
+        hidden_states = tf.nn.gelu(hidden_states)
+        return hidden_states
+
+    def build(self, input_shape=None):
+        if self.built:
+            return
+        self.built = True
+        if getattr(self, "dense", None) is not None:
+            with tf.name_scope(self.dense.name):
+                self.dense.build([None, None, self.config.hidden_size])
+
+
+class TFEsmOutput(keras.layers.Layer):
+    def __init__(self, config, name=None):
+        super().__init__(name=name)
+        self.dense = keras.layers.Dense(
+            config.hidden_size, kernel_initializer=get_initializer(config.initializer_range), name="dense"
+        )
+        self.dropout = keras.layers.Dropout(config.hidden_dropout_prob)
+        self.config = config
+
+    def call(self, hidden_states, input_tensor, training=False):
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.dropout(hidden_states, training=training)
+        hidden_states += input_tensor
+        return hidden_states
+
+    def build(self, input_shape=None):
+        if self.built:
+            return
+        self.built = True
+        if getattr(self, "dense", None) is not None:
+            with tf.name_scope(self.dense.name):
+                self.dense.build([None, None, self.config.intermediate_size])
+
+
+class TFEsmLayer(keras.layers.Layer):
+    def __init__(self, config, name=None):
+        super().__init__(name=name)
+        self.chunk_size_feed_forward = config.chunk_size_feed_forward
+        self.seq_len_dim = 1
+        self.attention = TFEsmAttention(config, name="attention")
+        self.is_decoder = config.is_decoder
+        self.add_cross_attention = config.add_cross_attention
+        if self.add_cross_attention:
+            if not self.is_decoder:
+                raise RuntimeError(f"{self} should be used as a decoder model if cross attention is added")
+            self.crossattention = TFEsmAttention(config)
+        self.intermediate = TFEsmIntermediate(config, name="intermediate")
+        self.output_layer = TFEsmOutput(config, name="output")
+        self.LayerNorm = keras.layers.LayerNormalization(epsilon=config.layer_norm_eps, name="LayerNorm")
+        self.config = config
+
+    def call(
+        self,
+        hidden_states,
+        attention_mask=None,
+        head_mask=None,
+        encoder_hidden_states=None,
+        encoder_attention_mask=None,
+        past_key_value=None,
+        output_attentions=False,
+        training=False,
+    ):
+        # decoder uni-directional self-attention cached key/values tuple is at positions 1,2
+        self_attn_past_key_value = past_key_value[:2] if past_key_value is not None else None
+        self_attention_outputs = self.attention(
+            hidden_states,
+            attention_mask,
+            head_mask,
+            output_attentions=output_attentions,
+            past_key_value=self_attn_past_key_value,
+            training=training,
+        )
+        attention_output = self_attention_outputs[0]
+
+        # if decoder, the last output is tuple of self-attn cache
+        if self.is_decoder:
+            outputs = self_attention_outputs[1:-1]
+            present_key_value = self_attention_outputs[-1]
+        else:
+            outputs = self_attention_outputs[1:]  # add self attentions if we output attention weights
+
+        cross_attn_present_key_value = None
+        if self.is_decoder and encoder_hidden_states is not None:
+            if not hasattr(self, "crossattention"):
+                raise AttributeError(
+                    f"If `encoder_hidden_states` are passed, {self} has to be instantiated"
+                    " with cross-attention layers by setting `config.add_cross_attention=True`"
+                )
+
+            # cross_attn cached key/values tuple is at positions 3,4 of past_key_value tuple
+            cross_attn_past_key_value = past_key_value[-2:] if past_key_value is not None else None
+            cross_attention_outputs = self.crossattention(
+                attention_output,
+                attention_mask,
+                head_mask,
+                encoder_hidden_states,
+                encoder_attention_mask,
+                cross_attn_past_key_value,
+                output_attentions,
+                training=training,
+            )
+            attention_output = cross_attention_outputs[0]
+            outputs = outputs + cross_attention_outputs[1:-1]  # add cross attentions if we output attention weights
+
+            # add cross-attn cache to positions 3,4 of present_key_value tuple
+            cross_attn_present_key_value = cross_attention_outputs[-1]
+            present_key_value = present_key_value + cross_attn_present_key_value
+
+        layernorm_output = self.LayerNorm(attention_output)
+        intermediate_output = self.intermediate(hidden_states=layernorm_output)
+        layer_output = self.output_layer(
+            hidden_states=intermediate_output, input_tensor=attention_output, training=training
+        )
+        outputs = (layer_output,) + outputs  # add attentions if we output them
+
+        # if decoder, return the attn key/values as the last output
+        if self.is_decoder:
+            outputs = outputs + (present_key_value,)
+
+        return outputs
+
+    def build(self, input_shape=None):
+        if self.built:
+            return
+        self.built = True
+        if getattr(self, "attention", None) is not None:
+            with tf.name_scope(self.attention.name):
+                self.attention.build(None)
+        if getattr(self, "intermediate", None) is not None:
+            with tf.name_scope(self.intermediate.name):
+                self.intermediate.build(None)
+        if getattr(self, "output_layer", None) is not None:
+            with tf.name_scope(self.output_layer.name):
+                self.output_layer.build(None)
+        if getattr(self, "LayerNorm", None) is not None:
+            with tf.name_scope(self.LayerNorm.name):
+                self.LayerNorm.build([None, None, self.config.hidden_size])
+
+
+class TFEsmEncoder(keras.layers.Layer):
+    def __init__(self, config, name=None):
+        super().__init__(name=name)
+        self.config = config
+        self.layer = [TFEsmLayer(config, name=f"layer_._{i}") for i in range(config.num_hidden_layers)]
+        self.emb_layer_norm_after = keras.layers.LayerNormalization(
+            epsilon=config.layer_norm_eps, name="emb_layer_norm_after"
+        )
+
+    def call(
+        self,
+        hidden_states,
+        attention_mask=None,
+        head_mask=None,
+        encoder_hidden_states=None,
+        encoder_attention_mask=None,
+        past_key_values=None,
+        use_cache=None,
+        output_attentions=False,
+        output_hidden_states=False,
+        return_dict=True,
+        training=False,
+    ):
+        all_hidden_states = () if output_hidden_states else None
+        all_self_attentions = () if output_attentions else None
+        all_cross_attentions = () if output_attentions and self.config.add_cross_attention else None
+
+        next_decoder_cache = () if use_cache else None
+        for i, layer_module in enumerate(self.layer):
+            if output_hidden_states:
+                all_hidden_states = all_hidden_states + (hidden_states,)
+
+            layer_head_mask = head_mask[i] if head_mask is not None else None
+            past_key_value = past_key_values[i] if past_key_values is not None else None
+
+            layer_outputs = layer_module(
+                hidden_states,
+                attention_mask,
+                layer_head_mask,
+                encoder_hidden_states,
+                encoder_attention_mask,
+                past_key_value,
+                output_attentions,
+                training,
+            )
+
+            hidden_states = layer_outputs[0]
+            if use_cache:
+                next_decoder_cache += (layer_outputs[-1],)
+            if output_attentions:
+                all_self_attentions = all_self_attentions + (layer_outputs[1],)
+                if self.config.add_cross_attention:
+                    all_cross_attentions = all_cross_attentions + (layer_outputs[2],)
+
+        if self.emb_layer_norm_after:
+            hidden_states = self.emb_layer_norm_after(hidden_states)
+
+        if output_hidden_states:
+            all_hidden_states = all_hidden_states + (hidden_states,)
+
+        if not return_dict:
+            return tuple(
+                v
+                for v in [
+                    hidden_states,
+                    next_decoder_cache,
+                    all_hidden_states,
+                    all_self_attentions,
+                    all_cross_attentions,
+                ]
+                if v is not None
+            )
+        return TFBaseModelOutputWithPastAndCrossAttentions(
+            last_hidden_state=hidden_states,
+            past_key_values=next_decoder_cache,
+            hidden_states=all_hidden_states,
+            attentions=all_self_attentions,
+            cross_attentions=all_cross_attentions,
+        )
+
+    def build(self, input_shape=None):
+        if self.built:
+            return
+        self.built = True
+        if getattr(self, "emb_layer_norm_after", None) is not None:
+            with tf.name_scope(self.emb_layer_norm_after.name):
+                self.emb_layer_norm_after.build([None, None, self.config.hidden_size])
+        if getattr(self, "layer", None) is not None:
+            for layer in self.layer:
+                with tf.name_scope(layer.name):
+                    layer.build(None)
+
+
+# Copied from transformers.models.bert.modeling_tf_bert.TFBertPooler with Bert->Esm
+class TFEsmPooler(keras.layers.Layer):
+    def __init__(self, config: EsmConfig, **kwargs):
+        super().__init__(**kwargs)
+
+        self.dense = keras.layers.Dense(
+            units=config.hidden_size,
+            kernel_initializer=get_initializer(config.initializer_range),
+            activation="tanh",
+            name="dense",
+        )
+        self.config = config
+
+    def call(self, hidden_states: tf.Tensor) -> tf.Tensor:
+        # We "pool" the model by simply taking the hidden state corresponding
+        # to the first token.
+        first_token_tensor = hidden_states[:, 0]
+        pooled_output = self.dense(inputs=first_token_tensor)
+
+        return pooled_output
+
+    def build(self, input_shape=None):
+        if self.built:
+            return
+        self.built = True
+        if getattr(self, "dense", None) is not None:
+            with tf.name_scope(self.dense.name):
+                self.dense.build([None, None, self.config.hidden_size])
+
+
+class TFEsmPreTrainedModel(TFPreTrainedModel):
+    """
+    An abstract class to handle weights initialization and a simple interface for downloading and loading pretrained
+    models.
+    """
+
+    config_class = EsmConfig
+    base_model_prefix = "esm"
+
+
+ESM_START_DOCSTRING = r"""
+
+    This model inherits from [`TFPreTrainedModel`]. Check the superclass documentation for the generic methods the
+    library implements for all its model (such as downloading or saving, resizing the input embeddings, pruning heads
+    etc.)
+
+    This model is also a Keras [Model](https://www.tensorflow.org/api_docs/python/tf/keras/Model) subclass. Use it as a
+    regular Keras model and refer to the TF/Keras documentation for all matters related to general usage and behavior.
+
+    Parameters:
+        config ([`EsmConfig`]): Model configuration class with all the parameters of the
+            model. Initializing with a config file does not load the weights associated with the model, only the
+            configuration. Check out the [`~TFPreTrainedModel.from_pretrained`] method to load the model weights.
+"""
+
+ESM_INPUTS_DOCSTRING = r"""
+    Args:
+        input_ids (`tf.Tensor` of shape `({0})`):
+            Indices of input sequence tokens in the vocabulary.
+
+            Indices can be obtained using [`AutoTokenizer`]. See [`PreTrainedTokenizer.encode`] and
+            [`PreTrainedTokenizer.__call__`] for details.
+
+            [What are input IDs?](../glossary#input-ids)
+        attention_mask (`tf.Tensor` of shape `({0})`, *optional*):
+            Mask to avoid performing attention on padding token indices. Mask values selected in `[0, 1]`:
+
+            - 1 for tokens that are **not masked**,
+            - 0 for tokens that are **masked**.
+
+            [What are attention masks?](../glossary#attention-mask)
+        position_ids (`tf.Tensor` of shape `({0})`, *optional*):
+            Indices of positions of each input sequence tokens in the position embeddings. Selected in the range `[0,
+            config.max_position_embeddings - 1]`.
+
+            [What are position IDs?](../glossary#position-ids)
+        head_mask (`tf.Tensor` of shape `(num_heads,)` or `(num_layers, num_heads)`, *optional*):
+            Mask to nullify selected heads of the self-attention modules. Mask values selected in `[0, 1]`:
+
+            - 1 indicates the head is **not masked**,
+            - 0 indicates the head is **masked**.
+
+        inputs_embeds (`tf.Tensor` of shape `({0}, hidden_size)`, *optional*):
+            Optionally, instead of passing `input_ids` you can choose to directly pass an embedded representation. This
+            is useful if you want more control over how to convert `input_ids` indices into associated vectors than the
+            model's internal embedding lookup matrix.
+        output_attentions (`bool`, *optional*):
+            Whether or not to return the attentions tensors of all attention layers. See `attentions` under returned
+            tensors for more detail.
+        output_hidden_states (`bool`, *optional*):
+            Whether or not to return the hidden states of all layers. See `hidden_states` under returned tensors for
+            more detail.
+        return_dict (`bool`, *optional*):
+            Whether or not to return a [`~file_utils.ModelOutput`] instead of a plain tuple.
+"""
+
+
+@add_start_docstrings(
+    "The bare ESM Model transformer outputting raw hidden-states without any specific head on top.",
+    ESM_START_DOCSTRING,
+)
+class TFEsmMainLayer(keras.layers.Layer):
+    """
+
+    The model can behave as an encoder (with only self-attention) as well as a decoder, in which case a layer of
+    cross-attention is added between the self-attention layers, following the architecture described in [Attention is
+    all you need](https://arxiv.org/abs/1706.03762) by Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit,
+    Llion Jones, Aidan N. Gomez, Lukasz Kaiser and Illia Polosukhin.
+
+    To behave as an decoder the model needs to be initialized with the `is_decoder` argument of the configuration set
+    to `True`. To be used in a Seq2Seq model, the model needs to initialized with both `is_decoder` argument and
+    `add_cross_attention` set to `True`; an `encoder_hidden_states` is then expected as an input to the forward pass.
+    """
+
+    _keys_to_ignore_on_load_missing = [r"position_ids"]
+
+    def __init__(self, config, add_pooling_layer=True, name=None, **kwargs):
+        super().__init__(name=name, **kwargs)
+
+        self.config = config
+        self.is_decoder = config.is_decoder
+
+        self.embeddings = TFEsmEmbeddings(config, name="embeddings")
+        self.encoder = TFEsmEncoder(config, name="encoder")
+        self.pooler = TFEsmPooler(config, name="pooler") if add_pooling_layer else None
+
+        self.contact_head = TFEsmContactPredictionHead(
+            in_features=self.config.num_hidden_layers * self.config.num_attention_heads, bias=True, name="contact_head"
+        )
+
+    def build(self, input_shape=None):
+        if self.built:
+            return
+        self.built = True
+        if getattr(self, "embeddings", None) is not None:
+            with tf.name_scope(self.embeddings.name):
+                self.embeddings.build(None)
+        if getattr(self, "encoder", None) is not None:
+            with tf.name_scope(self.encoder.name):
+                self.encoder.build(None)
+        if getattr(self, "pooler", None) is not None:
+            with tf.name_scope(self.pooler.name):
+                self.pooler.build(None)
+        if getattr(self, "contact_head", None) is not None:
+            with tf.name_scope(self.contact_head.name):
+                self.contact_head.build(None)
+
+    def get_input_embeddings(self):
+        return self.embeddings.word_embeddings
+
+    def set_input_embeddings(self, value: tf.Variable):
+        self.embeddings.word_embeddings.weight = value
+        self.embeddings.vocab_size = shape_list(value)[0]
+
+    def _prune_heads(self, heads_to_prune):
+        raise NotImplementedError
+
+    def call(
+        self,
+        input_ids: TFModelInputType | None = None,
+        attention_mask: np.ndarray | tf.Tensor | None = None,
+        position_ids: np.ndarray | tf.Tensor | None = None,
+        head_mask: np.ndarray | tf.Tensor | None = None,
+        inputs_embeds: np.ndarray | tf.Tensor | None = None,
+        encoder_hidden_states: np.ndarray | tf.Tensor | None = None,
+        encoder_attention_mask: np.ndarray | tf.Tensor | None = None,
+        past_key_values: Optional[Tuple[Tuple[Union[np.ndarray, tf.Tensor]]]] = None,
+        use_cache: Optional[bool] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+        training: bool = False,
+    ) -> Union[TFBaseModelOutputWithPoolingAndCrossAttentions, Tuple[tf.Tensor]]:
+        if not self.config.is_decoder:
+            use_cache = False
+
+        if input_ids is not None and inputs_embeds is not None:
+            raise ValueError("You cannot specify both input_ids and inputs_embeds at the same time")
+        elif input_ids is not None:
+            input_shape = shape_list(input_ids)
+        elif inputs_embeds is not None:
+            input_shape = shape_list(inputs_embeds)[:-1]
+        else:
+            raise ValueError("You have to specify either input_ids or inputs_embeds")
+
+        batch_size, seq_length = input_shape
+
+        if past_key_values is None:
+            past_key_values_length = 0
+            past_key_values = [None] * len(self.encoder.layer)
+        else:
+            past_key_values_length = shape_list(past_key_values[0][0])[-2]
+
+        if attention_mask is None:
+            attention_mask = tf.fill(dims=(batch_size, seq_length + past_key_values_length), value=1)
+
+        embedding_output = self.embeddings(
+            input_ids=input_ids,
+            attention_mask=attention_mask,
+            position_ids=position_ids,
+            inputs_embeds=inputs_embeds,
+            past_key_values_length=past_key_values_length,
+            training=training,
+        )
+
+        # We create a 3D attention mask from a 2D tensor mask.
+        # Sizes are [batch_size, 1, 1, to_seq_length]
+        # So we can broadcast to [batch_size, num_heads, from_seq_length, to_seq_length]
+        # this attention mask is more simple than the triangular masking of causal attention
+        # used in OpenAI GPT, we just need to prepare the broadcast dimension here.
+        attention_mask_shape = shape_list(attention_mask)
+
+        mask_seq_length = seq_length + past_key_values_length
+        # Copied from `modeling_tf_t5.py`
+        # Provided a padding mask of dimensions [batch_size, mask_seq_length]
+        # - if the model is a decoder, apply a causal mask in addition to the padding mask
+        # - if the model is an encoder, make the mask broadcastable to [batch_size, num_heads, mask_seq_length, mask_seq_length]
+        if self.is_decoder:
+            seq_ids = tf.range(mask_seq_length)
+            causal_mask = tf.less_equal(
+                tf.tile(seq_ids[None, None, :], (batch_size, mask_seq_length, 1)),
+                seq_ids[None, :, None],
+            )
+            causal_mask = tf.cast(causal_mask, dtype=attention_mask.dtype)
+            extended_attention_mask = causal_mask * attention_mask[:, None, :]
+            attention_mask_shape = shape_list(extended_attention_mask)
+            extended_attention_mask = tf.reshape(
+                extended_attention_mask, (attention_mask_shape[0], 1, attention_mask_shape[1], attention_mask_shape[2])
+            )
+            if past_key_values[0] is not None:
+                # attention_mask needs to be sliced to the shape `[batch_size, 1, from_seq_length - cached_seq_length, to_seq_length]
+                extended_attention_mask = extended_attention_mask[:, :, -seq_length:, :]
+        else:
+            extended_attention_mask = tf.reshape(
+                attention_mask, (attention_mask_shape[0], 1, 1, attention_mask_shape[1])
+            )
+
+        # Since attention_mask is 1.0 for positions we want to attend and 0.0 for
+        # masked positions, this operation will create a tensor which is 0.0 for
+        # positions we want to attend and -10000.0 for masked positions.
+        # Since we are adding it to the raw scores before the softmax, this is
+        # effectively the same as removing these entirely.
+        extended_attention_mask = tf.cast(extended_attention_mask, dtype=embedding_output.dtype)
+        one_cst = tf.constant(1.0, dtype=embedding_output.dtype)
+        ten_thousand_cst = tf.constant(-10000.0, dtype=embedding_output.dtype)
+        extended_attention_mask = tf.multiply(tf.subtract(one_cst, extended_attention_mask), ten_thousand_cst)
+
+        # Copied from `modeling_tf_t5.py` with -1e9 -> -10000
+        if self.is_decoder and encoder_attention_mask is not None:
+            # If a 2D ou 3D attention mask is provided for the cross-attention
+            # we need to make broadcastable to [batch_size, num_heads, mask_seq_length, mask_seq_length]
+            # we need to make broadcastable to [batch_size, num_heads, seq_length, seq_length]
+            encoder_attention_mask = tf.cast(encoder_attention_mask, dtype=extended_attention_mask.dtype)
+            num_dims_encoder_attention_mask = len(shape_list(encoder_attention_mask))
+            if num_dims_encoder_attention_mask == 3:
+                encoder_extended_attention_mask = encoder_attention_mask[:, None, :, :]
+            if num_dims_encoder_attention_mask == 2:
+                encoder_extended_attention_mask = encoder_attention_mask[:, None, None, :]
+
+            # T5 has a mask that can compare sequence ids, we can simulate this here with this transposition
+            # Cf. https://github.com/tensorflow/mesh/blob/8d2465e9bc93129b913b5ccc6a59aa97abd96ec6/mesh_tensorflow/transformer/transformer_layers.py#L270
+            # encoder_extended_attention_mask = tf.math.equal(encoder_extended_attention_mask,
+            #                                         tf.transpose(encoder_extended_attention_mask, perm=(-1, -2)))
+
+            encoder_extended_attention_mask = (1.0 - encoder_extended_attention_mask) * -10000.0
+        else:
+            encoder_extended_attention_mask = None
+
+        # Prepare head mask if needed
+        # 1.0 in head_mask indicate we keep the head
+        # attention_probs has shape bsz x n_heads x N x N
+        # input head_mask has shape [num_heads] or [num_hidden_layers x num_heads]
+        # and head_mask is converted to shape [num_hidden_layers x batch x num_heads x seq_length x seq_length]
+        if head_mask is not None:
+            raise NotImplementedError
+        else:
+            head_mask = [None] * self.config.num_hidden_layers
+
+        encoder_outputs = self.encoder(
+            hidden_states=embedding_output,
+            attention_mask=extended_attention_mask,
+            head_mask=head_mask,
+            encoder_hidden_states=encoder_hidden_states,
+            encoder_attention_mask=encoder_extended_attention_mask,
+            past_key_values=past_key_values,
+            use_cache=use_cache,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+            training=training,
+        )
+
+        sequence_output = encoder_outputs[0]
+        pooled_output = self.pooler(hidden_states=sequence_output) if self.pooler is not None else None
+
+        if not return_dict:
+            return (
+                sequence_output,
+                pooled_output,
+            ) + encoder_outputs[1:]
+
+        return TFBaseModelOutputWithPoolingAndCrossAttentions(
+            last_hidden_state=sequence_output,
+            pooler_output=pooled_output,
+            past_key_values=encoder_outputs.past_key_values,
+            hidden_states=encoder_outputs.hidden_states,
+            attentions=encoder_outputs.attentions,
+            cross_attentions=encoder_outputs.cross_attentions,
+        )
+
+    def predict_contacts(self, tokens, attention_mask):
+        attns = self(tokens, attention_mask=attention_mask, return_dict=True, output_attentions=True).attentions
+        attns = tf.stack(attns, axis=1)  # Matches the original model layout
+        # In the original model, attentions for padding tokens are completely zeroed out.
+        # This makes no difference most of the time because the other tokens won't attend to them,
+        # but it does for the contact prediction task, which takes attentions as input,
+        # so we have to mimic that here.
+        attention_mask = tf.cast(attention_mask, attns.dtype)
+        attns *= attention_mask[:, None, None, None]
+        attns *= attention_mask[:, None, None, :, None]
+        return self.contact_head(tokens, attns)
+
+
+@add_start_docstrings(
+    "The bare ESM Model transformer outputting raw hidden-states without any specific head on top.",
+    ESM_START_DOCSTRING,
+)
+class TFEsmModel(TFEsmPreTrainedModel):
+    def __init__(self, config: EsmConfig, add_pooling_layer=True, *inputs, **kwargs):
+        super().__init__(config, *inputs, **kwargs)
+
+        self.esm = TFEsmMainLayer(config, add_pooling_layer=add_pooling_layer, name="esm")
+
+    @unpack_inputs
+    @add_start_docstrings_to_model_forward(ESM_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @add_code_sample_docstrings(
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=TFBaseModelOutputWithPoolingAndCrossAttentions,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def call(
+        self,
+        input_ids: TFModelInputType | None = None,
+        attention_mask: np.ndarray | tf.Tensor | None = None,
+        position_ids: np.ndarray | tf.Tensor | None = None,
+        head_mask: np.ndarray | tf.Tensor | None = None,
+        inputs_embeds: np.ndarray | tf.Tensor | None = None,
+        encoder_hidden_states: np.ndarray | tf.Tensor | None = None,
+        encoder_attention_mask: np.ndarray | tf.Tensor | None = None,
+        past_key_values: Optional[Tuple[Tuple[Union[np.ndarray, tf.Tensor]]]] = None,
+        use_cache: Optional[bool] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+        training: Optional[bool] = False,
+    ) -> Union[TFBaseModelOutputWithPoolingAndCrossAttentions, Tuple[tf.Tensor]]:
+        r"""
+        encoder_hidden_states  (`tf.Tensor` of shape `(batch_size, sequence_length, hidden_size)`, *optional*):
+            Sequence of hidden-states at the output of the last layer of the encoder. Used in the cross-attention if
+            the model is configured as a decoder.
+        encoder_attention_mask (`tf.Tensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Mask to avoid performing attention on the padding token indices of the encoder input. This mask is used in
+            the cross-attention if the model is configured as a decoder. Mask values selected in `[0, 1]`:
+
+            - 1 for tokens that are **not masked**,
+            - 0 for tokens that are **masked**.
+
+        past_key_values (`Tuple[Tuple[tf.Tensor]]` of length `config.n_layers`)
+            contains precomputed key and value hidden states of the attention blocks. Can be used to speed up decoding.
+            If `past_key_values` are used, the user can optionally input only the last `decoder_input_ids` (those that
+            don't have their past key value states given to this model) of shape `(batch_size, 1)` instead of all
+            `decoder_input_ids` of shape `(batch_size, sequence_length)`.
+        use_cache (`bool`, *optional*, defaults to `True`):
+            If set to `True`, `past_key_values` key value states are returned and can be used to speed up decoding (see
+            `past_key_values`). Set to `False` during training, `True` during generation
+        """
+        outputs = self.esm(
+            input_ids=input_ids,
+            attention_mask=attention_mask,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            encoder_hidden_states=encoder_hidden_states,
+            encoder_attention_mask=encoder_attention_mask,
+            past_key_values=past_key_values,
+            use_cache=use_cache,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+            training=training,
+        )
+        return outputs
+
+    def predict_contacts(self, tokens, attention_mask):
+        return self.esm.predict_contacts(tokens, attention_mask)
+
+    def build(self, input_shape=None):
+        if self.built:
+            return
+        self.built = True
+        if getattr(self, "esm", None) is not None:
+            with tf.name_scope(self.esm.name):
+                self.esm.build(None)
+
+
+@add_start_docstrings("""ESM Model with a `language modeling` head on top.""", ESM_START_DOCSTRING)
+class TFEsmForMaskedLM(TFEsmPreTrainedModel, TFMaskedLanguageModelingLoss):
+    _keys_to_ignore_on_load_missing = [r"position_ids"]
+    _keys_to_ignore_on_load_unexpected = [r"pooler"]
+
+    def __init__(self, config):
+        super().__init__(config)
+
+        if config.is_decoder:
+            logger.warning(
+                "If you want to use `EsmForMaskedLM` make sure `config.is_decoder=False` for "
+                "bi-directional self-attention."
+            )
+
+        self.esm = TFEsmMainLayer(config, add_pooling_layer=False, name="esm")
+        self.lm_head = TFEsmLMHead(config, name="lm_head")
+        if config.tie_word_embeddings:
+            # Ensure word embeddings are built so that we actually have something to tie
+            with tf.name_scope(os.path.join(self._name_scope(), "esm", "embeddings", "word_embeddings")):
+                self.esm.embeddings.word_embeddings.build((None, None))
+            self.lm_head.decoder = self.esm.embeddings.word_embeddings.weights[0]
+
+    def get_output_embeddings(self):
+        return self.lm_head.decoder
+
+    def set_output_embeddings(self, new_embeddings):
+        self.lm_head.decoder = new_embeddings
+
+    def get_lm_head(self):
+        return self.lm_head
+
+    @unpack_inputs
+    @add_start_docstrings_to_model_forward(ESM_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @add_code_sample_docstrings(
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=TFMaskedLMOutput,
+        config_class=_CONFIG_FOR_DOC,
+        mask="<mask>",
+    )
+    def call(
+        self,
+        input_ids: TFModelInputType | None = None,
+        attention_mask: np.ndarray | tf.Tensor | None = None,
+        position_ids: np.ndarray | tf.Tensor | None = None,
+        head_mask: np.ndarray | tf.Tensor | None = None,
+        inputs_embeds: np.ndarray | tf.Tensor | None = None,
+        encoder_hidden_states: np.ndarray | tf.Tensor | None = None,
+        encoder_attention_mask: np.ndarray | tf.Tensor | None = None,
+        labels: np.ndarray | tf.Tensor | None = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+        training: bool = False,
+    ) -> Union[TFMaskedLMOutput, Tuple[tf.Tensor]]:
+        r"""
+        labels (`tf.Tensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Labels for computing the masked language modeling loss. Indices should be in `[-100, 0, ...,
+            config.vocab_size]` (see `input_ids` docstring) Tokens with indices set to `-100` are ignored (masked), the
+            loss is only computed for the tokens with labels in `[0, ..., config.vocab_size]`
+        kwargs (`Dict[str, any]`, optional, defaults to *{}*):
+            Used to hide legacy arguments that have been deprecated.
+        """
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.esm(
+            input_ids,
+            attention_mask=attention_mask,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            encoder_hidden_states=encoder_hidden_states,
+            encoder_attention_mask=encoder_attention_mask,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+            training=training,
+        )
+        sequence_output = outputs[0]
+        prediction_scores = self.lm_head(sequence_output)
+
+        masked_lm_loss = None
+        if labels is not None:
+            masked_lm_loss = self.hf_compute_loss(labels=labels, logits=prediction_scores)
+
+        if not return_dict:
+            output = (prediction_scores,) + outputs[2:]
+            return ((masked_lm_loss,) + output) if masked_lm_loss is not None else output
+
+        return TFMaskedLMOutput(
+            loss=masked_lm_loss,
+            logits=prediction_scores,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+    def predict_contacts(self, tokens, attention_mask):
+        return self.esm.predict_contacts(tokens, attention_mask)
+
+    def build(self, input_shape=None):
+        if self.built:
+            return
+        self.built = True
+        if getattr(self, "esm", None) is not None:
+            with tf.name_scope(self.esm.name):
+                self.esm.build(None)
+        if getattr(self, "lm_head", None) is not None:
+            with tf.name_scope(self.lm_head.name):
+                self.lm_head.build(None)
+
+
+class TFEsmLMHead(keras.layers.Layer):
+    """ESM Head for masked language modeling."""
+
+    def __init__(self, config, name=None):
+        super().__init__(name=name)
+        self.dense = keras.layers.Dense(
+            config.hidden_size, kernel_initializer=get_initializer(config.initializer_range), name="dense"
+        )
+
+        self.layer_norm = keras.layers.LayerNormalization(epsilon=config.layer_norm_eps, name="layer_norm")
+        if config.tie_word_embeddings:
+            self.decoder = None
+        else:
+            self.decoder = keras.layers.Dense(
+                config.vocab_size,
+                kernel_initializer=get_initializer(config.initializer_range),
+                name="decoder",
+                use_bias=False,
+            )
+        self.config = config
+
+    def build(self, input_shape=None):
+        # Separate bias to match the PT model and allow weight cross-loading to work
+        # Put it in the build so it gets the right name when adding it as a weight
+        if self.built:
+            return
+        self.built = True
+        self.bias = self.add_weight("bias", shape=(self.config.vocab_size,), initializer="zeros", trainable=True)
+        if getattr(self, "dense", None) is not None:
+            with tf.name_scope(self.dense.name):
+                self.dense.build([None, None, self.config.hidden_size])
+        if getattr(self, "layer_norm", None) is not None:
+            with tf.name_scope(self.layer_norm.name):
+                self.layer_norm.build([None, None, self.config.hidden_size])
+        if getattr(self, "decoder", None) is not None and not self.config.tie_word_embeddings:
+            with tf.name_scope(self.decoder.name):
+                self.decoder.build([None, None, self.config.hidden_size])
+
+    def get_bias(self):
+        return {"bias": self.bias}
+
+    def call(self, features):
+        x = self.dense(features)
+        x = tf.nn.gelu(x)
+        x = self.layer_norm(x)
+
+        # project back to size of vocabulary with bias
+        if self.config.tie_word_embeddings:
+            x = tf.matmul(x, self.decoder, transpose_b=True) + self.bias
+        else:
+            x = self.decoder(x) + self.bias
+        return x
+
+
+@add_start_docstrings(
+    """
+    ESM Model transformer with a sequence classification/regression head on top (a linear layer on top of the pooled
+    output) e.g. for GLUE tasks.
+    """,
+    ESM_START_DOCSTRING,
+)
+class TFEsmForSequenceClassification(TFEsmPreTrainedModel, TFSequenceClassificationLoss):
+    _keys_to_ignore_on_load_missing = [r"position_ids"]
+
+    def __init__(self, config):
+        super().__init__(config)
+        self.num_labels = config.num_labels
+        self.config = config
+
+        self.esm = TFEsmMainLayer(config, add_pooling_layer=False, name="esm")
+        self.classifier = TFEsmClassificationHead(config, name="classifier")
+
+    @unpack_inputs
+    @add_start_docstrings_to_model_forward(ESM_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @add_code_sample_docstrings(
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=TFSequenceClassifierOutput,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def call(
+        self,
+        input_ids: TFModelInputType | None = None,
+        attention_mask: np.ndarray | tf.Tensor | None = None,
+        position_ids: np.ndarray | tf.Tensor | None = None,
+        head_mask: np.ndarray | tf.Tensor | None = None,
+        inputs_embeds: np.ndarray | tf.Tensor | None = None,
+        labels: np.ndarray | tf.Tensor | None = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+        training: bool = False,
+    ) -> Union[TFSequenceClassifierOutput, Tuple[tf.Tensor]]:
+        r"""
+        labels (`tf.Tensor` of shape `(batch_size,)`, *optional*):
+            Labels for computing the sequence classification/regression loss. Indices should be in `[0, ...,
+            config.num_labels - 1]`. If `config.num_labels == 1` a regression loss is computed (Mean-Square loss), If
+            `config.num_labels > 1` a classification loss is computed (Cross-Entropy).
+        """
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.esm(
+            input_ids,
+            attention_mask=attention_mask,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+            training=training,
+        )
+        sequence_output = outputs[0]
+        logits = self.classifier(sequence_output)
+
+        loss = None if labels is None else self.hf_compute_loss(labels, logits)
+
+        if not return_dict:
+            output = (logits,) + outputs[2:]
+            return ((loss,) + output) if loss is not None else output
+
+        return TFSequenceClassifierOutput(
+            loss=loss,
+            logits=logits,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+    def build(self, input_shape=None):
+        if self.built:
+            return
+        self.built = True
+        if getattr(self, "esm", None) is not None:
+            with tf.name_scope(self.esm.name):
+                self.esm.build(None)
+        if getattr(self, "classifier", None) is not None:
+            with tf.name_scope(self.classifier.name):
+                self.classifier.build(None)
+
+
+@add_start_docstrings(
+    """
+    ESM Model with a token classification head on top (a linear layer on top of the hidden-states output) e.g. for
+    Named-Entity-Recognition (NER) tasks.
+    """,
+    ESM_START_DOCSTRING,
+)
+class TFEsmForTokenClassification(TFEsmPreTrainedModel, TFTokenClassificationLoss):
+    _keys_to_ignore_on_load_unexpected = [r"pooler"]
+    _keys_to_ignore_on_load_missing = [r"position_ids"]
+
+    def __init__(self, config):
+        super().__init__(config)
+        self.num_labels = config.num_labels
+
+        self.esm = TFEsmMainLayer(config, add_pooling_layer=False, name="esm")
+        self.dropout = keras.layers.Dropout(config.hidden_dropout_prob)
+        self.classifier = keras.layers.Dense(config.num_labels, name="classifier")
+        self.config = config
+
+    @unpack_inputs
+    @add_start_docstrings_to_model_forward(ESM_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @add_code_sample_docstrings(
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=TFTokenClassifierOutput,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def call(
+        self,
+        input_ids: TFModelInputType | None = None,
+        attention_mask: np.ndarray | tf.Tensor | None = None,
+        position_ids: np.ndarray | tf.Tensor | None = None,
+        head_mask: np.ndarray | tf.Tensor | None = None,
+        inputs_embeds: np.ndarray | tf.Tensor | None = None,
+        labels: np.ndarray | tf.Tensor | None = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+        training: bool = False,
+    ) -> Union[TFTokenClassifierOutput, Tuple[tf.Tensor]]:
+        r"""
+        labels (`tf.Tensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Labels for computing the token classification loss. Indices should be in `[0, ..., config.num_labels - 1]`.
+        """
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.esm(
+            input_ids,
+            attention_mask=attention_mask,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+            training=training,
+        )
+
+        sequence_output = outputs[0]
+
+        sequence_output = self.dropout(sequence_output, training=training)
+        logits = self.classifier(sequence_output)
+
+        loss = None if labels is None else self.hf_compute_loss(labels, logits)
+
+        if not return_dict:
+            output = (logits,) + outputs[2:]
+            return ((loss,) + output) if loss is not None else output
+
+        return TFTokenClassifierOutput(
+            loss=loss,
+            logits=logits,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+    def build(self, input_shape=None):
+        if self.built:
+            return
+        self.built = True
+        if getattr(self, "esm", None) is not None:
+            with tf.name_scope(self.esm.name):
+                self.esm.build(None)
+        if getattr(self, "classifier", None) is not None:
+            with tf.name_scope(self.classifier.name):
+                self.classifier.build([None, None, self.config.hidden_size])
+
+
+class TFEsmClassificationHead(keras.layers.Layer):
+    """Head for sentence-level classification tasks."""
+
+    def __init__(self, config, name=None):
+        super().__init__(name=name)
+        self.dense = keras.layers.Dense(
+            config.hidden_size,
+            kernel_initializer=get_initializer(config.initializer_range),
+            activation="tanh",
+            name="dense",
+        )
+        self.dropout = keras.layers.Dropout(config.hidden_dropout_prob)
+        self.out_proj = keras.layers.Dense(
+            config.num_labels,
+            kernel_initializer=get_initializer(config.initializer_range),
+            activation="linear",
+            name="out_proj",
+        )
+        self.config = config
+
+    def call(self, features, training=False):
+        x = features[:, 0, :]  # take <s> token (equiv. to [CLS])
+        x = self.dropout(x, training=training)
+        x = self.dense(x)
+        x = self.dropout(x, training=training)
+        x = self.out_proj(x)
+        return x
+
+    def build(self, input_shape=None):
+        if self.built:
+            return
+        self.built = True
+        if getattr(self, "dense", None) is not None:
+            with tf.name_scope(self.dense.name):
+                self.dense.build([None, None, self.config.hidden_size])
+        if getattr(self, "out_proj", None) is not None:
+            with tf.name_scope(self.out_proj.name):
+                self.out_proj.build([None, None, self.config.hidden_size])
+
+
+def create_position_ids_from_input_ids(input_ids, padding_idx, past_key_values_length=0):
+    """
+    Replace non-padding symbols with their position numbers. Position numbers begin at padding_idx+1. Padding symbols
+    are ignored. This is modified from fairseq's `utils.make_positions`.
+
+    Args:
+        x: tf.Tensor x:
+
+    Returns: tf.Tensor
+    """
+    # The series of casts and type-conversions here are carefully balanced to both work with ONNX export and XLA.
+    mask = tf.cast(input_ids != padding_idx, tf.int64)
+    incremental_indices = (tf.cumsum(mask, axis=1) + past_key_values_length) * mask
+    return incremental_indices + padding_idx

llmeval-env/lib/python3.10/site-packages/transformers/models/esm/openfold_utils/feats.py

@@ -0,0 +1,255 @@
+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from typing import Dict, Tuple, overload
+
+import torch
+import torch.types
+from torch import nn
+
+from . import residue_constants as rc
+from .rigid_utils import Rigid, Rotation
+from .tensor_utils import batched_gather
+
+
+@overload
+def pseudo_beta_fn(aatype: torch.Tensor, all_atom_positions: torch.Tensor, all_atom_masks: None) -> torch.Tensor:
+    ...
+
+
+@overload
+def pseudo_beta_fn(
+    aatype: torch.Tensor, all_atom_positions: torch.Tensor, all_atom_masks: torch.Tensor
+) -> Tuple[torch.Tensor, torch.Tensor]:
+    ...
+
+
+def pseudo_beta_fn(aatype, all_atom_positions, all_atom_masks):
+    is_gly = aatype == rc.restype_order["G"]
+    ca_idx = rc.atom_order["CA"]
+    cb_idx = rc.atom_order["CB"]
+    pseudo_beta = torch.where(
+        is_gly[..., None].expand(*((-1,) * len(is_gly.shape)), 3),
+        all_atom_positions[..., ca_idx, :],
+        all_atom_positions[..., cb_idx, :],
+    )
+
+    if all_atom_masks is not None:
+        pseudo_beta_mask = torch.where(
+            is_gly,
+            all_atom_masks[..., ca_idx],
+            all_atom_masks[..., cb_idx],
+        )
+        return pseudo_beta, pseudo_beta_mask
+    else:
+        return pseudo_beta
+
+
+def atom14_to_atom37(atom14: torch.Tensor, batch: Dict[str, torch.Tensor]) -> torch.Tensor:
+    atom37_data = batched_gather(
+        atom14,
+        batch["residx_atom37_to_atom14"],
+        dim=-2,
+        no_batch_dims=len(atom14.shape[:-2]),
+    )
+
+    atom37_data = atom37_data * batch["atom37_atom_exists"][..., None]
+
+    return atom37_data
+
+
+def build_template_angle_feat(template_feats: Dict[str, torch.Tensor]) -> torch.Tensor:
+    template_aatype = template_feats["template_aatype"]
+    torsion_angles_sin_cos = template_feats["template_torsion_angles_sin_cos"]
+    alt_torsion_angles_sin_cos = template_feats["template_alt_torsion_angles_sin_cos"]
+    torsion_angles_mask = template_feats["template_torsion_angles_mask"]
+    template_angle_feat = torch.cat(
+        [
+            nn.functional.one_hot(template_aatype, 22),
+            torsion_angles_sin_cos.reshape(*torsion_angles_sin_cos.shape[:-2], 14),
+            alt_torsion_angles_sin_cos.reshape(*alt_torsion_angles_sin_cos.shape[:-2], 14),
+            torsion_angles_mask,
+        ],
+        dim=-1,
+    )
+
+    return template_angle_feat
+
+
+def build_template_pair_feat(
+    batch: Dict[str, torch.Tensor],
+    min_bin: torch.types.Number,
+    max_bin: torch.types.Number,
+    no_bins: int,
+    use_unit_vector: bool = False,
+    eps: float = 1e-20,
+    inf: float = 1e8,
+) -> torch.Tensor:
+    template_mask = batch["template_pseudo_beta_mask"]
+    template_mask_2d = template_mask[..., None] * template_mask[..., None, :]
+
+    # Compute distogram (this seems to differ slightly from Alg. 5)
+    tpb = batch["template_pseudo_beta"]
+    dgram = torch.sum((tpb[..., None, :] - tpb[..., None, :, :]) ** 2, dim=-1, keepdim=True)
+    lower = torch.linspace(min_bin, max_bin, no_bins, device=tpb.device) ** 2
+    upper = torch.cat([lower[1:], lower.new_tensor([inf])], dim=-1)
+    dgram = ((dgram > lower) * (dgram < upper)).type(dgram.dtype)
+
+    to_concat = [dgram, template_mask_2d[..., None]]
+
+    aatype_one_hot: torch.LongTensor = nn.functional.one_hot(
+        batch["template_aatype"],
+        rc.restype_num + 2,
+    )
+
+    n_res = batch["template_aatype"].shape[-1]
+    to_concat.append(aatype_one_hot[..., None, :, :].expand(*aatype_one_hot.shape[:-2], n_res, -1, -1))
+    to_concat.append(aatype_one_hot[..., None, :].expand(*aatype_one_hot.shape[:-2], -1, n_res, -1))
+
+    n, ca, c = [rc.atom_order[a] for a in ["N", "CA", "C"]]
+    rigids = Rigid.make_transform_from_reference(
+        n_xyz=batch["template_all_atom_positions"][..., n, :],
+        ca_xyz=batch["template_all_atom_positions"][..., ca, :],
+        c_xyz=batch["template_all_atom_positions"][..., c, :],
+        eps=eps,
+    )
+    points = rigids.get_trans()[..., None, :, :]
+    rigid_vec = rigids[..., None].invert_apply(points)
+
+    inv_distance_scalar = torch.rsqrt(eps + torch.sum(rigid_vec**2, dim=-1))
+
+    t_aa_masks = batch["template_all_atom_mask"]
+    template_mask = t_aa_masks[..., n] * t_aa_masks[..., ca] * t_aa_masks[..., c]
+    template_mask_2d = template_mask[..., None] * template_mask[..., None, :]
+
+    inv_distance_scalar = inv_distance_scalar * template_mask_2d
+    unit_vector = rigid_vec * inv_distance_scalar[..., None]
+
+    if not use_unit_vector:
+        unit_vector = unit_vector * 0.0
+
+    to_concat.extend(torch.unbind(unit_vector[..., None, :], dim=-1))
+    to_concat.append(template_mask_2d[..., None])
+
+    act = torch.cat(to_concat, dim=-1)
+    act = act * template_mask_2d[..., None]
+
+    return act
+
+
+def build_extra_msa_feat(batch: Dict[str, torch.Tensor]) -> torch.Tensor:
+    msa_1hot: torch.LongTensor = nn.functional.one_hot(batch["extra_msa"], 23)
+    msa_feat = [
+        msa_1hot,
+        batch["extra_has_deletion"].unsqueeze(-1),
+        batch["extra_deletion_value"].unsqueeze(-1),
+    ]
+    return torch.cat(msa_feat, dim=-1)
+
+
+def torsion_angles_to_frames(
+    r: Rigid,
+    alpha: torch.Tensor,
+    aatype: torch.Tensor,
+    rrgdf: torch.Tensor,
+) -> Rigid:
+    # [*, N, 8, 4, 4]
+    default_4x4 = rrgdf[aatype, ...]
+
+    # [*, N, 8] transformations, i.e.
+    #   One [*, N, 8, 3, 3] rotation matrix and
+    #   One [*, N, 8, 3]    translation matrix
+    default_r = r.from_tensor_4x4(default_4x4)
+
+    bb_rot = alpha.new_zeros((*((1,) * len(alpha.shape[:-1])), 2))
+    bb_rot[..., 1] = 1
+
+    # [*, N, 8, 2]
+    alpha = torch.cat([bb_rot.expand(*alpha.shape[:-2], -1, -1), alpha], dim=-2)
+
+    # [*, N, 8, 3, 3]
+    # Produces rotation matrices of the form:
+    # [
+    #   [1, 0  , 0  ],
+    #   [0, a_2,-a_1],
+    #   [0, a_1, a_2]
+    # ]
+    # This follows the original code rather than the supplement, which uses
+    # different indices.
+
+    all_rots = alpha.new_zeros(default_r.get_rots().get_rot_mats().shape)
+    all_rots[..., 0, 0] = 1
+    all_rots[..., 1, 1] = alpha[..., 1]
+    all_rots[..., 1, 2] = -alpha[..., 0]
+    all_rots[..., 2, 1:] = alpha
+
+    all_frames = default_r.compose(Rigid(Rotation(rot_mats=all_rots), None))
+
+    chi2_frame_to_frame = all_frames[..., 5]
+    chi3_frame_to_frame = all_frames[..., 6]
+    chi4_frame_to_frame = all_frames[..., 7]
+
+    chi1_frame_to_bb = all_frames[..., 4]
+    chi2_frame_to_bb = chi1_frame_to_bb.compose(chi2_frame_to_frame)
+    chi3_frame_to_bb = chi2_frame_to_bb.compose(chi3_frame_to_frame)
+    chi4_frame_to_bb = chi3_frame_to_bb.compose(chi4_frame_to_frame)
+
+    all_frames_to_bb = Rigid.cat(
+        [
+            all_frames[..., :5],
+            chi2_frame_to_bb.unsqueeze(-1),
+            chi3_frame_to_bb.unsqueeze(-1),
+            chi4_frame_to_bb.unsqueeze(-1),
+        ],
+        dim=-1,
+    )
+
+    all_frames_to_global = r[..., None].compose(all_frames_to_bb)
+
+    return all_frames_to_global
+
+
+def frames_and_literature_positions_to_atom14_pos(
+    r: Rigid,
+    aatype: torch.Tensor,
+    default_frames: torch.Tensor,
+    group_idx: torch.Tensor,
+    atom_mask: torch.Tensor,
+    lit_positions: torch.Tensor,
+) -> torch.Tensor:
+    # [*, N, 14]
+    group_mask = group_idx[aatype, ...]
+
+    # [*, N, 14, 8]
+    group_mask_one_hot: torch.LongTensor = nn.functional.one_hot(
+        group_mask,
+        num_classes=default_frames.shape[-3],
+    )
+
+    # [*, N, 14, 8]
+    t_atoms_to_global = r[..., None, :] * group_mask_one_hot
+
+    # [*, N, 14]
+    t_atoms_to_global = t_atoms_to_global.map_tensor_fn(lambda x: torch.sum(x, dim=-1))
+
+    # [*, N, 14, 1]
+    atom_mask = atom_mask[aatype, ...].unsqueeze(-1)
+
+    # [*, N, 14, 3]
+    lit_positions = lit_positions[aatype, ...]
+    pred_positions = t_atoms_to_global.apply(lit_positions)
+    pred_positions = pred_positions * atom_mask
+
+    return pred_positions

llmeval-env/lib/python3.10/site-packages/transformers/models/esm/tokenization_esm.py

@@ -0,0 +1,143 @@
+# coding=utf-8
+# Copyright 2022 Meta and The HuggingFace Inc. team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Tokenization classes for ESM."""
+import os
+from typing import List, Optional
+
+from ...tokenization_utils import PreTrainedTokenizer
+from ...utils import logging
+
+
+logger = logging.get_logger(__name__)
+
+VOCAB_FILES_NAMES = {"vocab_file": "vocab.txt"}
+
+
+def load_vocab_file(vocab_file):
+    with open(vocab_file, "r") as f:
+        lines = f.read().splitlines()
+        return [l.strip() for l in lines]
+
+
+class EsmTokenizer(PreTrainedTokenizer):
+    """
+    Constructs an ESM tokenizer.
+    """
+
+    vocab_files_names = VOCAB_FILES_NAMES
+    model_input_names = ["input_ids", "attention_mask"]
+
+    def __init__(
+        self,
+        vocab_file,
+        unk_token="<unk>",
+        cls_token="<cls>",
+        pad_token="<pad>",
+        mask_token="<mask>",
+        eos_token="<eos>",
+        **kwargs,
+    ):
+        self.all_tokens = load_vocab_file(vocab_file)
+        self._id_to_token = dict(enumerate(self.all_tokens))
+        self._token_to_id = {tok: ind for ind, tok in enumerate(self.all_tokens)}
+        super().__init__(
+            unk_token=unk_token,
+            cls_token=cls_token,
+            pad_token=pad_token,
+            mask_token=mask_token,
+            eos_token=eos_token,
+            **kwargs,
+        )
+
+        # TODO, all the tokens are added? But they are also part of the vocab... bit strange.
+        # none of them are special, but they all need special splitting.
+
+        self.unique_no_split_tokens = self.all_tokens
+        self._update_trie(self.unique_no_split_tokens)
+
+    def _convert_id_to_token(self, index: int) -> str:
+        return self._id_to_token.get(index, self.unk_token)
+
+    def _convert_token_to_id(self, token: str) -> int:
+        return self._token_to_id.get(token, self._token_to_id.get(self.unk_token))
+
+    def _tokenize(self, text, **kwargs):
+        return text.split()
+
+    def get_vocab(self):
+        base_vocab = self._token_to_id.copy()
+        base_vocab.update(self.added_tokens_encoder)
+        return base_vocab
+
+    def token_to_id(self, token: str) -> int:
+        return self._token_to_id.get(token, self._token_to_id.get(self.unk_token))
+
+    def id_to_token(self, index: int) -> str:
+        return self._id_to_token.get(index, self.unk_token)
+
+    def build_inputs_with_special_tokens(
+        self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None
+    ) -> List[int]:
+        cls = [self.cls_token_id]
+        sep = [self.eos_token_id]  # No sep token in ESM vocabulary
+        if token_ids_1 is None:
+            if self.eos_token_id is None:
+                return cls + token_ids_0
+            else:
+                return cls + token_ids_0 + sep
+        elif self.eos_token_id is None:
+            raise ValueError("Cannot tokenize multiple sequences when EOS token is not set!")
+        return cls + token_ids_0 + sep + token_ids_1 + sep  # Multiple inputs always have an EOS token
+
+    def get_special_tokens_mask(
+        self, token_ids_0: List, token_ids_1: Optional[List] = None, already_has_special_tokens: bool = False
+    ) -> List[int]:
+        """
+        Retrieves sequence ids from a token list that has no special tokens added. This method is called when adding
+        special tokens using the tokenizer `prepare_for_model` or `encode_plus` methods.
+
+        Args:
+            token_ids_0 (`List[int]`):
+                List of ids of the first sequence.
+            token_ids_1 (`List[int]`, *optional*):
+                List of ids of the second sequence.
+            already_has_special_tokens (`bool`, *optional*, defaults to `False`):
+                Whether or not the token list is already formatted with special tokens for the model.
+
+        Returns:
+            A list of integers in the range [0, 1]: 1 for a special token, 0 for a sequence token.
+        """
+        if already_has_special_tokens:
+            if token_ids_1 is not None:
+                raise ValueError(
+                    "You should not supply a second sequence if the provided sequence of "
+                    "ids is already formatted with special tokens for the model."
+                )
+
+            return [1 if token in self.all_special_ids else 0 for token in token_ids_0]
+        mask = [1] + ([0] * len(token_ids_0)) + [1]
+        if token_ids_1 is not None:
+            mask += [0] * len(token_ids_1) + [1]
+        return mask
+
+    def save_vocabulary(self, save_directory, filename_prefix):
+        vocab_file = os.path.join(save_directory, (filename_prefix + "-" if filename_prefix else "") + "vocab.txt")
+        with open(vocab_file, "w") as f:
+            f.write("\n".join(self.all_tokens))
+        return (vocab_file,)
+
+    @property
+    def vocab_size(self) -> int:
+        return len(self.all_tokens)

llmeval-env/lib/python3.10/site-packages/transformers/models/layoutlmv2/__init__.py

@@ -0,0 +1,104 @@
+# Copyright 2021 The HuggingFace Team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from typing import TYPE_CHECKING
+
+from ...utils import (
+    OptionalDependencyNotAvailable,
+    _LazyModule,
+    is_tokenizers_available,
+    is_torch_available,
+    is_vision_available,
+)
+
+
+_import_structure = {
+    "configuration_layoutlmv2": ["LAYOUTLMV2_PRETRAINED_CONFIG_ARCHIVE_MAP", "LayoutLMv2Config"],
+    "processing_layoutlmv2": ["LayoutLMv2Processor"],
+    "tokenization_layoutlmv2": ["LayoutLMv2Tokenizer"],
+}
+
+try:
+    if not is_tokenizers_available():
+        raise OptionalDependencyNotAvailable()
+except OptionalDependencyNotAvailable:
+    pass
+else:
+    _import_structure["tokenization_layoutlmv2_fast"] = ["LayoutLMv2TokenizerFast"]
+
+try:
+    if not is_vision_available():
+        raise OptionalDependencyNotAvailable()
+except OptionalDependencyNotAvailable:
+    pass
+else:
+    _import_structure["feature_extraction_layoutlmv2"] = ["LayoutLMv2FeatureExtractor"]
+    _import_structure["image_processing_layoutlmv2"] = ["LayoutLMv2ImageProcessor"]
+
+try:
+    if not is_torch_available():
+        raise OptionalDependencyNotAvailable()
+except OptionalDependencyNotAvailable:
+    pass
+else:
+    _import_structure["modeling_layoutlmv2"] = [
+        "LAYOUTLMV2_PRETRAINED_MODEL_ARCHIVE_LIST",
+        "LayoutLMv2ForQuestionAnswering",
+        "LayoutLMv2ForSequenceClassification",
+        "LayoutLMv2ForTokenClassification",
+        "LayoutLMv2Layer",
+        "LayoutLMv2Model",
+        "LayoutLMv2PreTrainedModel",
+    ]
+
+if TYPE_CHECKING:
+    from .configuration_layoutlmv2 import LAYOUTLMV2_PRETRAINED_CONFIG_ARCHIVE_MAP, LayoutLMv2Config
+    from .processing_layoutlmv2 import LayoutLMv2Processor
+    from .tokenization_layoutlmv2 import LayoutLMv2Tokenizer
+
+    try:
+        if not is_tokenizers_available():
+            raise OptionalDependencyNotAvailable()
+    except OptionalDependencyNotAvailable:
+        pass
+    else:
+        from .tokenization_layoutlmv2_fast import LayoutLMv2TokenizerFast
+
+    try:
+        if not is_vision_available():
+            raise OptionalDependencyNotAvailable()
+    except OptionalDependencyNotAvailable:
+        pass
+    else:
+        from .feature_extraction_layoutlmv2 import LayoutLMv2FeatureExtractor, LayoutLMv2ImageProcessor
+
+    try:
+        if not is_torch_available():
+            raise OptionalDependencyNotAvailable()
+    except OptionalDependencyNotAvailable:
+        pass
+    else:
+        from .modeling_layoutlmv2 import (
+            LAYOUTLMV2_PRETRAINED_MODEL_ARCHIVE_LIST,
+            LayoutLMv2ForQuestionAnswering,
+            LayoutLMv2ForSequenceClassification,
+            LayoutLMv2ForTokenClassification,
+            LayoutLMv2Layer,
+            LayoutLMv2Model,
+            LayoutLMv2PreTrainedModel,
+        )
+else:
+    import sys
+
+    sys.modules[__name__] = _LazyModule(__name__, globals()["__file__"], _import_structure, module_spec=__spec__)

llmeval-env/lib/python3.10/site-packages/transformers/models/layoutlmv2/configuration_layoutlmv2.py

@@ -0,0 +1,222 @@
+# coding=utf-8
+# Copyright Microsoft Research and The HuggingFace Inc. team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+""" LayoutLMv2 model configuration"""
+
+from ...configuration_utils import PretrainedConfig
+from ...utils import is_detectron2_available, logging
+
+
+logger = logging.get_logger(__name__)
+
+
+from ..deprecated._archive_maps import LAYOUTLMV2_PRETRAINED_CONFIG_ARCHIVE_MAP  # noqa: F401, E402
+
+
+# soft dependency
+if is_detectron2_available():
+    import detectron2
+
+
+class LayoutLMv2Config(PretrainedConfig):
+    r"""
+    This is the configuration class to store the configuration of a [`LayoutLMv2Model`]. It is used to instantiate an
+    LayoutLMv2 model according to the specified arguments, defining the model architecture. Instantiating a
+    configuration with the defaults will yield a similar configuration to that of the LayoutLMv2
+    [microsoft/layoutlmv2-base-uncased](https://huggingface.co/microsoft/layoutlmv2-base-uncased) architecture.
+
+    Configuration objects inherit from [`PretrainedConfig`] and can be used to control the model outputs. Read the
+    documentation from [`PretrainedConfig`] for more information.
+
+    Args:
+        vocab_size (`int`, *optional*, defaults to 30522):
+            Vocabulary size of the LayoutLMv2 model. Defines the number of different tokens that can be represented by
+            the `inputs_ids` passed when calling [`LayoutLMv2Model`] or [`TFLayoutLMv2Model`].
+        hidden_size (`int`, *optional*, defaults to 768):
+            Dimension of the encoder layers and the pooler layer.
+        num_hidden_layers (`int`, *optional*, defaults to 12):
+            Number of hidden layers in the Transformer encoder.
+        num_attention_heads (`int`, *optional*, defaults to 12):
+            Number of attention heads for each attention layer in the Transformer encoder.
+        intermediate_size (`int`, *optional*, defaults to 3072):
+            Dimension of the "intermediate" (i.e., feed-forward) layer in the Transformer encoder.
+        hidden_act (`str` or `function`, *optional*, defaults to `"gelu"`):
+            The non-linear activation function (function or string) in the encoder and pooler. If string, `"gelu"`,
+            `"relu"`, `"selu"` and `"gelu_new"` are supported.
+        hidden_dropout_prob (`float`, *optional*, defaults to 0.1):
+            The dropout probability for all fully connected layers in the embeddings, encoder, and pooler.
+        attention_probs_dropout_prob (`float`, *optional*, defaults to 0.1):
+            The dropout ratio for the attention probabilities.
+        max_position_embeddings (`int`, *optional*, defaults to 512):
+            The maximum sequence length that this model might ever be used with. Typically set this to something large
+            just in case (e.g., 512 or 1024 or 2048).
+        type_vocab_size (`int`, *optional*, defaults to 2):
+            The vocabulary size of the `token_type_ids` passed when calling [`LayoutLMv2Model`] or
+            [`TFLayoutLMv2Model`].
+        initializer_range (`float`, *optional*, defaults to 0.02):
+            The standard deviation of the truncated_normal_initializer for initializing all weight matrices.
+        layer_norm_eps (`float`, *optional*, defaults to 1e-12):
+            The epsilon used by the layer normalization layers.
+        max_2d_position_embeddings (`int`, *optional*, defaults to 1024):
+            The maximum value that the 2D position embedding might ever be used with. Typically set this to something
+            large just in case (e.g., 1024).
+        max_rel_pos (`int`, *optional*, defaults to 128):
+            The maximum number of relative positions to be used in the self-attention mechanism.
+        rel_pos_bins (`int`, *optional*, defaults to 32):
+            The number of relative position bins to be used in the self-attention mechanism.
+        fast_qkv (`bool`, *optional*, defaults to `True`):
+            Whether or not to use a single matrix for the queries, keys, values in the self-attention layers.
+        max_rel_2d_pos (`int`, *optional*, defaults to 256):
+            The maximum number of relative 2D positions in the self-attention mechanism.
+        rel_2d_pos_bins (`int`, *optional*, defaults to 64):
+            The number of 2D relative position bins in the self-attention mechanism.
+        image_feature_pool_shape (`List[int]`, *optional*, defaults to [7, 7, 256]):
+            The shape of the average-pooled feature map.
+        coordinate_size (`int`, *optional*, defaults to 128):
+            Dimension of the coordinate embeddings.
+        shape_size (`int`, *optional*, defaults to 128):
+            Dimension of the width and height embeddings.
+        has_relative_attention_bias (`bool`, *optional*, defaults to `True`):
+            Whether or not to use a relative attention bias in the self-attention mechanism.
+        has_spatial_attention_bias (`bool`, *optional*, defaults to `True`):
+            Whether or not to use a spatial attention bias in the self-attention mechanism.
+        has_visual_segment_embedding (`bool`, *optional*, defaults to `False`):
+            Whether or not to add visual segment embeddings.
+        detectron2_config_args (`dict`, *optional*):
+            Dictionary containing the configuration arguments of the Detectron2 visual backbone. Refer to [this
+            file](https://github.com/microsoft/unilm/blob/master/layoutlmft/layoutlmft/models/layoutlmv2/detectron2_config.py)
+            for details regarding default values.
+
+    Example:
+
+    ```python
+    >>> from transformers import LayoutLMv2Config, LayoutLMv2Model
+
+    >>> # Initializing a LayoutLMv2 microsoft/layoutlmv2-base-uncased style configuration
+    >>> configuration = LayoutLMv2Config()
+
+    >>> # Initializing a model (with random weights) from the microsoft/layoutlmv2-base-uncased style configuration
+    >>> model = LayoutLMv2Model(configuration)
+
+    >>> # Accessing the model configuration
+    >>> configuration = model.config
+    ```"""
+
+    model_type = "layoutlmv2"
+
+    def __init__(
+        self,
+        vocab_size=30522,
+        hidden_size=768,
+        num_hidden_layers=12,
+        num_attention_heads=12,
+        intermediate_size=3072,
+        hidden_act="gelu",
+        hidden_dropout_prob=0.1,
+        attention_probs_dropout_prob=0.1,
+        max_position_embeddings=512,
+        type_vocab_size=2,
+        initializer_range=0.02,
+        layer_norm_eps=1e-12,
+        pad_token_id=0,
+        max_2d_position_embeddings=1024,
+        max_rel_pos=128,
+        rel_pos_bins=32,
+        fast_qkv=True,
+        max_rel_2d_pos=256,
+        rel_2d_pos_bins=64,
+        convert_sync_batchnorm=True,
+        image_feature_pool_shape=[7, 7, 256],
+        coordinate_size=128,
+        shape_size=128,
+        has_relative_attention_bias=True,
+        has_spatial_attention_bias=True,
+        has_visual_segment_embedding=False,
+        detectron2_config_args=None,
+        **kwargs,
+    ):
+        super().__init__(
+            vocab_size=vocab_size,
+            hidden_size=hidden_size,
+            num_hidden_layers=num_hidden_layers,
+            num_attention_heads=num_attention_heads,
+            intermediate_size=intermediate_size,
+            hidden_act=hidden_act,
+            hidden_dropout_prob=hidden_dropout_prob,
+            attention_probs_dropout_prob=attention_probs_dropout_prob,
+            max_position_embeddings=max_position_embeddings,
+            type_vocab_size=type_vocab_size,
+            initializer_range=initializer_range,
+            layer_norm_eps=layer_norm_eps,
+            pad_token_id=pad_token_id,
+            **kwargs,
+        )
+        self.max_2d_position_embeddings = max_2d_position_embeddings
+        self.max_rel_pos = max_rel_pos
+        self.rel_pos_bins = rel_pos_bins
+        self.fast_qkv = fast_qkv
+        self.max_rel_2d_pos = max_rel_2d_pos
+        self.rel_2d_pos_bins = rel_2d_pos_bins
+        self.convert_sync_batchnorm = convert_sync_batchnorm
+        self.image_feature_pool_shape = image_feature_pool_shape
+        self.coordinate_size = coordinate_size
+        self.shape_size = shape_size
+        self.has_relative_attention_bias = has_relative_attention_bias
+        self.has_spatial_attention_bias = has_spatial_attention_bias
+        self.has_visual_segment_embedding = has_visual_segment_embedding
+        self.detectron2_config_args = (
+            detectron2_config_args if detectron2_config_args is not None else self.get_default_detectron2_config()
+        )
+
+    @classmethod
+    def get_default_detectron2_config(self):
+        return {
+            "MODEL.MASK_ON": True,
+            "MODEL.PIXEL_STD": [57.375, 57.120, 58.395],
+            "MODEL.BACKBONE.NAME": "build_resnet_fpn_backbone",
+            "MODEL.FPN.IN_FEATURES": ["res2", "res3", "res4", "res5"],
+            "MODEL.ANCHOR_GENERATOR.SIZES": [[32], [64], [128], [256], [512]],
+            "MODEL.RPN.IN_FEATURES": ["p2", "p3", "p4", "p5", "p6"],
+            "MODEL.RPN.PRE_NMS_TOPK_TRAIN": 2000,
+            "MODEL.RPN.PRE_NMS_TOPK_TEST": 1000,
+            "MODEL.RPN.POST_NMS_TOPK_TRAIN": 1000,
+            "MODEL.POST_NMS_TOPK_TEST": 1000,
+            "MODEL.ROI_HEADS.NAME": "StandardROIHeads",
+            "MODEL.ROI_HEADS.NUM_CLASSES": 5,
+            "MODEL.ROI_HEADS.IN_FEATURES": ["p2", "p3", "p4", "p5"],
+            "MODEL.ROI_BOX_HEAD.NAME": "FastRCNNConvFCHead",
+            "MODEL.ROI_BOX_HEAD.NUM_FC": 2,
+            "MODEL.ROI_BOX_HEAD.POOLER_RESOLUTION": 14,
+            "MODEL.ROI_MASK_HEAD.NAME": "MaskRCNNConvUpsampleHead",
+            "MODEL.ROI_MASK_HEAD.NUM_CONV": 4,
+            "MODEL.ROI_MASK_HEAD.POOLER_RESOLUTION": 7,
+            "MODEL.RESNETS.DEPTH": 101,
+            "MODEL.RESNETS.SIZES": [[32], [64], [128], [256], [512]],
+            "MODEL.RESNETS.ASPECT_RATIOS": [[0.5, 1.0, 2.0]],
+            "MODEL.RESNETS.OUT_FEATURES": ["res2", "res3", "res4", "res5"],
+            "MODEL.RESNETS.NUM_GROUPS": 32,
+            "MODEL.RESNETS.WIDTH_PER_GROUP": 8,
+            "MODEL.RESNETS.STRIDE_IN_1X1": False,
+        }
+
+    def get_detectron2_config(self):
+        detectron2_config = detectron2.config.get_cfg()
+        for k, v in self.detectron2_config_args.items():
+            attributes = k.split(".")
+            to_set = detectron2_config
+            for attribute in attributes[:-1]:
+                to_set = getattr(to_set, attribute)
+            setattr(to_set, attributes[-1], v)
+
+        return detectron2_config

llmeval-env/lib/python3.10/site-packages/transformers/models/layoutlmv2/feature_extraction_layoutlmv2.py

@@ -0,0 +1,35 @@
+# coding=utf-8
+# Copyright 2021 The HuggingFace Inc. team.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+Feature extractor class for LayoutLMv2.
+"""
+
+import warnings
+
+from ...utils import logging
+from .image_processing_layoutlmv2 import LayoutLMv2ImageProcessor
+
+
+logger = logging.get_logger(__name__)
+
+
+class LayoutLMv2FeatureExtractor(LayoutLMv2ImageProcessor):
+    def __init__(self, *args, **kwargs) -> None:
+        warnings.warn(
+            "The class LayoutLMv2FeatureExtractor is deprecated and will be removed in version 5 of Transformers."
+            " Please use LayoutLMv2ImageProcessor instead.",
+            FutureWarning,
+        )
+        super().__init__(*args, **kwargs)

llmeval-env/lib/python3.10/site-packages/transformers/models/layoutlmv2/modeling_layoutlmv2.py

@@ -0,0 +1,1407 @@
+# coding=utf-8
+# Copyright 2021 Microsoft Research The HuggingFace Inc. team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+""" PyTorch LayoutLMv2 model."""
+
+import math
+from typing import Optional, Tuple, Union
+
+import torch
+import torch.utils.checkpoint
+from torch import nn
+from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss
+
+from ...activations import ACT2FN
+from ...modeling_outputs import (
+    BaseModelOutput,
+    BaseModelOutputWithPooling,
+    QuestionAnsweringModelOutput,
+    SequenceClassifierOutput,
+    TokenClassifierOutput,
+)
+from ...modeling_utils import PreTrainedModel
+from ...pytorch_utils import apply_chunking_to_forward
+from ...utils import (
+    add_start_docstrings,
+    add_start_docstrings_to_model_forward,
+    is_detectron2_available,
+    logging,
+    replace_return_docstrings,
+    requires_backends,
+)
+from .configuration_layoutlmv2 import LayoutLMv2Config
+
+
+# soft dependency
+if is_detectron2_available():
+    import detectron2
+    from detectron2.modeling import META_ARCH_REGISTRY
+
+logger = logging.get_logger(__name__)
+
+_CHECKPOINT_FOR_DOC = "microsoft/layoutlmv2-base-uncased"
+_CONFIG_FOR_DOC = "LayoutLMv2Config"
+
+
+from ..deprecated._archive_maps import LAYOUTLMV2_PRETRAINED_MODEL_ARCHIVE_LIST  # noqa: F401, E402
+
+
+class LayoutLMv2Embeddings(nn.Module):
+    """Construct the embeddings from word, position and token_type embeddings."""
+
+    def __init__(self, config):
+        super(LayoutLMv2Embeddings, self).__init__()
+        self.word_embeddings = nn.Embedding(config.vocab_size, config.hidden_size, padding_idx=config.pad_token_id)
+        self.position_embeddings = nn.Embedding(config.max_position_embeddings, config.hidden_size)
+
+        self.x_position_embeddings = nn.Embedding(config.max_2d_position_embeddings, config.coordinate_size)
+        self.y_position_embeddings = nn.Embedding(config.max_2d_position_embeddings, config.coordinate_size)
+        self.h_position_embeddings = nn.Embedding(config.max_2d_position_embeddings, config.shape_size)
+        self.w_position_embeddings = nn.Embedding(config.max_2d_position_embeddings, config.shape_size)
+        self.token_type_embeddings = nn.Embedding(config.type_vocab_size, config.hidden_size)
+
+        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+
+        self.register_buffer(
+            "position_ids", torch.arange(config.max_position_embeddings).expand((1, -1)), persistent=False
+        )
+
+    def _calc_spatial_position_embeddings(self, bbox):
+        try:
+            left_position_embeddings = self.x_position_embeddings(bbox[:, :, 0])
+            upper_position_embeddings = self.y_position_embeddings(bbox[:, :, 1])
+            right_position_embeddings = self.x_position_embeddings(bbox[:, :, 2])
+            lower_position_embeddings = self.y_position_embeddings(bbox[:, :, 3])
+        except IndexError as e:
+            raise IndexError("The `bbox` coordinate values should be within 0-1000 range.") from e
+
+        h_position_embeddings = self.h_position_embeddings(bbox[:, :, 3] - bbox[:, :, 1])
+        w_position_embeddings = self.w_position_embeddings(bbox[:, :, 2] - bbox[:, :, 0])
+
+        spatial_position_embeddings = torch.cat(
+            [
+                left_position_embeddings,
+                upper_position_embeddings,
+                right_position_embeddings,
+                lower_position_embeddings,
+                h_position_embeddings,
+                w_position_embeddings,
+            ],
+            dim=-1,
+        )
+        return spatial_position_embeddings
+
+
+class LayoutLMv2SelfAttention(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        if config.hidden_size % config.num_attention_heads != 0 and not hasattr(config, "embedding_size"):
+            raise ValueError(
+                f"The hidden size ({config.hidden_size}) is not a multiple of the number of attention "
+                f"heads ({config.num_attention_heads})"
+            )
+        self.fast_qkv = config.fast_qkv
+        self.num_attention_heads = config.num_attention_heads
+        self.attention_head_size = int(config.hidden_size / config.num_attention_heads)
+        self.all_head_size = self.num_attention_heads * self.attention_head_size
+
+        self.has_relative_attention_bias = config.has_relative_attention_bias
+        self.has_spatial_attention_bias = config.has_spatial_attention_bias
+
+        if config.fast_qkv:
+            self.qkv_linear = nn.Linear(config.hidden_size, 3 * self.all_head_size, bias=False)
+            self.q_bias = nn.Parameter(torch.zeros(1, 1, self.all_head_size))
+            self.v_bias = nn.Parameter(torch.zeros(1, 1, self.all_head_size))
+        else:
+            self.query = nn.Linear(config.hidden_size, self.all_head_size)
+            self.key = nn.Linear(config.hidden_size, self.all_head_size)
+            self.value = nn.Linear(config.hidden_size, self.all_head_size)
+
+        self.dropout = nn.Dropout(config.attention_probs_dropout_prob)
+
+    def transpose_for_scores(self, x):
+        new_x_shape = x.size()[:-1] + (self.num_attention_heads, self.attention_head_size)
+        x = x.view(*new_x_shape)
+        return x.permute(0, 2, 1, 3)
+
+    def compute_qkv(self, hidden_states):
+        if self.fast_qkv:
+            qkv = self.qkv_linear(hidden_states)
+            q, k, v = torch.chunk(qkv, 3, dim=-1)
+            if q.ndimension() == self.q_bias.ndimension():
+                q = q + self.q_bias
+                v = v + self.v_bias
+            else:
+                _sz = (1,) * (q.ndimension() - 1) + (-1,)
+                q = q + self.q_bias.view(*_sz)
+                v = v + self.v_bias.view(*_sz)
+        else:
+            q = self.query(hidden_states)
+            k = self.key(hidden_states)
+            v = self.value(hidden_states)
+        return q, k, v
+
+    def forward(
+        self,
+        hidden_states,
+        attention_mask=None,
+        head_mask=None,
+        output_attentions=False,
+        rel_pos=None,
+        rel_2d_pos=None,
+    ):
+        q, k, v = self.compute_qkv(hidden_states)
+
+        # (B, L, H*D) -> (B, H, L, D)
+        query_layer = self.transpose_for_scores(q)
+        key_layer = self.transpose_for_scores(k)
+        value_layer = self.transpose_for_scores(v)
+
+        query_layer = query_layer / math.sqrt(self.attention_head_size)
+        # [BSZ, NAT, L, L]
+        attention_scores = torch.matmul(query_layer, key_layer.transpose(-1, -2))
+        if self.has_relative_attention_bias:
+            attention_scores += rel_pos
+        if self.has_spatial_attention_bias:
+            attention_scores += rel_2d_pos
+        attention_scores = attention_scores.float().masked_fill_(
+            attention_mask.to(torch.bool), torch.finfo(attention_scores.dtype).min
+        )
+        attention_probs = nn.functional.softmax(attention_scores, dim=-1, dtype=torch.float32).type_as(value_layer)
+        # This is actually dropping out entire tokens to attend to, which might
+        # seem a bit unusual, but is taken from the original Transformer paper.
+        attention_probs = self.dropout(attention_probs)
+
+        # Mask heads if we want to
+        if head_mask is not None:
+            attention_probs = attention_probs * head_mask
+
+        context_layer = torch.matmul(attention_probs, value_layer)
+        context_layer = context_layer.permute(0, 2, 1, 3).contiguous()
+        new_context_layer_shape = context_layer.size()[:-2] + (self.all_head_size,)
+        context_layer = context_layer.view(*new_context_layer_shape)
+
+        outputs = (context_layer, attention_probs) if output_attentions else (context_layer,)
+        return outputs
+
+
+class LayoutLMv2Attention(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.self = LayoutLMv2SelfAttention(config)
+        self.output = LayoutLMv2SelfOutput(config)
+
+    def forward(
+        self,
+        hidden_states,
+        attention_mask=None,
+        head_mask=None,
+        output_attentions=False,
+        rel_pos=None,
+        rel_2d_pos=None,
+    ):
+        self_outputs = self.self(
+            hidden_states,
+            attention_mask,
+            head_mask,
+            output_attentions,
+            rel_pos=rel_pos,
+            rel_2d_pos=rel_2d_pos,
+        )
+        attention_output = self.output(self_outputs[0], hidden_states)
+        outputs = (attention_output,) + self_outputs[1:]  # add attentions if we output them
+        return outputs
+
+
+class LayoutLMv2SelfOutput(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
+        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+
+    def forward(self, hidden_states, input_tensor):
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.dropout(hidden_states)
+        hidden_states = self.LayerNorm(hidden_states + input_tensor)
+        return hidden_states
+
+
+# Copied from transformers.models.bert.modeling_bert.BertIntermediate with Bert->LayoutLMv2
+class LayoutLMv2Intermediate(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.intermediate_size)
+        if isinstance(config.hidden_act, str):
+            self.intermediate_act_fn = ACT2FN[config.hidden_act]
+        else:
+            self.intermediate_act_fn = config.hidden_act
+
+    def forward(self, hidden_states: torch.Tensor) -> torch.Tensor:
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.intermediate_act_fn(hidden_states)
+        return hidden_states
+
+
+# Copied from transformers.models.bert.modeling_bert.BertOutput with Bert->LayoutLM
+class LayoutLMv2Output(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.intermediate_size, config.hidden_size)
+        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+
+    def forward(self, hidden_states: torch.Tensor, input_tensor: torch.Tensor) -> torch.Tensor:
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.dropout(hidden_states)
+        hidden_states = self.LayerNorm(hidden_states + input_tensor)
+        return hidden_states
+
+
+class LayoutLMv2Layer(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.chunk_size_feed_forward = config.chunk_size_feed_forward
+        self.seq_len_dim = 1
+        self.attention = LayoutLMv2Attention(config)
+        self.intermediate = LayoutLMv2Intermediate(config)
+        self.output = LayoutLMv2Output(config)
+
+    def forward(
+        self,
+        hidden_states,
+        attention_mask=None,
+        head_mask=None,
+        output_attentions=False,
+        rel_pos=None,
+        rel_2d_pos=None,
+    ):
+        self_attention_outputs = self.attention(
+            hidden_states,
+            attention_mask,
+            head_mask,
+            output_attentions=output_attentions,
+            rel_pos=rel_pos,
+            rel_2d_pos=rel_2d_pos,
+        )
+        attention_output = self_attention_outputs[0]
+
+        outputs = self_attention_outputs[1:]  # add self attentions if we output attention weights
+
+        layer_output = apply_chunking_to_forward(
+            self.feed_forward_chunk, self.chunk_size_feed_forward, self.seq_len_dim, attention_output
+        )
+        outputs = (layer_output,) + outputs
+
+        return outputs
+
+    def feed_forward_chunk(self, attention_output):
+        intermediate_output = self.intermediate(attention_output)
+        layer_output = self.output(intermediate_output, attention_output)
+        return layer_output
+
+
+def relative_position_bucket(relative_position, bidirectional=True, num_buckets=32, max_distance=128):
+    """
+    Adapted from Mesh Tensorflow:
+    https://github.com/tensorflow/mesh/blob/0cb87fe07da627bf0b7e60475d59f95ed6b5be3d/mesh_tensorflow/transformer/transformer_layers.py#L593
+    Translate relative position to a bucket number for relative attention. The relative position is defined as
+    memory_position - query_position, i.e. the distance in tokens from the attending position to the attended-to
+    position. If bidirectional=False, then positive relative positions are invalid. We use smaller buckets for small
+    absolute relative_position and larger buckets for larger absolute relative_positions. All relative positions
+    >=max_distance map to the same bucket. All relative positions <=-max_distance map to the same bucket. This should
+    allow for more graceful generalization to longer sequences than the model has been trained on.
+
+    Args:
+        relative_position: an int32 Tensor
+        bidirectional: a boolean - whether the attention is bidirectional
+        num_buckets: an integer
+        max_distance: an integer
+
+    Returns:
+        a Tensor with the same shape as relative_position, containing int32 values in the range [0, num_buckets)
+    """
+
+    ret = 0
+    if bidirectional:
+        num_buckets //= 2
+        ret += (relative_position > 0).long() * num_buckets
+        n = torch.abs(relative_position)
+    else:
+        n = torch.max(-relative_position, torch.zeros_like(relative_position))
+    # now n is in the range [0, inf)
+
+    # half of the buckets are for exact increments in positions
+    max_exact = num_buckets // 2
+    is_small = n < max_exact
+
+    # The other half of the buckets are for logarithmically bigger bins in positions up to max_distance
+    val_if_large = max_exact + (
+        torch.log(n.float() / max_exact) / math.log(max_distance / max_exact) * (num_buckets - max_exact)
+    ).to(torch.long)
+    val_if_large = torch.min(val_if_large, torch.full_like(val_if_large, num_buckets - 1))
+
+    ret += torch.where(is_small, n, val_if_large)
+    return ret
+
+
+class LayoutLMv2Encoder(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.config = config
+        self.layer = nn.ModuleList([LayoutLMv2Layer(config) for _ in range(config.num_hidden_layers)])
+
+        self.has_relative_attention_bias = config.has_relative_attention_bias
+        self.has_spatial_attention_bias = config.has_spatial_attention_bias
+
+        if self.has_relative_attention_bias:
+            self.rel_pos_bins = config.rel_pos_bins
+            self.max_rel_pos = config.max_rel_pos
+            self.rel_pos_bias = nn.Linear(self.rel_pos_bins, config.num_attention_heads, bias=False)
+
+        if self.has_spatial_attention_bias:
+            self.max_rel_2d_pos = config.max_rel_2d_pos
+            self.rel_2d_pos_bins = config.rel_2d_pos_bins
+            self.rel_pos_x_bias = nn.Linear(self.rel_2d_pos_bins, config.num_attention_heads, bias=False)
+            self.rel_pos_y_bias = nn.Linear(self.rel_2d_pos_bins, config.num_attention_heads, bias=False)
+
+        self.gradient_checkpointing = False
+
+    def _calculate_1d_position_embeddings(self, position_ids):
+        rel_pos_mat = position_ids.unsqueeze(-2) - position_ids.unsqueeze(-1)
+        rel_pos = relative_position_bucket(
+            rel_pos_mat,
+            num_buckets=self.rel_pos_bins,
+            max_distance=self.max_rel_pos,
+        )
+        rel_pos = self.rel_pos_bias.weight.t()[rel_pos].permute(0, 3, 1, 2)
+        rel_pos = rel_pos.contiguous()
+        return rel_pos
+
+    def _calculate_2d_position_embeddings(self, bbox):
+        position_coord_x = bbox[:, :, 0]
+        position_coord_y = bbox[:, :, 3]
+        rel_pos_x_2d_mat = position_coord_x.unsqueeze(-2) - position_coord_x.unsqueeze(-1)
+        rel_pos_y_2d_mat = position_coord_y.unsqueeze(-2) - position_coord_y.unsqueeze(-1)
+        rel_pos_x = relative_position_bucket(
+            rel_pos_x_2d_mat,
+            num_buckets=self.rel_2d_pos_bins,
+            max_distance=self.max_rel_2d_pos,
+        )
+        rel_pos_y = relative_position_bucket(
+            rel_pos_y_2d_mat,
+            num_buckets=self.rel_2d_pos_bins,
+            max_distance=self.max_rel_2d_pos,
+        )
+        rel_pos_x = self.rel_pos_x_bias.weight.t()[rel_pos_x].permute(0, 3, 1, 2)
+        rel_pos_y = self.rel_pos_y_bias.weight.t()[rel_pos_y].permute(0, 3, 1, 2)
+        rel_pos_x = rel_pos_x.contiguous()
+        rel_pos_y = rel_pos_y.contiguous()
+        rel_2d_pos = rel_pos_x + rel_pos_y
+        return rel_2d_pos
+
+    def forward(
+        self,
+        hidden_states,
+        attention_mask=None,
+        head_mask=None,
+        output_attentions=False,
+        output_hidden_states=False,
+        return_dict=True,
+        bbox=None,
+        position_ids=None,
+    ):
+        all_hidden_states = () if output_hidden_states else None
+        all_self_attentions = () if output_attentions else None
+
+        rel_pos = self._calculate_1d_position_embeddings(position_ids) if self.has_relative_attention_bias else None
+        rel_2d_pos = self._calculate_2d_position_embeddings(bbox) if self.has_spatial_attention_bias else None
+
+        for i, layer_module in enumerate(self.layer):
+            if output_hidden_states:
+                all_hidden_states = all_hidden_states + (hidden_states,)
+
+            layer_head_mask = head_mask[i] if head_mask is not None else None
+
+            if self.gradient_checkpointing and self.training:
+                layer_outputs = self._gradient_checkpointing_func(
+                    layer_module.__call__,
+                    hidden_states,
+                    attention_mask,
+                    layer_head_mask,
+                    output_attentions,
+                    rel_pos=rel_pos,
+                    rel_2d_pos=rel_2d_pos,
+                )
+            else:
+                layer_outputs = layer_module(
+                    hidden_states,
+                    attention_mask,
+                    layer_head_mask,
+                    output_attentions,
+                    rel_pos=rel_pos,
+                    rel_2d_pos=rel_2d_pos,
+                )
+
+            hidden_states = layer_outputs[0]
+            if output_attentions:
+                all_self_attentions = all_self_attentions + (layer_outputs[1],)
+
+        if output_hidden_states:
+            all_hidden_states = all_hidden_states + (hidden_states,)
+
+        if not return_dict:
+            return tuple(
+                v
+                for v in [
+                    hidden_states,
+                    all_hidden_states,
+                    all_self_attentions,
+                ]
+                if v is not None
+            )
+        return BaseModelOutput(
+            last_hidden_state=hidden_states,
+            hidden_states=all_hidden_states,
+            attentions=all_self_attentions,
+        )
+
+
+class LayoutLMv2PreTrainedModel(PreTrainedModel):
+    """
+    An abstract class to handle weights initialization and a simple interface for downloading and loading pretrained
+    models.
+    """
+
+    config_class = LayoutLMv2Config
+    base_model_prefix = "layoutlmv2"
+
+    def _init_weights(self, module):
+        """Initialize the weights"""
+        if isinstance(module, nn.Linear):
+            # Slightly different from the TF version which uses truncated_normal for initialization
+            # cf https://github.com/pytorch/pytorch/pull/5617
+            module.weight.data.normal_(mean=0.0, std=self.config.initializer_range)
+            if module.bias is not None:
+                module.bias.data.zero_()
+        elif isinstance(module, nn.Embedding):
+            module.weight.data.normal_(mean=0.0, std=self.config.initializer_range)
+            if module.padding_idx is not None:
+                module.weight.data[module.padding_idx].zero_()
+        elif isinstance(module, nn.LayerNorm):
+            module.bias.data.zero_()
+            module.weight.data.fill_(1.0)
+
+
+def my_convert_sync_batchnorm(module, process_group=None):
+    # same as `nn.modules.SyncBatchNorm.convert_sync_batchnorm` but allowing converting from `detectron2.layers.FrozenBatchNorm2d`
+    if isinstance(module, torch.nn.modules.batchnorm._BatchNorm):
+        return nn.modules.SyncBatchNorm.convert_sync_batchnorm(module, process_group)
+    module_output = module
+    if isinstance(module, detectron2.layers.FrozenBatchNorm2d):
+        module_output = torch.nn.SyncBatchNorm(
+            num_features=module.num_features,
+            eps=module.eps,
+            affine=True,
+            track_running_stats=True,
+            process_group=process_group,
+        )
+        module_output.weight = torch.nn.Parameter(module.weight)
+        module_output.bias = torch.nn.Parameter(module.bias)
+        module_output.running_mean = module.running_mean
+        module_output.running_var = module.running_var
+        module_output.num_batches_tracked = torch.tensor(0, dtype=torch.long, device=module.running_mean.device)
+    for name, child in module.named_children():
+        module_output.add_module(name, my_convert_sync_batchnorm(child, process_group))
+    del module
+    return module_output
+
+
+class LayoutLMv2VisualBackbone(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.cfg = config.get_detectron2_config()
+        meta_arch = self.cfg.MODEL.META_ARCHITECTURE
+        model = META_ARCH_REGISTRY.get(meta_arch)(self.cfg)
+        assert isinstance(model.backbone, detectron2.modeling.backbone.FPN)
+        self.backbone = model.backbone
+
+        assert len(self.cfg.MODEL.PIXEL_MEAN) == len(self.cfg.MODEL.PIXEL_STD)
+        num_channels = len(self.cfg.MODEL.PIXEL_MEAN)
+        self.register_buffer(
+            "pixel_mean",
+            torch.Tensor(self.cfg.MODEL.PIXEL_MEAN).view(num_channels, 1, 1),
+            persistent=False,
+        )
+        self.register_buffer(
+            "pixel_std", torch.Tensor(self.cfg.MODEL.PIXEL_STD).view(num_channels, 1, 1), persistent=False
+        )
+        self.out_feature_key = "p2"
+        if torch.are_deterministic_algorithms_enabled():
+            logger.warning("using `AvgPool2d` instead of `AdaptiveAvgPool2d`")
+            input_shape = (224, 224)
+            backbone_stride = self.backbone.output_shape()[self.out_feature_key].stride
+            self.pool = nn.AvgPool2d(
+                (
+                    math.ceil(math.ceil(input_shape[0] / backbone_stride) / config.image_feature_pool_shape[0]),
+                    math.ceil(math.ceil(input_shape[1] / backbone_stride) / config.image_feature_pool_shape[1]),
+                )
+            )
+        else:
+            self.pool = nn.AdaptiveAvgPool2d(config.image_feature_pool_shape[:2])
+        if len(config.image_feature_pool_shape) == 2:
+            config.image_feature_pool_shape.append(self.backbone.output_shape()[self.out_feature_key].channels)
+        assert self.backbone.output_shape()[self.out_feature_key].channels == config.image_feature_pool_shape[2]
+
+    def forward(self, images):
+        images_input = ((images if torch.is_tensor(images) else images.tensor) - self.pixel_mean) / self.pixel_std
+        features = self.backbone(images_input)
+        features = features[self.out_feature_key]
+        features = self.pool(features).flatten(start_dim=2).transpose(1, 2).contiguous()
+        return features
+
+    def synchronize_batch_norm(self):
+        if not (
+            torch.distributed.is_available()
+            and torch.distributed.is_initialized()
+            and torch.distributed.get_rank() > -1
+        ):
+            raise RuntimeError("Make sure torch.distributed is set up properly.")
+
+        self_rank = torch.distributed.get_rank()
+        node_size = torch.cuda.device_count()
+        world_size = torch.distributed.get_world_size()
+        if not (world_size % node_size == 0):
+            raise RuntimeError("Make sure the number of processes can be divided by the number of nodes")
+
+        node_global_ranks = [list(range(i * node_size, (i + 1) * node_size)) for i in range(world_size // node_size)]
+        sync_bn_groups = [
+            torch.distributed.new_group(ranks=node_global_ranks[i]) for i in range(world_size // node_size)
+        ]
+        node_rank = self_rank // node_size
+
+        self.backbone = my_convert_sync_batchnorm(self.backbone, process_group=sync_bn_groups[node_rank])
+
+
+LAYOUTLMV2_START_DOCSTRING = r"""
+    This model is a PyTorch [torch.nn.Module](https://pytorch.org/docs/stable/nn.html#torch.nn.Module) sub-class. Use
+    it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage and
+    behavior.
+
+    Parameters:
+        config ([`LayoutLMv2Config`]): Model configuration class with all the parameters of the model.
+            Initializing with a config file does not load the weights associated with the model, only the
+            configuration. Check out the [`~PreTrainedModel.from_pretrained`] method to load the model weights.
+"""
+
+LAYOUTLMV2_INPUTS_DOCSTRING = r"""
+    Args:
+        input_ids (`torch.LongTensor` of shape `{0}`):
+            Indices of input sequence tokens in the vocabulary.
+
+            Indices can be obtained using [`AutoTokenizer`]. See [`PreTrainedTokenizer.encode`] and
+            [`PreTrainedTokenizer.__call__`] for details.
+
+            [What are input IDs?](../glossary#input-ids)
+
+        bbox (`torch.LongTensor` of shape `({0}, 4)`, *optional*):
+            Bounding boxes of each input sequence tokens. Selected in the range `[0,
+            config.max_2d_position_embeddings-1]`. Each bounding box should be a normalized version in (x0, y0, x1, y1)
+            format, where (x0, y0) corresponds to the position of the upper left corner in the bounding box, and (x1,
+            y1) represents the position of the lower right corner.
+
+        image (`torch.FloatTensor` of shape `(batch_size, num_channels, height, width)` or `detectron.structures.ImageList` whose `tensors` is of shape `(batch_size, num_channels, height, width)`):
+            Batch of document images.
+
+        attention_mask (`torch.FloatTensor` of shape `{0}`, *optional*):
+            Mask to avoid performing attention on padding token indices. Mask values selected in `[0, 1]`:
+
+            - 1 for tokens that are **not masked**,
+            - 0 for tokens that are **masked**.
+
+            [What are attention masks?](../glossary#attention-mask)
+        token_type_ids (`torch.LongTensor` of shape `{0}`, *optional*):
+            Segment token indices to indicate first and second portions of the inputs. Indices are selected in `[0,
+            1]`:
+
+            - 0 corresponds to a *sentence A* token,
+            - 1 corresponds to a *sentence B* token.
+
+            [What are token type IDs?](../glossary#token-type-ids)
+        position_ids (`torch.LongTensor` of shape `{0}`, *optional*):
+            Indices of positions of each input sequence tokens in the position embeddings. Selected in the range `[0,
+            config.max_position_embeddings - 1]`.
+
+            [What are position IDs?](../glossary#position-ids)
+        head_mask (`torch.FloatTensor` of shape `(num_heads,)` or `(num_layers, num_heads)`, *optional*):
+            Mask to nullify selected heads of the self-attention modules. Mask values selected in `[0, 1]`:
+
+            - 1 indicates the head is **not masked**,
+            - 0 indicates the head is **masked**.
+
+        inputs_embeds (`torch.FloatTensor` of shape `(batch_size, sequence_length, hidden_size)`, *optional*):
+            Optionally, instead of passing `input_ids` you can choose to directly pass an embedded representation. This
+            is useful if you want more control over how to convert *input_ids* indices into associated vectors than the
+            model's internal embedding lookup matrix.
+        output_attentions (`bool`, *optional*):
+            Whether or not to return the attentions tensors of all attention layers. See `attentions` under returned
+            tensors for more detail.
+        output_hidden_states (`bool`, *optional*):
+            Whether or not to return the hidden states of all layers. See `hidden_states` under returned tensors for
+            more detail.
+        return_dict (`bool`, *optional*):
+            Whether or not to return a [`~utils.ModelOutput`] instead of a plain tuple.
+"""
+
+
+class LayoutLMv2Pooler(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
+        self.activation = nn.Tanh()
+
+    def forward(self, hidden_states):
+        # We "pool" the model by simply taking the hidden state corresponding
+        # to the first token.
+        first_token_tensor = hidden_states[:, 0]
+        pooled_output = self.dense(first_token_tensor)
+        pooled_output = self.activation(pooled_output)
+        return pooled_output
+
+
+@add_start_docstrings(
+    "The bare LayoutLMv2 Model transformer outputting raw hidden-states without any specific head on top.",
+    LAYOUTLMV2_START_DOCSTRING,
+)
+class LayoutLMv2Model(LayoutLMv2PreTrainedModel):
+    def __init__(self, config):
+        requires_backends(self, "detectron2")
+        super().__init__(config)
+        self.config = config
+        self.has_visual_segment_embedding = config.has_visual_segment_embedding
+        self.embeddings = LayoutLMv2Embeddings(config)
+
+        self.visual = LayoutLMv2VisualBackbone(config)
+        self.visual_proj = nn.Linear(config.image_feature_pool_shape[-1], config.hidden_size)
+        if self.has_visual_segment_embedding:
+            self.visual_segment_embedding = nn.Parameter(nn.Embedding(1, config.hidden_size).weight[0])
+        self.visual_LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+        self.visual_dropout = nn.Dropout(config.hidden_dropout_prob)
+
+        self.encoder = LayoutLMv2Encoder(config)
+        self.pooler = LayoutLMv2Pooler(config)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    def get_input_embeddings(self):
+        return self.embeddings.word_embeddings
+
+    def set_input_embeddings(self, value):
+        self.embeddings.word_embeddings = value
+
+    def _calc_text_embeddings(self, input_ids, bbox, position_ids, token_type_ids, inputs_embeds=None):
+        if input_ids is not None:
+            input_shape = input_ids.size()
+        else:
+            input_shape = inputs_embeds.size()[:-1]
+
+        seq_length = input_shape[1]
+
+        if position_ids is None:
+            position_ids = torch.arange(seq_length, dtype=torch.long, device=input_ids.device)
+            position_ids = position_ids.unsqueeze(0).expand_as(input_ids)
+        if token_type_ids is None:
+            token_type_ids = torch.zeros_like(input_ids)
+
+        if inputs_embeds is None:
+            inputs_embeds = self.embeddings.word_embeddings(input_ids)
+        position_embeddings = self.embeddings.position_embeddings(position_ids)
+        spatial_position_embeddings = self.embeddings._calc_spatial_position_embeddings(bbox)
+        token_type_embeddings = self.embeddings.token_type_embeddings(token_type_ids)
+
+        embeddings = inputs_embeds + position_embeddings + spatial_position_embeddings + token_type_embeddings
+        embeddings = self.embeddings.LayerNorm(embeddings)
+        embeddings = self.embeddings.dropout(embeddings)
+        return embeddings
+
+    def _calc_img_embeddings(self, image, bbox, position_ids):
+        visual_embeddings = self.visual_proj(self.visual(image))
+        position_embeddings = self.embeddings.position_embeddings(position_ids)
+        spatial_position_embeddings = self.embeddings._calc_spatial_position_embeddings(bbox)
+        embeddings = visual_embeddings + position_embeddings + spatial_position_embeddings
+        if self.has_visual_segment_embedding:
+            embeddings += self.visual_segment_embedding
+        embeddings = self.visual_LayerNorm(embeddings)
+        embeddings = self.visual_dropout(embeddings)
+        return embeddings
+
+    def _calc_visual_bbox(self, image_feature_pool_shape, bbox, device, final_shape):
+        visual_bbox_x = torch.div(
+            torch.arange(
+                0,
+                1000 * (image_feature_pool_shape[1] + 1),
+                1000,
+                device=device,
+                dtype=bbox.dtype,
+            ),
+            self.config.image_feature_pool_shape[1],
+            rounding_mode="floor",
+        )
+        visual_bbox_y = torch.div(
+            torch.arange(
+                0,
+                1000 * (self.config.image_feature_pool_shape[0] + 1),
+                1000,
+                device=device,
+                dtype=bbox.dtype,
+            ),
+            self.config.image_feature_pool_shape[0],
+            rounding_mode="floor",
+        )
+        visual_bbox = torch.stack(
+            [
+                visual_bbox_x[:-1].repeat(image_feature_pool_shape[0], 1),
+                visual_bbox_y[:-1].repeat(image_feature_pool_shape[1], 1).transpose(0, 1),
+                visual_bbox_x[1:].repeat(image_feature_pool_shape[0], 1),
+                visual_bbox_y[1:].repeat(image_feature_pool_shape[1], 1).transpose(0, 1),
+            ],
+            dim=-1,
+        ).view(-1, bbox.size(-1))
+
+        visual_bbox = visual_bbox.repeat(final_shape[0], 1, 1)
+
+        return visual_bbox
+
+    def _get_input_shape(self, input_ids=None, inputs_embeds=None):
+        if input_ids is not None and inputs_embeds is not None:
+            raise ValueError("You cannot specify both input_ids and inputs_embeds at the same time")
+        elif input_ids is not None:
+            return input_ids.size()
+        elif inputs_embeds is not None:
+            return inputs_embeds.size()[:-1]
+        else:
+            raise ValueError("You have to specify either input_ids or inputs_embeds")
+
+    @add_start_docstrings_to_model_forward(LAYOUTLMV2_INPUTS_DOCSTRING.format("(batch_size, sequence_length)"))
+    @replace_return_docstrings(output_type=BaseModelOutput, config_class=_CONFIG_FOR_DOC)
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        bbox: Optional[torch.LongTensor] = None,
+        image: Optional[torch.FloatTensor] = None,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        token_type_ids: Optional[torch.LongTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple, BaseModelOutputWithPooling]:
+        r"""
+        Return:
+
+        Examples:
+
+        ```python
+        >>> from transformers import AutoProcessor, LayoutLMv2Model, set_seed
+        >>> from PIL import Image
+        >>> import torch
+        >>> from datasets import load_dataset
+
+        >>> set_seed(88)
+
+        >>> processor = AutoProcessor.from_pretrained("microsoft/layoutlmv2-base-uncased")
+        >>> model = LayoutLMv2Model.from_pretrained("microsoft/layoutlmv2-base-uncased")
+
+
+        >>> dataset = load_dataset("hf-internal-testing/fixtures_docvqa")
+        >>> image_path = dataset["test"][0]["file"]
+        >>> image = Image.open(image_path).convert("RGB")
+
+        >>> encoding = processor(image, return_tensors="pt")
+
+        >>> outputs = model(**encoding)
+        >>> last_hidden_states = outputs.last_hidden_state
+
+        >>> last_hidden_states.shape
+        torch.Size([1, 342, 768])
+        ```
+        """
+        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
+        output_hidden_states = (
+            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
+        )
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        input_shape = self._get_input_shape(input_ids, inputs_embeds)
+        device = input_ids.device if input_ids is not None else inputs_embeds.device
+
+        visual_shape = list(input_shape)
+        visual_shape[1] = self.config.image_feature_pool_shape[0] * self.config.image_feature_pool_shape[1]
+        visual_shape = torch.Size(visual_shape)
+        # needs a new copy of input_shape for tracing. Otherwise wrong dimensions will occur
+        final_shape = list(self._get_input_shape(input_ids, inputs_embeds))
+        final_shape[1] += visual_shape[1]
+        final_shape = torch.Size(final_shape)
+
+        visual_bbox = self._calc_visual_bbox(self.config.image_feature_pool_shape, bbox, device, final_shape)
+        final_bbox = torch.cat([bbox, visual_bbox], dim=1)
+
+        if attention_mask is None:
+            attention_mask = torch.ones(input_shape, device=device)
+
+        visual_attention_mask = torch.ones(visual_shape, device=device)
+        final_attention_mask = torch.cat([attention_mask, visual_attention_mask], dim=1)
+
+        if token_type_ids is None:
+            token_type_ids = torch.zeros(input_shape, dtype=torch.long, device=device)
+
+        if position_ids is None:
+            seq_length = input_shape[1]
+            position_ids = self.embeddings.position_ids[:, :seq_length]
+            position_ids = position_ids.expand(input_shape)
+
+        visual_position_ids = torch.arange(0, visual_shape[1], dtype=torch.long, device=device).repeat(
+            input_shape[0], 1
+        )
+        final_position_ids = torch.cat([position_ids, visual_position_ids], dim=1)
+
+        if bbox is None:
+            bbox = torch.zeros(tuple(list(input_shape) + [4]), dtype=torch.long, device=device)
+
+        text_layout_emb = self._calc_text_embeddings(
+            input_ids=input_ids,
+            bbox=bbox,
+            token_type_ids=token_type_ids,
+            position_ids=position_ids,
+            inputs_embeds=inputs_embeds,
+        )
+
+        visual_emb = self._calc_img_embeddings(
+            image=image,
+            bbox=visual_bbox,
+            position_ids=visual_position_ids,
+        )
+        final_emb = torch.cat([text_layout_emb, visual_emb], dim=1)
+
+        extended_attention_mask = final_attention_mask.unsqueeze(1).unsqueeze(2)
+
+        extended_attention_mask = extended_attention_mask.to(dtype=self.dtype)
+        extended_attention_mask = (1.0 - extended_attention_mask) * torch.finfo(self.dtype).min
+
+        if head_mask is not None:
+            if head_mask.dim() == 1:
+                head_mask = head_mask.unsqueeze(0).unsqueeze(0).unsqueeze(-1).unsqueeze(-1)
+                head_mask = head_mask.expand(self.config.num_hidden_layers, -1, -1, -1, -1)
+            elif head_mask.dim() == 2:
+                head_mask = head_mask.unsqueeze(1).unsqueeze(-1).unsqueeze(-1)
+            head_mask = head_mask.to(dtype=next(self.parameters()).dtype)
+        else:
+            head_mask = [None] * self.config.num_hidden_layers
+
+        encoder_outputs = self.encoder(
+            final_emb,
+            extended_attention_mask,
+            bbox=final_bbox,
+            position_ids=final_position_ids,
+            head_mask=head_mask,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+        sequence_output = encoder_outputs[0]
+        pooled_output = self.pooler(sequence_output)
+
+        if not return_dict:
+            return (sequence_output, pooled_output) + encoder_outputs[1:]
+
+        return BaseModelOutputWithPooling(
+            last_hidden_state=sequence_output,
+            pooler_output=pooled_output,
+            hidden_states=encoder_outputs.hidden_states,
+            attentions=encoder_outputs.attentions,
+        )
+
+
+@add_start_docstrings(
+    """
+    LayoutLMv2 Model with a sequence classification head on top (a linear layer on top of the concatenation of the
+    final hidden state of the [CLS] token, average-pooled initial visual embeddings and average-pooled final visual
+    embeddings, e.g. for document image classification tasks such as the
+    [RVL-CDIP](https://www.cs.cmu.edu/~aharley/rvl-cdip/) dataset.
+    """,
+    LAYOUTLMV2_START_DOCSTRING,
+)
+class LayoutLMv2ForSequenceClassification(LayoutLMv2PreTrainedModel):
+    def __init__(self, config):
+        super().__init__(config)
+        self.num_labels = config.num_labels
+        self.layoutlmv2 = LayoutLMv2Model(config)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+        self.classifier = nn.Linear(config.hidden_size * 3, config.num_labels)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    def get_input_embeddings(self):
+        return self.layoutlmv2.embeddings.word_embeddings
+
+    @add_start_docstrings_to_model_forward(LAYOUTLMV2_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @replace_return_docstrings(output_type=SequenceClassifierOutput, config_class=_CONFIG_FOR_DOC)
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        bbox: Optional[torch.LongTensor] = None,
+        image: Optional[torch.FloatTensor] = None,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        token_type_ids: Optional[torch.LongTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        labels: Optional[torch.LongTensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple, SequenceClassifierOutput]:
+        r"""
+        labels (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
+            Labels for computing the sequence classification/regression loss. Indices should be in `[0, ...,
+            config.num_labels - 1]`. If `config.num_labels == 1` a regression loss is computed (Mean-Square loss), If
+            `config.num_labels > 1` a classification loss is computed (Cross-Entropy).
+
+        Returns:
+
+        Example:
+
+        ```python
+        >>> from transformers import AutoProcessor, LayoutLMv2ForSequenceClassification, set_seed
+        >>> from PIL import Image
+        >>> import torch
+        >>> from datasets import load_dataset
+
+        >>> set_seed(88)
+
+        >>> dataset = load_dataset("rvl_cdip", split="train", streaming=True)
+        >>> data = next(iter(dataset))
+        >>> image = data["image"].convert("RGB")
+
+        >>> processor = AutoProcessor.from_pretrained("microsoft/layoutlmv2-base-uncased")
+        >>> model = LayoutLMv2ForSequenceClassification.from_pretrained(
+        ...     "microsoft/layoutlmv2-base-uncased", num_labels=dataset.info.features["label"].num_classes
+        ... )
+
+        >>> encoding = processor(image, return_tensors="pt")
+        >>> sequence_label = torch.tensor([data["label"]])
+
+        >>> outputs = model(**encoding, labels=sequence_label)
+
+        >>> loss, logits = outputs.loss, outputs.logits
+        >>> predicted_idx = logits.argmax(dim=-1).item()
+        >>> predicted_answer = dataset.info.features["label"].names[4]
+        >>> predicted_idx, predicted_answer
+        (4, 'advertisement')
+        ```
+        """
+
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        if input_ids is not None and inputs_embeds is not None:
+            raise ValueError("You cannot specify both input_ids and inputs_embeds at the same time")
+        elif input_ids is not None:
+            self.warn_if_padding_and_no_attention_mask(input_ids, attention_mask)
+            input_shape = input_ids.size()
+        elif inputs_embeds is not None:
+            input_shape = inputs_embeds.size()[:-1]
+        else:
+            raise ValueError("You have to specify either input_ids or inputs_embeds")
+
+        device = input_ids.device if input_ids is not None else inputs_embeds.device
+
+        visual_shape = list(input_shape)
+        visual_shape[1] = self.config.image_feature_pool_shape[0] * self.config.image_feature_pool_shape[1]
+        visual_shape = torch.Size(visual_shape)
+        final_shape = list(input_shape)
+        final_shape[1] += visual_shape[1]
+        final_shape = torch.Size(final_shape)
+
+        visual_bbox = self.layoutlmv2._calc_visual_bbox(
+            self.config.image_feature_pool_shape, bbox, device, final_shape
+        )
+
+        visual_position_ids = torch.arange(0, visual_shape[1], dtype=torch.long, device=device).repeat(
+            input_shape[0], 1
+        )
+
+        initial_image_embeddings = self.layoutlmv2._calc_img_embeddings(
+            image=image,
+            bbox=visual_bbox,
+            position_ids=visual_position_ids,
+        )
+
+        outputs = self.layoutlmv2(
+            input_ids=input_ids,
+            bbox=bbox,
+            image=image,
+            attention_mask=attention_mask,
+            token_type_ids=token_type_ids,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+        if input_ids is not None:
+            input_shape = input_ids.size()
+        else:
+            input_shape = inputs_embeds.size()[:-1]
+
+        seq_length = input_shape[1]
+        sequence_output, final_image_embeddings = outputs[0][:, :seq_length], outputs[0][:, seq_length:]
+
+        cls_final_output = sequence_output[:, 0, :]
+
+        # average-pool the visual embeddings
+        pooled_initial_image_embeddings = initial_image_embeddings.mean(dim=1)
+        pooled_final_image_embeddings = final_image_embeddings.mean(dim=1)
+        # concatenate with cls_final_output
+        sequence_output = torch.cat(
+            [cls_final_output, pooled_initial_image_embeddings, pooled_final_image_embeddings], dim=1
+        )
+        sequence_output = self.dropout(sequence_output)
+        logits = self.classifier(sequence_output)
+
+        loss = None
+        if labels is not None:
+            if self.config.problem_type is None:
+                if self.num_labels == 1:
+                    self.config.problem_type = "regression"
+                elif self.num_labels > 1 and (labels.dtype == torch.long or labels.dtype == torch.int):
+                    self.config.problem_type = "single_label_classification"
+                else:
+                    self.config.problem_type = "multi_label_classification"
+
+            if self.config.problem_type == "regression":
+                loss_fct = MSELoss()
+                if self.num_labels == 1:
+                    loss = loss_fct(logits.squeeze(), labels.squeeze())
+                else:
+                    loss = loss_fct(logits, labels)
+            elif self.config.problem_type == "single_label_classification":
+                loss_fct = CrossEntropyLoss()
+                loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1))
+            elif self.config.problem_type == "multi_label_classification":
+                loss_fct = BCEWithLogitsLoss()
+                loss = loss_fct(logits, labels)
+        if not return_dict:
+            output = (logits,) + outputs[2:]
+            return ((loss,) + output) if loss is not None else output
+
+        return SequenceClassifierOutput(
+            loss=loss,
+            logits=logits,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+
+@add_start_docstrings(
+    """
+    LayoutLMv2 Model with a token classification head on top (a linear layer on top of the text part of the hidden
+    states) e.g. for sequence labeling (information extraction) tasks such as
+    [FUNSD](https://guillaumejaume.github.io/FUNSD/), [SROIE](https://rrc.cvc.uab.es/?ch=13),
+    [CORD](https://github.com/clovaai/cord) and [Kleister-NDA](https://github.com/applicaai/kleister-nda).
+    """,
+    LAYOUTLMV2_START_DOCSTRING,
+)
+class LayoutLMv2ForTokenClassification(LayoutLMv2PreTrainedModel):
+    def __init__(self, config):
+        super().__init__(config)
+        self.num_labels = config.num_labels
+        self.layoutlmv2 = LayoutLMv2Model(config)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+        self.classifier = nn.Linear(config.hidden_size, config.num_labels)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    def get_input_embeddings(self):
+        return self.layoutlmv2.embeddings.word_embeddings
+
+    @add_start_docstrings_to_model_forward(LAYOUTLMV2_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @replace_return_docstrings(output_type=TokenClassifierOutput, config_class=_CONFIG_FOR_DOC)
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        bbox: Optional[torch.LongTensor] = None,
+        image: Optional[torch.FloatTensor] = None,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        token_type_ids: Optional[torch.LongTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        labels: Optional[torch.LongTensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple, TokenClassifierOutput]:
+        r"""
+        labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Labels for computing the token classification loss. Indices should be in `[0, ..., config.num_labels - 1]`.
+
+        Returns:
+
+        Example:
+
+        ```python
+        >>> from transformers import AutoProcessor, LayoutLMv2ForTokenClassification, set_seed
+        >>> from PIL import Image
+        >>> from datasets import load_dataset
+
+        >>> set_seed(88)
+
+        >>> datasets = load_dataset("nielsr/funsd", split="test")
+        >>> labels = datasets.features["ner_tags"].feature.names
+        >>> id2label = {v: k for v, k in enumerate(labels)}
+
+        >>> processor = AutoProcessor.from_pretrained("microsoft/layoutlmv2-base-uncased", revision="no_ocr")
+        >>> model = LayoutLMv2ForTokenClassification.from_pretrained(
+        ...     "microsoft/layoutlmv2-base-uncased", num_labels=len(labels)
+        ... )
+
+        >>> data = datasets[0]
+        >>> image = Image.open(data["image_path"]).convert("RGB")
+        >>> words = data["words"]
+        >>> boxes = data["bboxes"]  # make sure to normalize your bounding boxes
+        >>> word_labels = data["ner_tags"]
+        >>> encoding = processor(
+        ...     image,
+        ...     words,
+        ...     boxes=boxes,
+        ...     word_labels=word_labels,
+        ...     padding="max_length",
+        ...     truncation=True,
+        ...     return_tensors="pt",
+        ... )
+
+        >>> outputs = model(**encoding)
+        >>> logits, loss = outputs.logits, outputs.loss
+
+        >>> predicted_token_class_ids = logits.argmax(-1)
+        >>> predicted_tokens_classes = [id2label[t.item()] for t in predicted_token_class_ids[0]]
+        >>> predicted_tokens_classes[:5]
+        ['B-ANSWER', 'B-HEADER', 'B-HEADER', 'B-HEADER', 'B-HEADER']
+        ```
+        """
+
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.layoutlmv2(
+            input_ids=input_ids,
+            bbox=bbox,
+            image=image,
+            attention_mask=attention_mask,
+            token_type_ids=token_type_ids,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+        if input_ids is not None:
+            input_shape = input_ids.size()
+        else:
+            input_shape = inputs_embeds.size()[:-1]
+
+        seq_length = input_shape[1]
+        # only take the text part of the output representations
+        sequence_output = outputs[0][:, :seq_length]
+        sequence_output = self.dropout(sequence_output)
+        logits = self.classifier(sequence_output)
+
+        loss = None
+        if labels is not None:
+            loss_fct = CrossEntropyLoss()
+            loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1))
+
+        if not return_dict:
+            output = (logits,) + outputs[2:]
+            return ((loss,) + output) if loss is not None else output
+
+        return TokenClassifierOutput(
+            loss=loss,
+            logits=logits,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+
+@add_start_docstrings(
+    """
+    LayoutLMv2 Model with a span classification head on top for extractive question-answering tasks such as
+    [DocVQA](https://rrc.cvc.uab.es/?ch=17) (a linear layer on top of the text part of the hidden-states output to
+    compute `span start logits` and `span end logits`).
+    """,
+    LAYOUTLMV2_START_DOCSTRING,
+)
+class LayoutLMv2ForQuestionAnswering(LayoutLMv2PreTrainedModel):
+    def __init__(self, config, has_visual_segment_embedding=True):
+        super().__init__(config)
+        self.num_labels = config.num_labels
+        config.has_visual_segment_embedding = has_visual_segment_embedding
+        self.layoutlmv2 = LayoutLMv2Model(config)
+        self.qa_outputs = nn.Linear(config.hidden_size, config.num_labels)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    def get_input_embeddings(self):
+        return self.layoutlmv2.embeddings.word_embeddings
+
+    @add_start_docstrings_to_model_forward(LAYOUTLMV2_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @replace_return_docstrings(output_type=QuestionAnsweringModelOutput, config_class=_CONFIG_FOR_DOC)
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        bbox: Optional[torch.LongTensor] = None,
+        image: Optional[torch.FloatTensor] = None,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        token_type_ids: Optional[torch.LongTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        start_positions: Optional[torch.LongTensor] = None,
+        end_positions: Optional[torch.LongTensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple, QuestionAnsweringModelOutput]:
+        r"""
+        start_positions (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
+            Labels for position (index) of the start of the labelled span for computing the token classification loss.
+            Positions are clamped to the length of the sequence (`sequence_length`). Position outside of the sequence
+            are not taken into account for computing the loss.
+        end_positions (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
+            Labels for position (index) of the end of the labelled span for computing the token classification loss.
+            Positions are clamped to the length of the sequence (`sequence_length`). Position outside of the sequence
+            are not taken into account for computing the loss.
+
+        Returns:
+
+        Example:
+
+        In this example below, we give the LayoutLMv2 model an image (of texts) and ask it a question. It will give us
+        a prediction of what it thinks the answer is (the span of the answer within the texts parsed from the image).
+
+        ```python
+        >>> from transformers import AutoProcessor, LayoutLMv2ForQuestionAnswering, set_seed
+        >>> import torch
+        >>> from PIL import Image
+        >>> from datasets import load_dataset
+
+        >>> set_seed(88)
+        >>> processor = AutoProcessor.from_pretrained("microsoft/layoutlmv2-base-uncased")
+        >>> model = LayoutLMv2ForQuestionAnswering.from_pretrained("microsoft/layoutlmv2-base-uncased")
+
+        >>> dataset = load_dataset("hf-internal-testing/fixtures_docvqa")
+        >>> image_path = dataset["test"][0]["file"]
+        >>> image = Image.open(image_path).convert("RGB")
+        >>> question = "When is coffee break?"
+        >>> encoding = processor(image, question, return_tensors="pt")
+
+        >>> outputs = model(**encoding)
+        >>> predicted_start_idx = outputs.start_logits.argmax(-1).item()
+        >>> predicted_end_idx = outputs.end_logits.argmax(-1).item()
+        >>> predicted_start_idx, predicted_end_idx
+        (154, 287)
+
+        >>> predicted_answer_tokens = encoding.input_ids.squeeze()[predicted_start_idx : predicted_end_idx + 1]
+        >>> predicted_answer = processor.tokenizer.decode(predicted_answer_tokens)
+        >>> predicted_answer  # results are not very good without further fine-tuning
+        'council mem - bers conducted by trrf treasurer philip g. kuehn to get answers which the public ...
+        ```
+
+        ```python
+        >>> target_start_index = torch.tensor([7])
+        >>> target_end_index = torch.tensor([14])
+        >>> outputs = model(**encoding, start_positions=target_start_index, end_positions=target_end_index)
+        >>> predicted_answer_span_start = outputs.start_logits.argmax(-1).item()
+        >>> predicted_answer_span_end = outputs.end_logits.argmax(-1).item()
+        >>> predicted_answer_span_start, predicted_answer_span_end
+        (154, 287)
+        ```
+        """
+
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.layoutlmv2(
+            input_ids=input_ids,
+            bbox=bbox,
+            image=image,
+            attention_mask=attention_mask,
+            token_type_ids=token_type_ids,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        if input_ids is not None:
+            input_shape = input_ids.size()
+        else:
+            input_shape = inputs_embeds.size()[:-1]
+
+        seq_length = input_shape[1]
+        # only take the text part of the output representations
+        sequence_output = outputs[0][:, :seq_length]
+
+        logits = self.qa_outputs(sequence_output)
+        start_logits, end_logits = logits.split(1, dim=-1)
+        start_logits = start_logits.squeeze(-1).contiguous()
+        end_logits = end_logits.squeeze(-1).contiguous()
+
+        total_loss = None
+        if start_positions is not None and end_positions is not None:
+            # If we are on multi-GPU, split add a dimension
+            if len(start_positions.size()) > 1:
+                start_positions = start_positions.squeeze(-1)
+            if len(end_positions.size()) > 1:
+                end_positions = end_positions.squeeze(-1)
+            # sometimes the start/end positions are outside our model inputs, we ignore these terms
+            ignored_index = start_logits.size(1)
+            start_positions = start_positions.clamp(0, ignored_index)
+            end_positions = end_positions.clamp(0, ignored_index)
+
+            loss_fct = CrossEntropyLoss(ignore_index=ignored_index)
+            start_loss = loss_fct(start_logits, start_positions)
+            end_loss = loss_fct(end_logits, end_positions)
+            total_loss = (start_loss + end_loss) / 2
+
+        if not return_dict:
+            output = (start_logits, end_logits) + outputs[2:]
+            return ((total_loss,) + output) if total_loss is not None else output
+
+        return QuestionAnsweringModelOutput(
+            loss=total_loss,
+            start_logits=start_logits,
+            end_logits=end_logits,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )

llmeval-env/lib/python3.10/site-packages/transformers/models/layoutlmv2/processing_layoutlmv2.py

@@ -0,0 +1,201 @@
+# coding=utf-8
+# Copyright 2021 The HuggingFace Inc. team.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+Processor class for LayoutLMv2.
+"""
+
+import warnings
+from typing import List, Optional, Union
+
+from ...processing_utils import ProcessorMixin
+from ...tokenization_utils_base import BatchEncoding, PaddingStrategy, PreTokenizedInput, TextInput, TruncationStrategy
+from ...utils import TensorType
+
+
+class LayoutLMv2Processor(ProcessorMixin):
+    r"""
+    Constructs a LayoutLMv2 processor which combines a LayoutLMv2 image processor and a LayoutLMv2 tokenizer into a
+    single processor.
+
+    [`LayoutLMv2Processor`] offers all the functionalities you need to prepare data for the model.
+
+    It first uses [`LayoutLMv2ImageProcessor`] to resize document images to a fixed size, and optionally applies OCR to
+    get words and normalized bounding boxes. These are then provided to [`LayoutLMv2Tokenizer`] or
+    [`LayoutLMv2TokenizerFast`], which turns the words and bounding boxes into token-level `input_ids`,
+    `attention_mask`, `token_type_ids`, `bbox`. Optionally, one can provide integer `word_labels`, which are turned
+    into token-level `labels` for token classification tasks (such as FUNSD, CORD).
+
+    Args:
+        image_processor (`LayoutLMv2ImageProcessor`, *optional*):
+            An instance of [`LayoutLMv2ImageProcessor`]. The image processor is a required input.
+        tokenizer (`LayoutLMv2Tokenizer` or `LayoutLMv2TokenizerFast`, *optional*):
+            An instance of [`LayoutLMv2Tokenizer`] or [`LayoutLMv2TokenizerFast`]. The tokenizer is a required input.
+    """
+
+    attributes = ["image_processor", "tokenizer"]
+    image_processor_class = "LayoutLMv2ImageProcessor"
+    tokenizer_class = ("LayoutLMv2Tokenizer", "LayoutLMv2TokenizerFast")
+
+    def __init__(self, image_processor=None, tokenizer=None, **kwargs):
+        feature_extractor = None
+        if "feature_extractor" in kwargs:
+            warnings.warn(
+                "The `feature_extractor` argument is deprecated and will be removed in v5, use `image_processor`"
+                " instead.",
+                FutureWarning,
+            )
+            feature_extractor = kwargs.pop("feature_extractor")
+
+        image_processor = image_processor if image_processor is not None else feature_extractor
+        if image_processor is None:
+            raise ValueError("You need to specify an `image_processor`.")
+        if tokenizer is None:
+            raise ValueError("You need to specify a `tokenizer`.")
+
+        super().__init__(image_processor, tokenizer)
+
+    def __call__(
+        self,
+        images,
+        text: Union[TextInput, PreTokenizedInput, List[TextInput], List[PreTokenizedInput]] = None,
+        text_pair: Optional[Union[PreTokenizedInput, List[PreTokenizedInput]]] = None,
+        boxes: Union[List[List[int]], List[List[List[int]]]] = None,
+        word_labels: Optional[Union[List[int], List[List[int]]]] = None,
+        add_special_tokens: bool = True,
+        padding: Union[bool, str, PaddingStrategy] = False,
+        truncation: Union[bool, str, TruncationStrategy] = False,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+        return_tensors: Optional[Union[str, TensorType]] = None,
+        **kwargs,
+    ) -> BatchEncoding:
+        """
+        This method first forwards the `images` argument to [`~LayoutLMv2ImageProcessor.__call__`]. In case
+        [`LayoutLMv2ImageProcessor`] was initialized with `apply_ocr` set to `True`, it passes the obtained words and
+        bounding boxes along with the additional arguments to [`~LayoutLMv2Tokenizer.__call__`] and returns the output,
+        together with resized `images`. In case [`LayoutLMv2ImageProcessor`] was initialized with `apply_ocr` set to
+        `False`, it passes the words (`text`/``text_pair`) and `boxes` specified by the user along with the additional
+        arguments to [`~LayoutLMv2Tokenizer.__call__`] and returns the output, together with resized `images``.
+
+        Please refer to the docstring of the above two methods for more information.
+        """
+        # verify input
+        if self.image_processor.apply_ocr and (boxes is not None):
+            raise ValueError(
+                "You cannot provide bounding boxes if you initialized the image processor with apply_ocr set to True."
+            )
+
+        if self.image_processor.apply_ocr and (word_labels is not None):
+            raise ValueError(
+                "You cannot provide word labels if you initialized the image processor with apply_ocr set to True."
+            )
+
+        if return_overflowing_tokens is True and return_offsets_mapping is False:
+            raise ValueError("You cannot return overflowing tokens without returning the offsets mapping.")
+
+        # first, apply the image processor
+        features = self.image_processor(images=images, return_tensors=return_tensors)
+
+        # second, apply the tokenizer
+        if text is not None and self.image_processor.apply_ocr and text_pair is None:
+            if isinstance(text, str):
+                text = [text]  # add batch dimension (as the image processor always adds a batch dimension)
+            text_pair = features["words"]
+
+        encoded_inputs = self.tokenizer(
+            text=text if text is not None else features["words"],
+            text_pair=text_pair if text_pair is not None else None,
+            boxes=boxes if boxes is not None else features["boxes"],
+            word_labels=word_labels,
+            add_special_tokens=add_special_tokens,
+            padding=padding,
+            truncation=truncation,
+            max_length=max_length,
+            stride=stride,
+            pad_to_multiple_of=pad_to_multiple_of,
+            return_token_type_ids=return_token_type_ids,
+            return_attention_mask=return_attention_mask,
+            return_overflowing_tokens=return_overflowing_tokens,
+            return_special_tokens_mask=return_special_tokens_mask,
+            return_offsets_mapping=return_offsets_mapping,
+            return_length=return_length,
+            verbose=verbose,
+            return_tensors=return_tensors,
+            **kwargs,
+        )
+
+        # add pixel values
+        images = features.pop("pixel_values")
+        if return_overflowing_tokens is True:
+            images = self.get_overflowing_images(images, encoded_inputs["overflow_to_sample_mapping"])
+        encoded_inputs["image"] = images
+
+        return encoded_inputs
+
+    def get_overflowing_images(self, images, overflow_to_sample_mapping):
+        # in case there's an overflow, ensure each `input_ids` sample is mapped to its corresponding image
+        images_with_overflow = []
+        for sample_idx in overflow_to_sample_mapping:
+            images_with_overflow.append(images[sample_idx])
+
+        if len(images_with_overflow) != len(overflow_to_sample_mapping):
+            raise ValueError(
+                "Expected length of images to be the same as the length of `overflow_to_sample_mapping`, but got"
+                f" {len(images_with_overflow)} and {len(overflow_to_sample_mapping)}"
+            )
+
+        return images_with_overflow
+
+    def batch_decode(self, *args, **kwargs):
+        """
+        This method forwards all its arguments to PreTrainedTokenizer's [`~PreTrainedTokenizer.batch_decode`]. Please
+        refer to the docstring of this method for more information.
+        """
+        return self.tokenizer.batch_decode(*args, **kwargs)
+
+    def decode(self, *args, **kwargs):
+        """
+        This method forwards all its arguments to PreTrainedTokenizer's [`~PreTrainedTokenizer.decode`]. Please refer
+        to the docstring of this method for more information.
+        """
+        return self.tokenizer.decode(*args, **kwargs)
+
+    @property
+    def model_input_names(self):
+        return ["input_ids", "bbox", "token_type_ids", "attention_mask", "image"]
+
+    @property
+    def feature_extractor_class(self):
+        warnings.warn(
+            "`feature_extractor_class` is deprecated and will be removed in v5. Use `image_processor_class` instead.",
+            FutureWarning,
+        )
+        return self.image_processor_class
+
+    @property
+    def feature_extractor(self):
+        warnings.warn(
+            "`feature_extractor` is deprecated and will be removed in v5. Use `image_processor` instead.",
+            FutureWarning,
+        )
+        return self.image_processor

llmeval-env/lib/python3.10/site-packages/transformers/models/layoutlmv2/tokenization_layoutlmv2.py

@@ -0,0 +1,1542 @@
+# coding=utf-8
+# Copyright Microsoft Research and The HuggingFace Inc. team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Tokenization class for LayoutLMv2."""
+
+import collections
+import os
+import sys
+import unicodedata
+from typing import Dict, List, Optional, Tuple, Union
+
+from ...tokenization_utils import AddedToken, PreTrainedTokenizer, _is_control, _is_punctuation, _is_whitespace
+from ...tokenization_utils_base import (
+    BatchEncoding,
+    EncodedInput,
+    PreTokenizedInput,
+    TextInput,
+    TextInputPair,
+    TruncationStrategy,
+)
+from ...utils import PaddingStrategy, TensorType, add_end_docstrings, logging
+
+
+logger = logging.get_logger(__name__)
+
+VOCAB_FILES_NAMES = {"vocab_file": "vocab.txt"}
+
+
+LAYOUTLMV2_ENCODE_KWARGS_DOCSTRING = r"""
+            add_special_tokens (`bool`, *optional*, defaults to `True`):
+                Whether or not to encode the sequences with the special tokens relative to their model.
+            padding (`bool`, `str` or [`~file_utils.PaddingStrategy`], *optional*, defaults to `False`):
+                Activates and controls padding. Accepts the following values:
+
+                - `True` or `'longest'`: Pad to the longest sequence in the batch (or no padding if only a single
+                  sequence if provided).
+                - `'max_length'`: Pad to a maximum length specified with the argument `max_length` or to the maximum
+                  acceptable input length for the model if that argument is not provided.
+                - `False` or `'do_not_pad'` (default): No padding (i.e., can output a batch with sequences of different
+                  lengths).
+            truncation (`bool`, `str` or [`~tokenization_utils_base.TruncationStrategy`], *optional*, defaults to `False`):
+                Activates and controls truncation. Accepts the following values:
+
+                - `True` or `'longest_first'`: Truncate to a maximum length specified with the argument `max_length` or
+                  to the maximum acceptable input length for the model if that argument is not provided. This will
+                  truncate token by token, removing a token from the longest sequence in the pair if a pair of
+                  sequences (or a batch of pairs) is provided.
+                - `'only_first'`: Truncate to a maximum length specified with the argument `max_length` or to the
+                  maximum acceptable input length for the model if that argument is not provided. This will only
+                  truncate the first sequence of a pair if a pair of sequences (or a batch of pairs) is provided.
+                - `'only_second'`: Truncate to a maximum length specified with the argument `max_length` or to the
+                  maximum acceptable input length for the model if that argument is not provided. This will only
+                  truncate the second sequence of a pair if a pair of sequences (or a batch of pairs) is provided.
+                - `False` or `'do_not_truncate'` (default): No truncation (i.e., can output batch with sequence lengths
+                  greater than the model maximum admissible input size).
+            max_length (`int`, *optional*):
+                Controls the maximum length to use by one of the truncation/padding parameters.
+
+                If left unset or set to `None`, this will use the predefined model maximum length if a maximum length
+                is required by one of the truncation/padding parameters. If the model has no specific maximum input
+                length (like XLNet) truncation/padding to a maximum length will be deactivated.
+            stride (`int`, *optional*, defaults to 0):
+                If set to a number along with `max_length`, the overflowing tokens returned when
+                `return_overflowing_tokens=True` will contain some tokens from the end of the truncated sequence
+                returned to provide some overlap between truncated and overflowing sequences. The value of this
+                argument defines the number of overlapping tokens.
+            pad_to_multiple_of (`int`, *optional*):
+                If set will pad the sequence to a multiple of the provided value. This is especially useful to enable
+                the use of Tensor Cores on NVIDIA hardware with compute capability `>= 7.5` (Volta).
+            return_tensors (`str` or [`~file_utils.TensorType`], *optional*):
+                If set, will return tensors instead of list of python integers. Acceptable values are:
+
+                - `'tf'`: Return TensorFlow `tf.constant` objects.
+                - `'pt'`: Return PyTorch `torch.Tensor` objects.
+                - `'np'`: Return Numpy `np.ndarray` objects.
+"""
+
+LAYOUTLMV2_ENCODE_PLUS_ADDITIONAL_KWARGS_DOCSTRING = r"""
+            return_token_type_ids (`bool`, *optional*):
+                Whether to return token type IDs. If left to the default, will return the token type IDs according to
+                the specific tokenizer's default, defined by the `return_outputs` attribute.
+
+                [What are token type IDs?](../glossary#token-type-ids)
+            return_attention_mask (`bool`, *optional*):
+                Whether to return the attention mask. If left to the default, will return the attention mask according
+                to the specific tokenizer's default, defined by the `return_outputs` attribute.
+
+                [What are attention masks?](../glossary#attention-mask)
+            return_overflowing_tokens (`bool`, *optional*, defaults to `False`):
+                Whether or not to return overflowing token sequences. If a pair of sequences of input ids (or a batch
+                of pairs) is provided with `truncation_strategy = longest_first` or `True`, an error is raised instead
+                of returning overflowing tokens.
+            return_special_tokens_mask (`bool`, *optional*, defaults to `False`):
+                Whether or not to return special tokens mask information.
+            return_offsets_mapping (`bool`, *optional*, defaults to `False`):
+                Whether or not to return `(char_start, char_end)` for each token.
+
+                This is only available on fast tokenizers inheriting from [`PreTrainedTokenizerFast`], if using
+                Python's tokenizer, this method will raise `NotImplementedError`.
+            return_length  (`bool`, *optional*, defaults to `False`):
+                Whether or not to return the lengths of the encoded inputs.
+            verbose (`bool`, *optional*, defaults to `True`):
+                Whether or not to print more information and warnings.
+            **kwargs: passed to the `self.tokenize()` method
+
+        Return:
+            [`BatchEncoding`]: A [`BatchEncoding`] with the following fields:
+
+            - **input_ids** -- List of token ids to be fed to a model.
+
+              [What are input IDs?](../glossary#input-ids)
+
+            - **bbox** -- List of bounding boxes to be fed to a model.
+
+            - **token_type_ids** -- List of token type ids to be fed to a model (when `return_token_type_ids=True` or
+              if *"token_type_ids"* is in `self.model_input_names`).
+
+              [What are token type IDs?](../glossary#token-type-ids)
+
+            - **attention_mask** -- List of indices specifying which tokens should be attended to by the model (when
+              `return_attention_mask=True` or if *"attention_mask"* is in `self.model_input_names`).
+
+              [What are attention masks?](../glossary#attention-mask)
+
+            - **labels** -- List of labels to be fed to a model. (when `word_labels` is specified).
+            - **overflowing_tokens** -- List of overflowing tokens sequences (when a `max_length` is specified and
+              `return_overflowing_tokens=True`).
+            - **num_truncated_tokens** -- Number of tokens truncated (when a `max_length` is specified and
+              `return_overflowing_tokens=True`).
+            - **special_tokens_mask** -- List of 0s and 1s, with 1 specifying added special tokens and 0 specifying
+              regular sequence tokens (when `add_special_tokens=True` and `return_special_tokens_mask=True`).
+            - **length** -- The length of the inputs (when `return_length=True`).
+"""
+
+
+def load_vocab(vocab_file):
+    """Loads a vocabulary file into a dictionary."""
+    vocab = collections.OrderedDict()
+    with open(vocab_file, "r", encoding="utf-8") as reader:
+        tokens = reader.readlines()
+    for index, token in enumerate(tokens):
+        token = token.rstrip("\n")
+        vocab[token] = index
+    return vocab
+
+
+def whitespace_tokenize(text):
+    """Runs basic whitespace cleaning and splitting on a piece of text."""
+    text = text.strip()
+    if not text:
+        return []
+    tokens = text.split()
+    return tokens
+
+
+table = dict.fromkeys(i for i in range(sys.maxunicode) if unicodedata.category(chr(i)).startswith("P"))
+
+
+def subfinder(mylist, pattern):
+    matches = []
+    indices = []
+    for idx, i in enumerate(range(len(mylist))):
+        if mylist[i] == pattern[0] and mylist[i : i + len(pattern)] == pattern:
+            matches.append(pattern)
+            indices.append(idx)
+    if matches:
+        return matches[0], indices[0]
+    else:
+        return None, 0
+
+
+class LayoutLMv2Tokenizer(PreTrainedTokenizer):
+    r"""
+    Construct a LayoutLMv2 tokenizer. Based on WordPiece. [`LayoutLMv2Tokenizer`] can be used to turn words, word-level
+    bounding boxes and optional word labels to token-level `input_ids`, `attention_mask`, `token_type_ids`, `bbox`, and
+    optional `labels` (for token classification).
+
+    This tokenizer inherits from [`PreTrainedTokenizer`] which contains most of the main methods. Users should refer to
+    this superclass for more information regarding those methods.
+
+    [`LayoutLMv2Tokenizer`] runs end-to-end tokenization: punctuation splitting and wordpiece. It also turns the
+    word-level bounding boxes into token-level bounding boxes.
+
+    """
+
+    vocab_files_names = VOCAB_FILES_NAMES
+
+    def __init__(
+        self,
+        vocab_file,
+        do_lower_case=True,
+        do_basic_tokenize=True,
+        never_split=None,
+        unk_token="[UNK]",
+        sep_token="[SEP]",
+        pad_token="[PAD]",
+        cls_token="[CLS]",
+        mask_token="[MASK]",
+        cls_token_box=[0, 0, 0, 0],
+        sep_token_box=[1000, 1000, 1000, 1000],
+        pad_token_box=[0, 0, 0, 0],
+        pad_token_label=-100,
+        only_label_first_subword=True,
+        tokenize_chinese_chars=True,
+        strip_accents=None,
+        model_max_length: int = 512,
+        additional_special_tokens: Optional[List[str]] = None,
+        **kwargs,
+    ):
+        sep_token = AddedToken(sep_token, special=True) if isinstance(sep_token, str) else sep_token
+        unk_token = AddedToken(unk_token, special=True) if isinstance(unk_token, str) else unk_token
+        pad_token = AddedToken(pad_token, special=True) if isinstance(pad_token, str) else pad_token
+        cls_token = AddedToken(cls_token, special=True) if isinstance(cls_token, str) else cls_token
+        mask_token = AddedToken(mask_token, special=True) if isinstance(mask_token, str) else mask_token
+
+        if not os.path.isfile(vocab_file):
+            raise ValueError(
+                f"Can't find a vocabulary file at path '{vocab_file}'. To load the vocabulary from a Google pretrained"
+                " model use `tokenizer = BertTokenizer.from_pretrained(PRETRAINED_MODEL_NAME)`"
+            )
+        self.vocab = load_vocab(vocab_file)
+        self.ids_to_tokens = collections.OrderedDict([(ids, tok) for tok, ids in self.vocab.items()])
+        self.do_basic_tokenize = do_basic_tokenize
+        if do_basic_tokenize:
+            self.basic_tokenizer = BasicTokenizer(
+                do_lower_case=do_lower_case,
+                never_split=never_split,
+                tokenize_chinese_chars=tokenize_chinese_chars,
+                strip_accents=strip_accents,
+            )
+        self.wordpiece_tokenizer = WordpieceTokenizer(vocab=self.vocab, unk_token=str(unk_token))
+
+        # additional properties
+        self.cls_token_box = cls_token_box
+        self.sep_token_box = sep_token_box
+        self.pad_token_box = pad_token_box
+        self.pad_token_label = pad_token_label
+        self.only_label_first_subword = only_label_first_subword
+        super().__init__(
+            do_lower_case=do_lower_case,
+            do_basic_tokenize=do_basic_tokenize,
+            never_split=never_split,
+            unk_token=unk_token,
+            sep_token=sep_token,
+            pad_token=pad_token,
+            cls_token=cls_token,
+            mask_token=mask_token,
+            cls_token_box=cls_token_box,
+            sep_token_box=sep_token_box,
+            pad_token_box=pad_token_box,
+            pad_token_label=pad_token_label,
+            only_label_first_subword=only_label_first_subword,
+            tokenize_chinese_chars=tokenize_chinese_chars,
+            strip_accents=strip_accents,
+            model_max_length=model_max_length,
+            additional_special_tokens=additional_special_tokens,
+            **kwargs,
+        )
+
+    @property
+    def do_lower_case(self):
+        return self.basic_tokenizer.do_lower_case
+
+    @property
+    def vocab_size(self):
+        return len(self.vocab)
+
+    def get_vocab(self):
+        return dict(self.vocab, **self.added_tokens_encoder)
+
+    def _tokenize(self, text):
+        split_tokens = []
+        if self.do_basic_tokenize:
+            for token in self.basic_tokenizer.tokenize(text, never_split=self.all_special_tokens):
+                # If the token is part of the never_split set
+                if token in self.basic_tokenizer.never_split:
+                    split_tokens.append(token)
+                else:
+                    split_tokens += self.wordpiece_tokenizer.tokenize(token)
+        else:
+            split_tokens = self.wordpiece_tokenizer.tokenize(text)
+        return split_tokens
+
+    def _convert_token_to_id(self, token):
+        """Converts a token (str) in an id using the vocab."""
+        return self.vocab.get(token, self.vocab.get(self.unk_token))
+
+    def _convert_id_to_token(self, index):
+        """Converts an index (integer) in a token (str) using the vocab."""
+        return self.ids_to_tokens.get(index, self.unk_token)
+
+    def convert_tokens_to_string(self, tokens):
+        """Converts a sequence of tokens (string) in a single string."""
+        out_string = " ".join(tokens).replace(" ##", "").strip()
+        return out_string
+
+    def build_inputs_with_special_tokens(
+        self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None
+    ) -> List[int]:
+        """
+        Build model inputs from a sequence or a pair of sequence for sequence classification tasks by concatenating and
+        adding special tokens. A BERT sequence has the following format:
+
+        - single sequence: `[CLS] X [SEP]`
+        - pair of sequences: `[CLS] A [SEP] B [SEP]`
+
+        Args:
+            token_ids_0 (`List[int]`):
+                List of IDs to which the special tokens will be added.
+            token_ids_1 (`List[int]`, *optional*):
+                Optional second list of IDs for sequence pairs.
+
+        Returns:
+            `List[int]`: List of [input IDs](../glossary#input-ids) with the appropriate special tokens.
+        """
+        if token_ids_1 is None:
+            return [self.cls_token_id] + token_ids_0 + [self.sep_token_id]
+        cls = [self.cls_token_id]
+        sep = [self.sep_token_id]
+        return cls + token_ids_0 + sep + token_ids_1 + sep
+
+    def get_special_tokens_mask(
+        self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None, already_has_special_tokens: bool = False
+    ) -> List[int]:
+        """
+        Retrieve sequence ids from a token list that has no special tokens added. This method is called when adding
+        special tokens using the tokenizer `prepare_for_model` method.
+
+        Args:
+            token_ids_0 (`List[int]`):
+                List of IDs.
+            token_ids_1 (`List[int]`, *optional*):
+                Optional second list of IDs for sequence pairs.
+            already_has_special_tokens (`bool`, *optional*, defaults to `False`):
+                Whether or not the token list is already formatted with special tokens for the model.
+
+        Returns:
+            `List[int]`: A list of integers in the range [0, 1]: 1 for a special token, 0 for a sequence token.
+        """
+
+        if already_has_special_tokens:
+            return super().get_special_tokens_mask(
+                token_ids_0=token_ids_0, token_ids_1=token_ids_1, already_has_special_tokens=True
+            )
+
+        if token_ids_1 is not None:
+            return [1] + ([0] * len(token_ids_0)) + [1] + ([0] * len(token_ids_1)) + [1]
+        return [1] + ([0] * len(token_ids_0)) + [1]
+
+    def create_token_type_ids_from_sequences(
+        self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None
+    ) -> List[int]:
+        """
+        Create a mask from the two sequences passed to be used in a sequence-pair classification task. A BERT sequence
+        pair mask has the following format: :: 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 | first sequence | second
+        sequence | If `token_ids_1` is `None`, this method only returns the first portion of the mask (0s).
+
+        Args:
+            token_ids_0 (`List[int]`):
+                List of IDs.
+            token_ids_1 (`List[int]`, *optional*):
+                Optional second list of IDs for sequence pairs.
+
+        Returns:
+            `List[int]`: List of [token type IDs](../glossary#token-type-ids) according to the given sequence(s).
+        """
+        sep = [self.sep_token_id]
+        cls = [self.cls_token_id]
+        if token_ids_1 is None:
+            return len(cls + token_ids_0 + sep) * [0]
+        return len(cls + token_ids_0 + sep) * [0] + len(token_ids_1 + sep) * [1]
+
+    def save_vocabulary(self, save_directory: str, filename_prefix: Optional[str] = None) -> Tuple[str]:
+        index = 0
+        if os.path.isdir(save_directory):
+            vocab_file = os.path.join(
+                save_directory, (filename_prefix + "-" if filename_prefix else "") + VOCAB_FILES_NAMES["vocab_file"]
+            )
+        else:
+            vocab_file = (filename_prefix + "-" if filename_prefix else "") + save_directory
+        with open(vocab_file, "w", encoding="utf-8") as writer:
+            for token, token_index in sorted(self.vocab.items(), key=lambda kv: kv[1]):
+                if index != token_index:
+                    logger.warning(
+                        f"Saving vocabulary to {vocab_file}: vocabulary indices are not consecutive."
+                        " Please check that the vocabulary is not corrupted!"
+                    )
+                    index = token_index
+                writer.write(token + "\n")
+                index += 1
+        return (vocab_file,)
+
+    @add_end_docstrings(LAYOUTLMV2_ENCODE_KWARGS_DOCSTRING, LAYOUTLMV2_ENCODE_PLUS_ADDITIONAL_KWARGS_DOCSTRING)
+    def __call__(
+        self,
+        text: Union[TextInput, PreTokenizedInput, List[TextInput], List[PreTokenizedInput]],
+        text_pair: Optional[Union[PreTokenizedInput, List[PreTokenizedInput]]] = None,
+        boxes: Union[List[List[int]], List[List[List[int]]]] = None,
+        word_labels: Optional[Union[List[int], List[List[int]]]] = None,
+        add_special_tokens: bool = True,
+        padding: Union[bool, str, PaddingStrategy] = False,
+        truncation: Union[bool, str, TruncationStrategy] = None,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[Union[str, TensorType]] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+        **kwargs,
+    ) -> BatchEncoding:
+        """
+        Main method to tokenize and prepare for the model one or several sequence(s) or one or several pair(s) of
+        sequences with word-level normalized bounding boxes and optional labels.
+
+        Args:
+            text (`str`, `List[str]`, `List[List[str]]`):
+                The sequence or batch of sequences to be encoded. Each sequence can be a string, a list of strings
+                (words of a single example or questions of a batch of examples) or a list of list of strings (batch of
+                words).
+            text_pair (`List[str]`, `List[List[str]]`):
+                The sequence or batch of sequences to be encoded. Each sequence should be a list of strings
+                (pretokenized string).
+            boxes (`List[List[int]]`, `List[List[List[int]]]`):
+                Word-level bounding boxes. Each bounding box should be normalized to be on a 0-1000 scale.
+            word_labels (`List[int]`, `List[List[int]]`, *optional*):
+                Word-level integer labels (for token classification tasks such as FUNSD, CORD).
+        """
+
+        # Input type checking for clearer error
+        def _is_valid_text_input(t):
+            if isinstance(t, str):
+                # Strings are fine
+                return True
+            elif isinstance(t, (list, tuple)):
+                # List are fine as long as they are...
+                if len(t) == 0:
+                    # ... empty
+                    return True
+                elif isinstance(t[0], str):
+                    # ... list of strings
+                    return True
+                elif isinstance(t[0], (list, tuple)):
+                    # ... list with an empty list or with a list of strings
+                    return len(t[0]) == 0 or isinstance(t[0][0], str)
+                else:
+                    return False
+            else:
+                return False
+
+        if text_pair is not None:
+            # in case text + text_pair are provided, text = questions, text_pair = words
+            if not _is_valid_text_input(text):
+                raise ValueError("text input must of type `str` (single example) or `List[str]` (batch of examples). ")
+            if not isinstance(text_pair, (list, tuple)):
+                raise ValueError(
+                    "Words must be of type `List[str]` (single pretokenized example), "
+                    "or `List[List[str]]` (batch of pretokenized examples)."
+                )
+        else:
+            # in case only text is provided => must be words
+            if not isinstance(text, (list, tuple)):
+                raise ValueError(
+                    "Words must be of type `List[str]` (single pretokenized example), "
+                    "or `List[List[str]]` (batch of pretokenized examples)."
+                )
+
+        if text_pair is not None:
+            is_batched = isinstance(text, (list, tuple))
+        else:
+            is_batched = isinstance(text, (list, tuple)) and text and isinstance(text[0], (list, tuple))
+
+        words = text if text_pair is None else text_pair
+        if boxes is None:
+            raise ValueError("You must provide corresponding bounding boxes")
+        if is_batched:
+            if len(words) != len(boxes):
+                raise ValueError("You must provide words and boxes for an equal amount of examples")
+            for words_example, boxes_example in zip(words, boxes):
+                if len(words_example) != len(boxes_example):
+                    raise ValueError("You must provide as many words as there are bounding boxes")
+        else:
+            if len(words) != len(boxes):
+                raise ValueError("You must provide as many words as there are bounding boxes")
+
+        if is_batched:
+            if text_pair is not None and len(text) != len(text_pair):
+                raise ValueError(
+                    f"batch length of `text`: {len(text)} does not match batch length of `text_pair`:"
+                    f" {len(text_pair)}."
+                )
+            batch_text_or_text_pairs = list(zip(text, text_pair)) if text_pair is not None else text
+            is_pair = bool(text_pair is not None)
+            return self.batch_encode_plus(
+                batch_text_or_text_pairs=batch_text_or_text_pairs,
+                is_pair=is_pair,
+                boxes=boxes,
+                word_labels=word_labels,
+                add_special_tokens=add_special_tokens,
+                padding=padding,
+                truncation=truncation,
+                max_length=max_length,
+                stride=stride,
+                pad_to_multiple_of=pad_to_multiple_of,
+                return_tensors=return_tensors,
+                return_token_type_ids=return_token_type_ids,
+                return_attention_mask=return_attention_mask,
+                return_overflowing_tokens=return_overflowing_tokens,
+                return_special_tokens_mask=return_special_tokens_mask,
+                return_offsets_mapping=return_offsets_mapping,
+                return_length=return_length,
+                verbose=verbose,
+                **kwargs,
+            )
+        else:
+            return self.encode_plus(
+                text=text,
+                text_pair=text_pair,
+                boxes=boxes,
+                word_labels=word_labels,
+                add_special_tokens=add_special_tokens,
+                padding=padding,
+                truncation=truncation,
+                max_length=max_length,
+                stride=stride,
+                pad_to_multiple_of=pad_to_multiple_of,
+                return_tensors=return_tensors,
+                return_token_type_ids=return_token_type_ids,
+                return_attention_mask=return_attention_mask,
+                return_overflowing_tokens=return_overflowing_tokens,
+                return_special_tokens_mask=return_special_tokens_mask,
+                return_offsets_mapping=return_offsets_mapping,
+                return_length=return_length,
+                verbose=verbose,
+                **kwargs,
+            )
+
+    @add_end_docstrings(LAYOUTLMV2_ENCODE_KWARGS_DOCSTRING, LAYOUTLMV2_ENCODE_PLUS_ADDITIONAL_KWARGS_DOCSTRING)
+    def batch_encode_plus(
+        self,
+        batch_text_or_text_pairs: Union[
+            List[TextInput],
+            List[TextInputPair],
+            List[PreTokenizedInput],
+        ],
+        is_pair: bool = None,
+        boxes: Optional[List[List[List[int]]]] = None,
+        word_labels: Optional[Union[List[int], List[List[int]]]] = None,
+        add_special_tokens: bool = True,
+        padding: Union[bool, str, PaddingStrategy] = False,
+        truncation: Union[bool, str, TruncationStrategy] = None,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[Union[str, TensorType]] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+        **kwargs,
+    ) -> BatchEncoding:
+        # Backward compatibility for 'truncation_strategy', 'pad_to_max_length'
+        padding_strategy, truncation_strategy, max_length, kwargs = self._get_padding_truncation_strategies(
+            padding=padding,
+            truncation=truncation,
+            max_length=max_length,
+            pad_to_multiple_of=pad_to_multiple_of,
+            verbose=verbose,
+            **kwargs,
+        )
+
+        return self._batch_encode_plus(
+            batch_text_or_text_pairs=batch_text_or_text_pairs,
+            is_pair=is_pair,
+            boxes=boxes,
+            word_labels=word_labels,
+            add_special_tokens=add_special_tokens,
+            padding_strategy=padding_strategy,
+            truncation_strategy=truncation_strategy,
+            max_length=max_length,
+            stride=stride,
+            pad_to_multiple_of=pad_to_multiple_of,
+            return_tensors=return_tensors,
+            return_token_type_ids=return_token_type_ids,
+            return_attention_mask=return_attention_mask,
+            return_overflowing_tokens=return_overflowing_tokens,
+            return_special_tokens_mask=return_special_tokens_mask,
+            return_offsets_mapping=return_offsets_mapping,
+            return_length=return_length,
+            verbose=verbose,
+            **kwargs,
+        )
+
+    def _batch_encode_plus(
+        self,
+        batch_text_or_text_pairs: Union[
+            List[TextInput],
+            List[TextInputPair],
+            List[PreTokenizedInput],
+        ],
+        is_pair: bool = None,
+        boxes: Optional[List[List[List[int]]]] = None,
+        word_labels: Optional[List[List[int]]] = None,
+        add_special_tokens: bool = True,
+        padding_strategy: PaddingStrategy = PaddingStrategy.DO_NOT_PAD,
+        truncation_strategy: TruncationStrategy = TruncationStrategy.DO_NOT_TRUNCATE,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[Union[str, TensorType]] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+        **kwargs,
+    ) -> BatchEncoding:
+        if return_offsets_mapping:
+            raise NotImplementedError(
+                "return_offset_mapping is not available when using Python tokenizers. "
+                "To use this feature, change your tokenizer to one deriving from "
+                "transformers.PreTrainedTokenizerFast."
+            )
+
+        batch_outputs = self._batch_prepare_for_model(
+            batch_text_or_text_pairs=batch_text_or_text_pairs,
+            is_pair=is_pair,
+            boxes=boxes,
+            word_labels=word_labels,
+            add_special_tokens=add_special_tokens,
+            padding_strategy=padding_strategy,
+            truncation_strategy=truncation_strategy,
+            max_length=max_length,
+            stride=stride,
+            pad_to_multiple_of=pad_to_multiple_of,
+            return_attention_mask=return_attention_mask,
+            return_token_type_ids=return_token_type_ids,
+            return_overflowing_tokens=return_overflowing_tokens,
+            return_special_tokens_mask=return_special_tokens_mask,
+            return_length=return_length,
+            return_tensors=return_tensors,
+            verbose=verbose,
+        )
+
+        return BatchEncoding(batch_outputs)
+
+    @add_end_docstrings(LAYOUTLMV2_ENCODE_KWARGS_DOCSTRING, LAYOUTLMV2_ENCODE_PLUS_ADDITIONAL_KWARGS_DOCSTRING)
+    def _batch_prepare_for_model(
+        self,
+        batch_text_or_text_pairs,
+        is_pair: bool = None,
+        boxes: Optional[List[List[int]]] = None,
+        word_labels: Optional[List[List[int]]] = None,
+        add_special_tokens: bool = True,
+        padding_strategy: PaddingStrategy = PaddingStrategy.DO_NOT_PAD,
+        truncation_strategy: TruncationStrategy = TruncationStrategy.DO_NOT_TRUNCATE,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[str] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+    ) -> BatchEncoding:
+        """
+        Prepares a sequence of input id, or a pair of sequences of inputs ids so that it can be used by the model. It
+        adds special tokens, truncates sequences if overflowing while taking into account the special tokens and
+        manages a moving window (with user defined stride) for overflowing tokens.
+
+        Args:
+            batch_ids_pairs: list of tokenized input ids or input ids pairs
+        """
+
+        batch_outputs = {}
+        for idx, example in enumerate(zip(batch_text_or_text_pairs, boxes)):
+            batch_text_or_text_pair, boxes_example = example
+            outputs = self.prepare_for_model(
+                batch_text_or_text_pair[0] if is_pair else batch_text_or_text_pair,
+                batch_text_or_text_pair[1] if is_pair else None,
+                boxes_example,
+                word_labels=word_labels[idx] if word_labels is not None else None,
+                add_special_tokens=add_special_tokens,
+                padding=PaddingStrategy.DO_NOT_PAD.value,  # we pad in batch afterward
+                truncation=truncation_strategy.value,
+                max_length=max_length,
+                stride=stride,
+                pad_to_multiple_of=None,  # we pad in batch afterward
+                return_attention_mask=False,  # we pad in batch afterward
+                return_token_type_ids=return_token_type_ids,
+                return_overflowing_tokens=return_overflowing_tokens,
+                return_special_tokens_mask=return_special_tokens_mask,
+                return_length=return_length,
+                return_tensors=None,  # We convert the whole batch to tensors at the end
+                prepend_batch_axis=False,
+                verbose=verbose,
+            )
+
+            for key, value in outputs.items():
+                if key not in batch_outputs:
+                    batch_outputs[key] = []
+                batch_outputs[key].append(value)
+
+        batch_outputs = self.pad(
+            batch_outputs,
+            padding=padding_strategy.value,
+            max_length=max_length,
+            pad_to_multiple_of=pad_to_multiple_of,
+            return_attention_mask=return_attention_mask,
+        )
+
+        batch_outputs = BatchEncoding(batch_outputs, tensor_type=return_tensors)
+
+        return batch_outputs
+
+    @add_end_docstrings(LAYOUTLMV2_ENCODE_KWARGS_DOCSTRING)
+    def encode(
+        self,
+        text: Union[TextInput, PreTokenizedInput],
+        text_pair: Optional[PreTokenizedInput] = None,
+        boxes: Optional[List[List[int]]] = None,
+        word_labels: Optional[List[int]] = None,
+        add_special_tokens: bool = True,
+        padding: Union[bool, str, PaddingStrategy] = False,
+        truncation: Union[bool, str, TruncationStrategy] = None,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[Union[str, TensorType]] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+        **kwargs,
+    ) -> List[int]:
+        encoded_inputs = self.encode_plus(
+            text=text,
+            text_pair=text_pair,
+            boxes=boxes,
+            word_labels=word_labels,
+            add_special_tokens=add_special_tokens,
+            padding=padding,
+            truncation=truncation,
+            max_length=max_length,
+            stride=stride,
+            pad_to_multiple_of=pad_to_multiple_of,
+            return_tensors=return_tensors,
+            return_token_type_ids=return_token_type_ids,
+            return_attention_mask=return_attention_mask,
+            return_overflowing_tokens=return_overflowing_tokens,
+            return_special_tokens_mask=return_special_tokens_mask,
+            return_offsets_mapping=return_offsets_mapping,
+            return_length=return_length,
+            verbose=verbose,
+            **kwargs,
+        )
+
+        return encoded_inputs["input_ids"]
+
+    @add_end_docstrings(LAYOUTLMV2_ENCODE_KWARGS_DOCSTRING, LAYOUTLMV2_ENCODE_PLUS_ADDITIONAL_KWARGS_DOCSTRING)
+    def encode_plus(
+        self,
+        text: Union[TextInput, PreTokenizedInput],
+        text_pair: Optional[PreTokenizedInput] = None,
+        boxes: Optional[List[List[int]]] = None,
+        word_labels: Optional[List[int]] = None,
+        add_special_tokens: bool = True,
+        padding: Union[bool, str, PaddingStrategy] = False,
+        truncation: Union[bool, str, TruncationStrategy] = None,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[Union[str, TensorType]] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+        **kwargs,
+    ) -> BatchEncoding:
+        """
+        Tokenize and prepare for the model a sequence or a pair of sequences. .. warning:: This method is deprecated,
+        `__call__` should be used instead.
+
+        Args:
+            text (`str`, `List[str]`, `List[List[str]]`):
+                The first sequence to be encoded. This can be a string, a list of strings or a list of list of strings.
+            text_pair (`List[str]` or `List[int]`, *optional*):
+                Optional second sequence to be encoded. This can be a list of strings (words of a single example) or a
+                list of list of strings (words of a batch of examples).
+        """
+
+        # Backward compatibility for 'truncation_strategy', 'pad_to_max_length'
+        padding_strategy, truncation_strategy, max_length, kwargs = self._get_padding_truncation_strategies(
+            padding=padding,
+            truncation=truncation,
+            max_length=max_length,
+            pad_to_multiple_of=pad_to_multiple_of,
+            verbose=verbose,
+            **kwargs,
+        )
+
+        return self._encode_plus(
+            text=text,
+            boxes=boxes,
+            text_pair=text_pair,
+            word_labels=word_labels,
+            add_special_tokens=add_special_tokens,
+            padding_strategy=padding_strategy,
+            truncation_strategy=truncation_strategy,
+            max_length=max_length,
+            stride=stride,
+            pad_to_multiple_of=pad_to_multiple_of,
+            return_tensors=return_tensors,
+            return_token_type_ids=return_token_type_ids,
+            return_attention_mask=return_attention_mask,
+            return_overflowing_tokens=return_overflowing_tokens,
+            return_special_tokens_mask=return_special_tokens_mask,
+            return_offsets_mapping=return_offsets_mapping,
+            return_length=return_length,
+            verbose=verbose,
+            **kwargs,
+        )
+
+    def _encode_plus(
+        self,
+        text: Union[TextInput, PreTokenizedInput],
+        text_pair: Optional[PreTokenizedInput] = None,
+        boxes: Optional[List[List[int]]] = None,
+        word_labels: Optional[List[int]] = None,
+        add_special_tokens: bool = True,
+        padding_strategy: PaddingStrategy = PaddingStrategy.DO_NOT_PAD,
+        truncation_strategy: TruncationStrategy = TruncationStrategy.DO_NOT_TRUNCATE,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[Union[str, TensorType]] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+        **kwargs,
+    ) -> BatchEncoding:
+        if return_offsets_mapping:
+            raise NotImplementedError(
+                "return_offset_mapping is not available when using Python tokenizers. "
+                "To use this feature, change your tokenizer to one deriving from "
+                "transformers.PreTrainedTokenizerFast. "
+                "More information on available tokenizers at "
+                "https://github.com/huggingface/transformers/pull/2674"
+            )
+
+        return self.prepare_for_model(
+            text=text,
+            text_pair=text_pair,
+            boxes=boxes,
+            word_labels=word_labels,
+            add_special_tokens=add_special_tokens,
+            padding=padding_strategy.value,
+            truncation=truncation_strategy.value,
+            max_length=max_length,
+            stride=stride,
+            pad_to_multiple_of=pad_to_multiple_of,
+            return_tensors=return_tensors,
+            prepend_batch_axis=True,
+            return_attention_mask=return_attention_mask,
+            return_token_type_ids=return_token_type_ids,
+            return_overflowing_tokens=return_overflowing_tokens,
+            return_special_tokens_mask=return_special_tokens_mask,
+            return_length=return_length,
+            verbose=verbose,
+        )
+
+    @add_end_docstrings(LAYOUTLMV2_ENCODE_KWARGS_DOCSTRING, LAYOUTLMV2_ENCODE_PLUS_ADDITIONAL_KWARGS_DOCSTRING)
+    def prepare_for_model(
+        self,
+        text: Union[TextInput, PreTokenizedInput],
+        text_pair: Optional[PreTokenizedInput] = None,
+        boxes: Optional[List[List[int]]] = None,
+        word_labels: Optional[List[int]] = None,
+        add_special_tokens: bool = True,
+        padding: Union[bool, str, PaddingStrategy] = False,
+        truncation: Union[bool, str, TruncationStrategy] = None,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[Union[str, TensorType]] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+        prepend_batch_axis: bool = False,
+        **kwargs,
+    ) -> BatchEncoding:
+        """
+        Prepares a sequence or a pair of sequences so that it can be used by the model. It adds special tokens,
+        truncates sequences if overflowing while taking into account the special tokens and manages a moving window
+        (with user defined stride) for overflowing tokens. Please Note, for *text_pair* different than `None` and
+        *truncation_strategy = longest_first* or `True`, it is not possible to return overflowing tokens. Such a
+        combination of arguments will raise an error.
+
+        Word-level `boxes` are turned into token-level `bbox`. If provided, word-level `word_labels` are turned into
+        token-level `labels`. The word label is used for the first token of the word, while remaining tokens are
+        labeled with -100, such that they will be ignored by the loss function.
+
+        Args:
+            text (`str`, `List[str]`, `List[List[str]]`):
+                The first sequence to be encoded. This can be a string, a list of strings or a list of list of strings.
+            text_pair (`List[str]` or `List[int]`, *optional*):
+                Optional second sequence to be encoded. This can be a list of strings (words of a single example) or a
+                list of list of strings (words of a batch of examples).
+        """
+
+        # Backward compatibility for 'truncation_strategy', 'pad_to_max_length'
+        padding_strategy, truncation_strategy, max_length, kwargs = self._get_padding_truncation_strategies(
+            padding=padding,
+            truncation=truncation,
+            max_length=max_length,
+            pad_to_multiple_of=pad_to_multiple_of,
+            verbose=verbose,
+            **kwargs,
+        )
+
+        tokens = []
+        pair_tokens = []
+        token_boxes = []
+        pair_token_boxes = []
+        labels = []
+
+        if text_pair is None:
+            if word_labels is None:
+                # CASE 1: document image classification (training + inference) + CASE 2: token classification (inference)
+                for word, box in zip(text, boxes):
+                    if len(word) < 1:  # skip empty words
+                        continue
+                    word_tokens = self.tokenize(word)
+                    tokens.extend(word_tokens)
+                    token_boxes.extend([box] * len(word_tokens))
+            else:
+                # CASE 2: token classification (training)
+                for word, box, label in zip(text, boxes, word_labels):
+                    if len(word) < 1:  # skip empty words
+                        continue
+                    word_tokens = self.tokenize(word)
+                    tokens.extend(word_tokens)
+                    token_boxes.extend([box] * len(word_tokens))
+                    if self.only_label_first_subword:
+                        # Use the real label id for the first token of the word, and padding ids for the remaining tokens
+                        labels.extend([label] + [self.pad_token_label] * (len(word_tokens) - 1))
+                    else:
+                        labels.extend([label] * len(word_tokens))
+        else:
+            # CASE 3: document visual question answering (inference)
+            # text = question
+            # text_pair = words
+            tokens = self.tokenize(text)
+            token_boxes = [self.pad_token_box for _ in range(len(tokens))]
+
+            for word, box in zip(text_pair, boxes):
+                if len(word) < 1:  # skip empty words
+                    continue
+                word_tokens = self.tokenize(word)
+                pair_tokens.extend(word_tokens)
+                pair_token_boxes.extend([box] * len(word_tokens))
+
+        # Create ids + pair_ids
+        ids = self.convert_tokens_to_ids(tokens)
+        pair_ids = self.convert_tokens_to_ids(pair_tokens) if pair_tokens else None
+
+        if (
+            return_overflowing_tokens
+            and truncation_strategy == TruncationStrategy.LONGEST_FIRST
+            and pair_ids is not None
+        ):
+            raise ValueError(
+                "Not possible to return overflowing tokens for pair of sequences with the "
+                "`longest_first`. Please select another truncation strategy than `longest_first`, "
+                "for instance `only_second` or `only_first`."
+            )
+
+        # Compute the total size of the returned encodings
+        pair = bool(pair_ids is not None)
+        len_ids = len(ids)
+        len_pair_ids = len(pair_ids) if pair else 0
+        total_len = len_ids + len_pair_ids + (self.num_special_tokens_to_add(pair=pair) if add_special_tokens else 0)
+
+        # Truncation: Handle max sequence length
+        overflowing_tokens = []
+        overflowing_token_boxes = []
+        overflowing_labels = []
+        if truncation_strategy != TruncationStrategy.DO_NOT_TRUNCATE and max_length and total_len > max_length:
+            (
+                ids,
+                token_boxes,
+                pair_ids,
+                pair_token_boxes,
+                labels,
+                overflowing_tokens,
+                overflowing_token_boxes,
+                overflowing_labels,
+            ) = self.truncate_sequences(
+                ids,
+                token_boxes,
+                pair_ids=pair_ids,
+                pair_token_boxes=pair_token_boxes,
+                labels=labels,
+                num_tokens_to_remove=total_len - max_length,
+                truncation_strategy=truncation_strategy,
+                stride=stride,
+            )
+
+        if return_token_type_ids and not add_special_tokens:
+            raise ValueError(
+                "Asking to return token_type_ids while setting add_special_tokens to False "
+                "results in an undefined behavior. Please set add_special_tokens to True or "
+                "set return_token_type_ids to None."
+            )
+
+        # Load from model defaults
+        if return_token_type_ids is None:
+            return_token_type_ids = "token_type_ids" in self.model_input_names
+        if return_attention_mask is None:
+            return_attention_mask = "attention_mask" in self.model_input_names
+
+        encoded_inputs = {}
+
+        if return_overflowing_tokens:
+            encoded_inputs["overflowing_tokens"] = overflowing_tokens
+            encoded_inputs["overflowing_token_boxes"] = overflowing_token_boxes
+            encoded_inputs["overflowing_labels"] = overflowing_labels
+            encoded_inputs["num_truncated_tokens"] = total_len - max_length
+
+        # Add special tokens
+        if add_special_tokens:
+            sequence = self.build_inputs_with_special_tokens(ids, pair_ids)
+            token_type_ids = self.create_token_type_ids_from_sequences(ids, pair_ids)
+            token_boxes = [self.cls_token_box] + token_boxes + [self.sep_token_box]
+            if pair_token_boxes:
+                pair_token_boxes = pair_token_boxes + [self.sep_token_box]
+            if labels:
+                labels = [self.pad_token_label] + labels + [self.pad_token_label]
+        else:
+            sequence = ids + pair_ids if pair else ids
+            token_type_ids = [0] * len(ids) + ([0] * len(pair_ids) if pair else [])
+
+        # Build output dictionary
+        encoded_inputs["input_ids"] = sequence
+        encoded_inputs["bbox"] = token_boxes + pair_token_boxes
+        if return_token_type_ids:
+            encoded_inputs["token_type_ids"] = token_type_ids
+        if return_special_tokens_mask:
+            if add_special_tokens:
+                encoded_inputs["special_tokens_mask"] = self.get_special_tokens_mask(ids, pair_ids)
+            else:
+                encoded_inputs["special_tokens_mask"] = [0] * len(sequence)
+
+        if labels:
+            encoded_inputs["labels"] = labels
+
+        # Check lengths
+        self._eventual_warn_about_too_long_sequence(encoded_inputs["input_ids"], max_length, verbose)
+
+        # Padding
+        if padding_strategy != PaddingStrategy.DO_NOT_PAD or return_attention_mask:
+            encoded_inputs = self.pad(
+                encoded_inputs,
+                max_length=max_length,
+                padding=padding_strategy.value,
+                pad_to_multiple_of=pad_to_multiple_of,
+                return_attention_mask=return_attention_mask,
+            )
+
+        if return_length:
+            encoded_inputs["length"] = len(encoded_inputs["input_ids"])
+
+        batch_outputs = BatchEncoding(
+            encoded_inputs, tensor_type=return_tensors, prepend_batch_axis=prepend_batch_axis
+        )
+
+        return batch_outputs
+
+    def truncate_sequences(
+        self,
+        ids: List[int],
+        token_boxes: List[List[int]],
+        pair_ids: Optional[List[int]] = None,
+        pair_token_boxes: Optional[List[List[int]]] = None,
+        labels: Optional[List[int]] = None,
+        num_tokens_to_remove: int = 0,
+        truncation_strategy: Union[str, TruncationStrategy] = "longest_first",
+        stride: int = 0,
+    ) -> Tuple[List[int], List[int], List[int]]:
+        """
+        Truncates a sequence pair in-place following the strategy.
+
+        Args:
+            ids (`List[int]`):
+                Tokenized input ids of the first sequence. Can be obtained from a string by chaining the `tokenize` and
+                `convert_tokens_to_ids` methods.
+            token_boxes (`List[List[int]]`):
+                Bounding boxes of the first sequence.
+            pair_ids (`List[int]`, *optional*):
+                Tokenized input ids of the second sequence. Can be obtained from a string by chaining the `tokenize`
+                and `convert_tokens_to_ids` methods.
+            pair_token_boxes (`List[List[int]]`, *optional*):
+                Bounding boxes of the second sequence.
+            labels (`List[int]`, *optional*):
+                Labels of the first sequence (for token classification tasks).
+            num_tokens_to_remove (`int`, *optional*, defaults to 0):
+                Number of tokens to remove using the truncation strategy.
+            truncation_strategy (`str` or [`~tokenization_utils_base.TruncationStrategy`], *optional*, defaults to `False`):
+                The strategy to follow for truncation. Can be:
+
+                - `'longest_first'`: Truncate to a maximum length specified with the argument `max_length` or to the
+                  maximum acceptable input length for the model if that argument is not provided. This will truncate
+                  token by token, removing a token from the longest sequence in the pair if a pair of sequences (or a
+                  batch of pairs) is provided.
+                - `'only_first'`: Truncate to a maximum length specified with the argument `max_length` or to the
+                  maximum acceptable input length for the model if that argument is not provided. This will only
+                  truncate the first sequence of a pair if a pair of sequences (or a batch of pairs) is provided.
+                - `'only_second'`: Truncate to a maximum length specified with the argument `max_length` or to the
+                  maximum acceptable input length for the model if that argument is not provided. This will only
+                  truncate the second sequence of a pair if a pair of sequences (or a batch of pairs) is provided.
+                - `'do_not_truncate'` (default): No truncation (i.e., can output batch with sequence lengths greater
+                  than the model maximum admissible input size).
+            stride (`int`, *optional*, defaults to 0):
+                If set to a positive number, the overflowing tokens returned will contain some tokens from the main
+                sequence returned. The value of this argument defines the number of additional tokens.
+
+        Returns:
+            `Tuple[List[int], List[int], List[int]]`: The truncated `ids`, the truncated `pair_ids` and the list of
+            overflowing tokens. Note: The *longest_first* strategy returns empty list of overflowing tokens if a pair
+            of sequences (or a batch of pairs) is provided.
+        """
+        if num_tokens_to_remove <= 0:
+            return ids, token_boxes, pair_ids, pair_token_boxes, labels, [], [], []
+
+        if not isinstance(truncation_strategy, TruncationStrategy):
+            truncation_strategy = TruncationStrategy(truncation_strategy)
+
+        overflowing_tokens = []
+        overflowing_token_boxes = []
+        overflowing_labels = []
+        if truncation_strategy == TruncationStrategy.ONLY_FIRST or (
+            truncation_strategy == TruncationStrategy.LONGEST_FIRST and pair_ids is None
+        ):
+            if len(ids) > num_tokens_to_remove:
+                window_len = min(len(ids), stride + num_tokens_to_remove)
+                overflowing_tokens = ids[-window_len:]
+                overflowing_token_boxes = token_boxes[-window_len:]
+                overflowing_labels = labels[-window_len:]
+                ids = ids[:-num_tokens_to_remove]
+                token_boxes = token_boxes[:-num_tokens_to_remove]
+                labels = labels[:-num_tokens_to_remove]
+            else:
+                error_msg = (
+                    f"We need to remove {num_tokens_to_remove} to truncate the input "
+                    f"but the first sequence has a length {len(ids)}. "
+                )
+                if truncation_strategy == TruncationStrategy.ONLY_FIRST:
+                    error_msg = (
+                        error_msg + "Please select another truncation strategy than "
+                        f"{truncation_strategy}, for instance 'longest_first' or 'only_second'."
+                    )
+                logger.error(error_msg)
+        elif truncation_strategy == TruncationStrategy.LONGEST_FIRST:
+            logger.warning(
+                "Be aware, overflowing tokens are not returned for the setting you have chosen,"
+                f" i.e. sequence pairs with the '{TruncationStrategy.LONGEST_FIRST.value}' "
+                "truncation strategy. So the returned list will always be empty even if some "
+                "tokens have been removed."
+            )
+            for _ in range(num_tokens_to_remove):
+                if pair_ids is None or len(ids) > len(pair_ids):
+                    ids = ids[:-1]
+                    token_boxes = token_boxes[:-1]
+                    labels = labels[:-1]
+                else:
+                    pair_ids = pair_ids[:-1]
+                    pair_token_boxes = pair_token_boxes[:-1]
+        elif truncation_strategy == TruncationStrategy.ONLY_SECOND and pair_ids is not None:
+            if len(pair_ids) > num_tokens_to_remove:
+                window_len = min(len(pair_ids), stride + num_tokens_to_remove)
+                overflowing_tokens = pair_ids[-window_len:]
+                overflowing_token_boxes = pair_token_boxes[-window_len:]
+                pair_ids = pair_ids[:-num_tokens_to_remove]
+                pair_token_boxes = pair_token_boxes[:-num_tokens_to_remove]
+            else:
+                logger.error(
+                    f"We need to remove {num_tokens_to_remove} to truncate the input "
+                    f"but the second sequence has a length {len(pair_ids)}. "
+                    f"Please select another truncation strategy than {truncation_strategy}, "
+                    "for instance 'longest_first' or 'only_first'."
+                )
+
+        return (
+            ids,
+            token_boxes,
+            pair_ids,
+            pair_token_boxes,
+            labels,
+            overflowing_tokens,
+            overflowing_token_boxes,
+            overflowing_labels,
+        )
+
+    def _pad(
+        self,
+        encoded_inputs: Union[Dict[str, EncodedInput], BatchEncoding],
+        max_length: Optional[int] = None,
+        padding_strategy: PaddingStrategy = PaddingStrategy.DO_NOT_PAD,
+        pad_to_multiple_of: Optional[int] = None,
+        return_attention_mask: Optional[bool] = None,
+    ) -> dict:
+        """
+        Pad encoded inputs (on left/right and up to predefined length or max length in the batch)
+
+        Args:
+            encoded_inputs:
+                Dictionary of tokenized inputs (`List[int]`) or batch of tokenized inputs (`List[List[int]]`).
+            max_length: maximum length of the returned list and optionally padding length (see below).
+                Will truncate by taking into account the special tokens.
+            padding_strategy: PaddingStrategy to use for padding.
+
+                - PaddingStrategy.LONGEST Pad to the longest sequence in the batch
+                - PaddingStrategy.MAX_LENGTH: Pad to the max length (default)
+                - PaddingStrategy.DO_NOT_PAD: Do not pad
+                The tokenizer padding sides are defined in self.padding_side:
+
+                    - 'left': pads on the left of the sequences
+                    - 'right': pads on the right of the sequences
+            pad_to_multiple_of: (optional) Integer if set will pad the sequence to a multiple of the provided value.
+                This is especially useful to enable the use of Tensor Core on NVIDIA hardware with compute capability
+                `>= 7.5` (Volta).
+            return_attention_mask:
+                (optional) Set to False to avoid returning attention mask (default: set to model specifics)
+        """
+        # Load from model defaults
+        if return_attention_mask is None:
+            return_attention_mask = "attention_mask" in self.model_input_names
+
+        required_input = encoded_inputs[self.model_input_names[0]]
+
+        if padding_strategy == PaddingStrategy.LONGEST:
+            max_length = len(required_input)
+
+        if max_length is not None and pad_to_multiple_of is not None and (max_length % pad_to_multiple_of != 0):
+            max_length = ((max_length // pad_to_multiple_of) + 1) * pad_to_multiple_of
+
+        needs_to_be_padded = padding_strategy != PaddingStrategy.DO_NOT_PAD and len(required_input) != max_length
+
+        # Initialize attention mask if not present.
+        if return_attention_mask and "attention_mask" not in encoded_inputs:
+            encoded_inputs["attention_mask"] = [1] * len(required_input)
+
+        if needs_to_be_padded:
+            difference = max_length - len(required_input)
+            if self.padding_side == "right":
+                if return_attention_mask:
+                    encoded_inputs["attention_mask"] = encoded_inputs["attention_mask"] + [0] * difference
+                if "token_type_ids" in encoded_inputs:
+                    encoded_inputs["token_type_ids"] = (
+                        encoded_inputs["token_type_ids"] + [self.pad_token_type_id] * difference
+                    )
+                if "bbox" in encoded_inputs:
+                    encoded_inputs["bbox"] = encoded_inputs["bbox"] + [self.pad_token_box] * difference
+                if "labels" in encoded_inputs:
+                    encoded_inputs["labels"] = encoded_inputs["labels"] + [self.pad_token_label] * difference
+                if "special_tokens_mask" in encoded_inputs:
+                    encoded_inputs["special_tokens_mask"] = encoded_inputs["special_tokens_mask"] + [1] * difference
+                encoded_inputs[self.model_input_names[0]] = required_input + [self.pad_token_id] * difference
+            elif self.padding_side == "left":
+                if return_attention_mask:
+                    encoded_inputs["attention_mask"] = [0] * difference + encoded_inputs["attention_mask"]
+                if "token_type_ids" in encoded_inputs:
+                    encoded_inputs["token_type_ids"] = [self.pad_token_type_id] * difference + encoded_inputs[
+                        "token_type_ids"
+                    ]
+                if "bbox" in encoded_inputs:
+                    encoded_inputs["bbox"] = [self.pad_token_box] * difference + encoded_inputs["bbox"]
+                if "labels" in encoded_inputs:
+                    encoded_inputs["labels"] = [self.pad_token_label] * difference + encoded_inputs["labels"]
+                if "special_tokens_mask" in encoded_inputs:
+                    encoded_inputs["special_tokens_mask"] = [1] * difference + encoded_inputs["special_tokens_mask"]
+                encoded_inputs[self.model_input_names[0]] = [self.pad_token_id] * difference + required_input
+            else:
+                raise ValueError("Invalid padding strategy:" + str(self.padding_side))
+
+        return encoded_inputs
+
+
+# Copied from transformers.models.bert.tokenization_bert.BasicTokenizer
+class BasicTokenizer(object):
+    """
+    Constructs a BasicTokenizer that will run basic tokenization (punctuation splitting, lower casing, etc.).
+
+    Args:
+        do_lower_case (`bool`, *optional*, defaults to `True`):
+            Whether or not to lowercase the input when tokenizing.
+        never_split (`Iterable`, *optional*):
+            Collection of tokens which will never be split during tokenization. Only has an effect when
+            `do_basic_tokenize=True`
+        tokenize_chinese_chars (`bool`, *optional*, defaults to `True`):
+            Whether or not to tokenize Chinese characters.
+
+            This should likely be deactivated for Japanese (see this
+            [issue](https://github.com/huggingface/transformers/issues/328)).
+        strip_accents (`bool`, *optional*):
+            Whether or not to strip all accents. If this option is not specified, then it will be determined by the
+            value for `lowercase` (as in the original BERT).
+        do_split_on_punc (`bool`, *optional*, defaults to `True`):
+            In some instances we want to skip the basic punctuation splitting so that later tokenization can capture
+            the full context of the words, such as contractions.
+    """
+
+    def __init__(
+        self,
+        do_lower_case=True,
+        never_split=None,
+        tokenize_chinese_chars=True,
+        strip_accents=None,
+        do_split_on_punc=True,
+    ):
+        if never_split is None:
+            never_split = []
+        self.do_lower_case = do_lower_case
+        self.never_split = set(never_split)
+        self.tokenize_chinese_chars = tokenize_chinese_chars
+        self.strip_accents = strip_accents
+        self.do_split_on_punc = do_split_on_punc
+
+    def tokenize(self, text, never_split=None):
+        """
+        Basic Tokenization of a piece of text. For sub-word tokenization, see WordPieceTokenizer.
+
+        Args:
+            never_split (`List[str]`, *optional*)
+                Kept for backward compatibility purposes. Now implemented directly at the base class level (see
+                [`PreTrainedTokenizer.tokenize`]) List of token not to split.
+        """
+        # union() returns a new set by concatenating the two sets.
+        never_split = self.never_split.union(set(never_split)) if never_split else self.never_split
+        text = self._clean_text(text)
+
+        # This was added on November 1st, 2018 for the multilingual and Chinese
+        # models. This is also applied to the English models now, but it doesn't
+        # matter since the English models were not trained on any Chinese data
+        # and generally don't have any Chinese data in them (there are Chinese
+        # characters in the vocabulary because Wikipedia does have some Chinese
+        # words in the English Wikipedia.).
+        if self.tokenize_chinese_chars:
+            text = self._tokenize_chinese_chars(text)
+        # prevents treating the same character with different unicode codepoints as different characters
+        unicode_normalized_text = unicodedata.normalize("NFC", text)
+        orig_tokens = whitespace_tokenize(unicode_normalized_text)
+        split_tokens = []
+        for token in orig_tokens:
+            if token not in never_split:
+                if self.do_lower_case:
+                    token = token.lower()
+                    if self.strip_accents is not False:
+                        token = self._run_strip_accents(token)
+                elif self.strip_accents:
+                    token = self._run_strip_accents(token)
+            split_tokens.extend(self._run_split_on_punc(token, never_split))
+
+        output_tokens = whitespace_tokenize(" ".join(split_tokens))
+        return output_tokens
+
+    def _run_strip_accents(self, text):
+        """Strips accents from a piece of text."""
+        text = unicodedata.normalize("NFD", text)
+        output = []
+        for char in text:
+            cat = unicodedata.category(char)
+            if cat == "Mn":
+                continue
+            output.append(char)
+        return "".join(output)
+
+    def _run_split_on_punc(self, text, never_split=None):
+        """Splits punctuation on a piece of text."""
+        if not self.do_split_on_punc or (never_split is not None and text in never_split):
+            return [text]
+        chars = list(text)
+        i = 0
+        start_new_word = True
+        output = []
+        while i < len(chars):
+            char = chars[i]
+            if _is_punctuation(char):
+                output.append([char])
+                start_new_word = True
+            else:
+                if start_new_word:
+                    output.append([])
+                start_new_word = False
+                output[-1].append(char)
+            i += 1
+
+        return ["".join(x) for x in output]
+
+    def _tokenize_chinese_chars(self, text):
+        """Adds whitespace around any CJK character."""
+        output = []
+        for char in text:
+            cp = ord(char)
+            if self._is_chinese_char(cp):
+                output.append(" ")
+                output.append(char)
+                output.append(" ")
+            else:
+                output.append(char)
+        return "".join(output)
+
+    def _is_chinese_char(self, cp):
+        """Checks whether CP is the codepoint of a CJK character."""
+        # This defines a "chinese character" as anything in the CJK Unicode block:
+        #   https://en.wikipedia.org/wiki/CJK_Unified_Ideographs_(Unicode_block)
+        #
+        # Note that the CJK Unicode block is NOT all Japanese and Korean characters,
+        # despite its name. The modern Korean Hangul alphabet is a different block,
+        # as is Japanese Hiragana and Katakana. Those alphabets are used to write
+        # space-separated words, so they are not treated specially and handled
+        # like the all of the other languages.
+        if (
+            (cp >= 0x4E00 and cp <= 0x9FFF)
+            or (cp >= 0x3400 and cp <= 0x4DBF)  #
+            or (cp >= 0x20000 and cp <= 0x2A6DF)  #
+            or (cp >= 0x2A700 and cp <= 0x2B73F)  #
+            or (cp >= 0x2B740 and cp <= 0x2B81F)  #
+            or (cp >= 0x2B820 and cp <= 0x2CEAF)  #
+            or (cp >= 0xF900 and cp <= 0xFAFF)
+            or (cp >= 0x2F800 and cp <= 0x2FA1F)  #
+        ):  #
+            return True
+
+        return False
+
+    def _clean_text(self, text):
+        """Performs invalid character removal and whitespace cleanup on text."""
+        output = []
+        for char in text:
+            cp = ord(char)
+            if cp == 0 or cp == 0xFFFD or _is_control(char):
+                continue
+            if _is_whitespace(char):
+                output.append(" ")
+            else:
+                output.append(char)
+        return "".join(output)
+
+
+# Copied from transformers.models.bert.tokenization_bert.WordpieceTokenizer
+class WordpieceTokenizer(object):
+    """Runs WordPiece tokenization."""
+
+    def __init__(self, vocab, unk_token, max_input_chars_per_word=100):
+        self.vocab = vocab
+        self.unk_token = unk_token
+        self.max_input_chars_per_word = max_input_chars_per_word
+
+    def tokenize(self, text):
+        """
+        Tokenizes a piece of text into its word pieces. This uses a greedy longest-match-first algorithm to perform
+        tokenization using the given vocabulary.
+
+        For example, `input = "unaffable"` wil return as output `["un", "##aff", "##able"]`.
+
+        Args:
+            text: A single token or whitespace separated tokens. This should have
+                already been passed through *BasicTokenizer*.
+
+        Returns:
+            A list of wordpiece tokens.
+        """
+
+        output_tokens = []
+        for token in whitespace_tokenize(text):
+            chars = list(token)
+            if len(chars) > self.max_input_chars_per_word:
+                output_tokens.append(self.unk_token)
+                continue
+
+            is_bad = False
+            start = 0
+            sub_tokens = []
+            while start < len(chars):
+                end = len(chars)
+                cur_substr = None
+                while start < end:
+                    substr = "".join(chars[start:end])
+                    if start > 0:
+                        substr = "##" + substr
+                    if substr in self.vocab:
+                        cur_substr = substr
+                        break
+                    end -= 1
+                if cur_substr is None:
+                    is_bad = True
+                    break
+                sub_tokens.append(cur_substr)
+                start = end
+
+            if is_bad:
+                output_tokens.append(self.unk_token)
+            else:
+                output_tokens.extend(sub_tokens)
+        return output_tokens

llmeval-env/lib/python3.10/site-packages/transformers/models/layoutlmv2/tokenization_layoutlmv2_fast.py

@@ -0,0 +1,793 @@
+# coding=utf-8
+# Copyright 2021 The HuggingFace Inc. team.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+Fast tokenization class for LayoutLMv2. It overwrites 2 methods of the slow tokenizer class, namely _batch_encode_plus
+and _encode_plus, in which the Rust tokenizer is used.
+"""
+
+import json
+from typing import Dict, List, Optional, Tuple, Union
+
+from tokenizers import normalizers
+
+from ...tokenization_utils_base import (
+    BatchEncoding,
+    EncodedInput,
+    PaddingStrategy,
+    PreTokenizedInput,
+    TensorType,
+    TextInput,
+    TextInputPair,
+    TruncationStrategy,
+)
+from ...tokenization_utils_fast import PreTrainedTokenizerFast
+from ...utils import add_end_docstrings, logging
+from .tokenization_layoutlmv2 import (
+    LAYOUTLMV2_ENCODE_KWARGS_DOCSTRING,
+    LAYOUTLMV2_ENCODE_PLUS_ADDITIONAL_KWARGS_DOCSTRING,
+    LayoutLMv2Tokenizer,
+)
+
+
+logger = logging.get_logger(__name__)
+
+VOCAB_FILES_NAMES = {"vocab_file": "vocab.txt", "tokenizer_file": "tokenizer.json"}
+
+
+class LayoutLMv2TokenizerFast(PreTrainedTokenizerFast):
+    r"""
+    Construct a "fast" LayoutLMv2 tokenizer (backed by HuggingFace's *tokenizers* library). Based on WordPiece.
+
+    This tokenizer inherits from [`PreTrainedTokenizerFast`] which contains most of the main methods. Users should
+    refer to this superclass for more information regarding those methods.
+
+    Args:
+        vocab_file (`str`):
+            File containing the vocabulary.
+        do_lower_case (`bool`, *optional*, defaults to `True`):
+            Whether or not to lowercase the input when tokenizing.
+        unk_token (`str`, *optional*, defaults to `"[UNK]"`):
+            The unknown token. A token that is not in the vocabulary cannot be converted to an ID and is set to be this
+            token instead.
+        sep_token (`str`, *optional*, defaults to `"[SEP]"`):
+            The separator token, which is used when building a sequence from multiple sequences, e.g. two sequences for
+            sequence classification or for a text and a question for question answering. It is also used as the last
+            token of a sequence built with special tokens.
+        pad_token (`str`, *optional*, defaults to `"[PAD]"`):
+            The token used for padding, for example when batching sequences of different lengths.
+        cls_token (`str`, *optional*, defaults to `"[CLS]"`):
+            The classifier token which is used when doing sequence classification (classification of the whole sequence
+            instead of per-token classification). It is the first token of the sequence when built with special tokens.
+        mask_token (`str`, *optional*, defaults to `"[MASK]"`):
+            The token used for masking values. This is the token used when training this model with masked language
+            modeling. This is the token which the model will try to predict.
+        cls_token_box (`List[int]`, *optional*, defaults to `[0, 0, 0, 0]`):
+            The bounding box to use for the special [CLS] token.
+        sep_token_box (`List[int]`, *optional*, defaults to `[1000, 1000, 1000, 1000]`):
+            The bounding box to use for the special [SEP] token.
+        pad_token_box (`List[int]`, *optional*, defaults to `[0, 0, 0, 0]`):
+            The bounding box to use for the special [PAD] token.
+        pad_token_label (`int`, *optional*, defaults to -100):
+            The label to use for padding tokens. Defaults to -100, which is the `ignore_index` of PyTorch's
+            CrossEntropyLoss.
+        only_label_first_subword (`bool`, *optional*, defaults to `True`):
+            Whether or not to only label the first subword, in case word labels are provided.
+        tokenize_chinese_chars (`bool`, *optional*, defaults to `True`):
+            Whether or not to tokenize Chinese characters. This should likely be deactivated for Japanese (see [this
+            issue](https://github.com/huggingface/transformers/issues/328)).
+        strip_accents (`bool`, *optional*):
+            Whether or not to strip all accents. If this option is not specified, then it will be determined by the
+            value for `lowercase` (as in the original LayoutLMv2).
+    """
+
+    vocab_files_names = VOCAB_FILES_NAMES
+    slow_tokenizer_class = LayoutLMv2Tokenizer
+
+    def __init__(
+        self,
+        vocab_file=None,
+        tokenizer_file=None,
+        do_lower_case=True,
+        unk_token="[UNK]",
+        sep_token="[SEP]",
+        pad_token="[PAD]",
+        cls_token="[CLS]",
+        mask_token="[MASK]",
+        cls_token_box=[0, 0, 0, 0],
+        sep_token_box=[1000, 1000, 1000, 1000],
+        pad_token_box=[0, 0, 0, 0],
+        pad_token_label=-100,
+        only_label_first_subword=True,
+        tokenize_chinese_chars=True,
+        strip_accents=None,
+        **kwargs,
+    ):
+        super().__init__(
+            vocab_file,
+            tokenizer_file=tokenizer_file,
+            do_lower_case=do_lower_case,
+            unk_token=unk_token,
+            sep_token=sep_token,
+            pad_token=pad_token,
+            cls_token=cls_token,
+            mask_token=mask_token,
+            cls_token_box=cls_token_box,
+            sep_token_box=sep_token_box,
+            pad_token_box=pad_token_box,
+            pad_token_label=pad_token_label,
+            only_label_first_subword=only_label_first_subword,
+            tokenize_chinese_chars=tokenize_chinese_chars,
+            strip_accents=strip_accents,
+            **kwargs,
+        )
+
+        pre_tok_state = json.loads(self.backend_tokenizer.normalizer.__getstate__())
+        if (
+            pre_tok_state.get("lowercase", do_lower_case) != do_lower_case
+            or pre_tok_state.get("strip_accents", strip_accents) != strip_accents
+        ):
+            pre_tok_class = getattr(normalizers, pre_tok_state.pop("type"))
+            pre_tok_state["lowercase"] = do_lower_case
+            pre_tok_state["strip_accents"] = strip_accents
+            self.backend_tokenizer.normalizer = pre_tok_class(**pre_tok_state)
+
+        self.do_lower_case = do_lower_case
+
+        # additional properties
+        self.cls_token_box = cls_token_box
+        self.sep_token_box = sep_token_box
+        self.pad_token_box = pad_token_box
+        self.pad_token_label = pad_token_label
+        self.only_label_first_subword = only_label_first_subword
+
+    @add_end_docstrings(LAYOUTLMV2_ENCODE_KWARGS_DOCSTRING, LAYOUTLMV2_ENCODE_PLUS_ADDITIONAL_KWARGS_DOCSTRING)
+    def __call__(
+        self,
+        text: Union[TextInput, PreTokenizedInput, List[TextInput], List[PreTokenizedInput]],
+        text_pair: Optional[Union[PreTokenizedInput, List[PreTokenizedInput]]] = None,
+        boxes: Union[List[List[int]], List[List[List[int]]]] = None,
+        word_labels: Optional[Union[List[int], List[List[int]]]] = None,
+        add_special_tokens: bool = True,
+        padding: Union[bool, str, PaddingStrategy] = False,
+        truncation: Union[bool, str, TruncationStrategy] = None,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[Union[str, TensorType]] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+        **kwargs,
+    ) -> BatchEncoding:
+        """
+        Main method to tokenize and prepare for the model one or several sequence(s) or one or several pair(s) of
+        sequences with word-level normalized bounding boxes and optional labels.
+
+        Args:
+            text (`str`, `List[str]`, `List[List[str]]`):
+                The sequence or batch of sequences to be encoded. Each sequence can be a string, a list of strings
+                (words of a single example or questions of a batch of examples) or a list of list of strings (batch of
+                words).
+            text_pair (`List[str]`, `List[List[str]]`):
+                The sequence or batch of sequences to be encoded. Each sequence should be a list of strings
+                (pretokenized string).
+            boxes (`List[List[int]]`, `List[List[List[int]]]`):
+                Word-level bounding boxes. Each bounding box should be normalized to be on a 0-1000 scale.
+            word_labels (`List[int]`, `List[List[int]]`, *optional*):
+                Word-level integer labels (for token classification tasks such as FUNSD, CORD).
+        """
+
+        # Input type checking for clearer error
+        def _is_valid_text_input(t):
+            if isinstance(t, str):
+                # Strings are fine
+                return True
+            elif isinstance(t, (list, tuple)):
+                # List are fine as long as they are...
+                if len(t) == 0:
+                    # ... empty
+                    return True
+                elif isinstance(t[0], str):
+                    # ... list of strings
+                    return True
+                elif isinstance(t[0], (list, tuple)):
+                    # ... list with an empty list or with a list of strings
+                    return len(t[0]) == 0 or isinstance(t[0][0], str)
+                else:
+                    return False
+            else:
+                return False
+
+        if text_pair is not None:
+            # in case text + text_pair are provided, text = questions, text_pair = words
+            if not _is_valid_text_input(text):
+                raise ValueError("text input must of type `str` (single example) or `List[str]` (batch of examples). ")
+            if not isinstance(text_pair, (list, tuple)):
+                raise ValueError(
+                    "Words must be of type `List[str]` (single pretokenized example), "
+                    "or `List[List[str]]` (batch of pretokenized examples)."
+                )
+        else:
+            # in case only text is provided => must be words
+            if not isinstance(text, (list, tuple)):
+                raise ValueError(
+                    "Words must be of type `List[str]` (single pretokenized example), "
+                    "or `List[List[str]]` (batch of pretokenized examples)."
+                )
+
+        if text_pair is not None:
+            is_batched = isinstance(text, (list, tuple))
+        else:
+            is_batched = isinstance(text, (list, tuple)) and text and isinstance(text[0], (list, tuple))
+
+        words = text if text_pair is None else text_pair
+        if boxes is None:
+            raise ValueError("You must provide corresponding bounding boxes")
+        if is_batched:
+            if len(words) != len(boxes):
+                raise ValueError("You must provide words and boxes for an equal amount of examples")
+            for words_example, boxes_example in zip(words, boxes):
+                if len(words_example) != len(boxes_example):
+                    raise ValueError("You must provide as many words as there are bounding boxes")
+        else:
+            if len(words) != len(boxes):
+                raise ValueError("You must provide as many words as there are bounding boxes")
+
+        if is_batched:
+            if text_pair is not None and len(text) != len(text_pair):
+                raise ValueError(
+                    f"batch length of `text`: {len(text)} does not match batch length of `text_pair`:"
+                    f" {len(text_pair)}."
+                )
+            batch_text_or_text_pairs = list(zip(text, text_pair)) if text_pair is not None else text
+            is_pair = bool(text_pair is not None)
+            return self.batch_encode_plus(
+                batch_text_or_text_pairs=batch_text_or_text_pairs,
+                is_pair=is_pair,
+                boxes=boxes,
+                word_labels=word_labels,
+                add_special_tokens=add_special_tokens,
+                padding=padding,
+                truncation=truncation,
+                max_length=max_length,
+                stride=stride,
+                pad_to_multiple_of=pad_to_multiple_of,
+                return_tensors=return_tensors,
+                return_token_type_ids=return_token_type_ids,
+                return_attention_mask=return_attention_mask,
+                return_overflowing_tokens=return_overflowing_tokens,
+                return_special_tokens_mask=return_special_tokens_mask,
+                return_offsets_mapping=return_offsets_mapping,
+                return_length=return_length,
+                verbose=verbose,
+                **kwargs,
+            )
+        else:
+            return self.encode_plus(
+                text=text,
+                text_pair=text_pair,
+                boxes=boxes,
+                word_labels=word_labels,
+                add_special_tokens=add_special_tokens,
+                padding=padding,
+                truncation=truncation,
+                max_length=max_length,
+                stride=stride,
+                pad_to_multiple_of=pad_to_multiple_of,
+                return_tensors=return_tensors,
+                return_token_type_ids=return_token_type_ids,
+                return_attention_mask=return_attention_mask,
+                return_overflowing_tokens=return_overflowing_tokens,
+                return_special_tokens_mask=return_special_tokens_mask,
+                return_offsets_mapping=return_offsets_mapping,
+                return_length=return_length,
+                verbose=verbose,
+                **kwargs,
+            )
+
+    @add_end_docstrings(LAYOUTLMV2_ENCODE_KWARGS_DOCSTRING, LAYOUTLMV2_ENCODE_PLUS_ADDITIONAL_KWARGS_DOCSTRING)
+    def batch_encode_plus(
+        self,
+        batch_text_or_text_pairs: Union[
+            List[TextInput],
+            List[TextInputPair],
+            List[PreTokenizedInput],
+        ],
+        is_pair: bool = None,
+        boxes: Optional[List[List[List[int]]]] = None,
+        word_labels: Optional[Union[List[int], List[List[int]]]] = None,
+        add_special_tokens: bool = True,
+        padding: Union[bool, str, PaddingStrategy] = False,
+        truncation: Union[bool, str, TruncationStrategy] = None,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[Union[str, TensorType]] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+        **kwargs,
+    ) -> BatchEncoding:
+        # Backward compatibility for 'truncation_strategy', 'pad_to_max_length'
+        padding_strategy, truncation_strategy, max_length, kwargs = self._get_padding_truncation_strategies(
+            padding=padding,
+            truncation=truncation,
+            max_length=max_length,
+            pad_to_multiple_of=pad_to_multiple_of,
+            verbose=verbose,
+            **kwargs,
+        )
+
+        return self._batch_encode_plus(
+            batch_text_or_text_pairs=batch_text_or_text_pairs,
+            is_pair=is_pair,
+            boxes=boxes,
+            word_labels=word_labels,
+            add_special_tokens=add_special_tokens,
+            padding_strategy=padding_strategy,
+            truncation_strategy=truncation_strategy,
+            max_length=max_length,
+            stride=stride,
+            pad_to_multiple_of=pad_to_multiple_of,
+            return_tensors=return_tensors,
+            return_token_type_ids=return_token_type_ids,
+            return_attention_mask=return_attention_mask,
+            return_overflowing_tokens=return_overflowing_tokens,
+            return_special_tokens_mask=return_special_tokens_mask,
+            return_offsets_mapping=return_offsets_mapping,
+            return_length=return_length,
+            verbose=verbose,
+            **kwargs,
+        )
+
+    def tokenize(self, text: str, pair: Optional[str] = None, add_special_tokens: bool = False, **kwargs) -> List[str]:
+        batched_input = [(text, pair)] if pair else [text]
+        encodings = self._tokenizer.encode_batch(
+            batched_input, add_special_tokens=add_special_tokens, is_pretokenized=False, **kwargs
+        )
+
+        return encodings[0].tokens
+
+    @add_end_docstrings(LAYOUTLMV2_ENCODE_KWARGS_DOCSTRING, LAYOUTLMV2_ENCODE_PLUS_ADDITIONAL_KWARGS_DOCSTRING)
+    def encode_plus(
+        self,
+        text: Union[TextInput, PreTokenizedInput],
+        text_pair: Optional[PreTokenizedInput] = None,
+        boxes: Optional[List[List[int]]] = None,
+        word_labels: Optional[List[int]] = None,
+        add_special_tokens: bool = True,
+        padding: Union[bool, str, PaddingStrategy] = False,
+        truncation: Union[bool, str, TruncationStrategy] = None,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[Union[str, TensorType]] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+        **kwargs,
+    ) -> BatchEncoding:
+        """
+        Tokenize and prepare for the model a sequence or a pair of sequences. .. warning:: This method is deprecated,
+        `__call__` should be used instead.
+
+        Args:
+            text (`str`, `List[str]`, `List[List[str]]`):
+                The first sequence to be encoded. This can be a string, a list of strings or a list of list of strings.
+            text_pair (`List[str]` or `List[int]`, *optional*):
+                Optional second sequence to be encoded. This can be a list of strings (words of a single example) or a
+                list of list of strings (words of a batch of examples).
+        """
+
+        # Backward compatibility for 'truncation_strategy', 'pad_to_max_length'
+        padding_strategy, truncation_strategy, max_length, kwargs = self._get_padding_truncation_strategies(
+            padding=padding,
+            truncation=truncation,
+            max_length=max_length,
+            pad_to_multiple_of=pad_to_multiple_of,
+            verbose=verbose,
+            **kwargs,
+        )
+
+        return self._encode_plus(
+            text=text,
+            boxes=boxes,
+            text_pair=text_pair,
+            word_labels=word_labels,
+            add_special_tokens=add_special_tokens,
+            padding_strategy=padding_strategy,
+            truncation_strategy=truncation_strategy,
+            max_length=max_length,
+            stride=stride,
+            pad_to_multiple_of=pad_to_multiple_of,
+            return_tensors=return_tensors,
+            return_token_type_ids=return_token_type_ids,
+            return_attention_mask=return_attention_mask,
+            return_overflowing_tokens=return_overflowing_tokens,
+            return_special_tokens_mask=return_special_tokens_mask,
+            return_offsets_mapping=return_offsets_mapping,
+            return_length=return_length,
+            verbose=verbose,
+            **kwargs,
+        )
+
+    def _batch_encode_plus(
+        self,
+        batch_text_or_text_pairs: Union[
+            List[TextInput],
+            List[TextInputPair],
+            List[PreTokenizedInput],
+        ],
+        is_pair: bool = None,
+        boxes: Optional[List[List[List[int]]]] = None,
+        word_labels: Optional[List[List[int]]] = None,
+        add_special_tokens: bool = True,
+        padding_strategy: PaddingStrategy = PaddingStrategy.DO_NOT_PAD,
+        truncation_strategy: TruncationStrategy = TruncationStrategy.DO_NOT_TRUNCATE,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[str] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+    ) -> BatchEncoding:
+        if not isinstance(batch_text_or_text_pairs, list):
+            raise TypeError(f"batch_text_or_text_pairs has to be a list (got {type(batch_text_or_text_pairs)})")
+
+        # Set the truncation and padding strategy and restore the initial configuration
+        self.set_truncation_and_padding(
+            padding_strategy=padding_strategy,
+            truncation_strategy=truncation_strategy,
+            max_length=max_length,
+            stride=stride,
+            pad_to_multiple_of=pad_to_multiple_of,
+        )
+
+        if is_pair:
+            batch_text_or_text_pairs = [(text.split(), text_pair) for text, text_pair in batch_text_or_text_pairs]
+
+        encodings = self._tokenizer.encode_batch(
+            batch_text_or_text_pairs,
+            add_special_tokens=add_special_tokens,
+            is_pretokenized=True,  # we set this to True as LayoutLMv2 always expects pretokenized inputs
+        )
+
+        # Convert encoding to dict
+        # `Tokens` has type: Tuple[
+        #                       List[Dict[str, List[List[int]]]] or List[Dict[str, 2D-Tensor]],
+        #                       List[EncodingFast]
+        #                    ]
+        # with nested dimensions corresponding to batch, overflows, sequence length
+        tokens_and_encodings = [
+            self._convert_encoding(
+                encoding=encoding,
+                return_token_type_ids=return_token_type_ids,
+                return_attention_mask=return_attention_mask,
+                return_overflowing_tokens=return_overflowing_tokens,
+                return_special_tokens_mask=return_special_tokens_mask,
+                return_offsets_mapping=True
+                if word_labels is not None
+                else return_offsets_mapping,  # we use offsets to create the labels
+                return_length=return_length,
+                verbose=verbose,
+            )
+            for encoding in encodings
+        ]
+
+        # Convert the output to have dict[list] from list[dict] and remove the additional overflows dimension
+        # From (variable) shape (batch, overflows, sequence length) to ~ (batch * overflows, sequence length)
+        # (we say ~ because the number of overflow varies with the example in the batch)
+        #
+        # To match each overflowing sample with the original sample in the batch
+        # we add an overflow_to_sample_mapping array (see below)
+        sanitized_tokens = {}
+        for key in tokens_and_encodings[0][0].keys():
+            stack = [e for item, _ in tokens_and_encodings for e in item[key]]
+            sanitized_tokens[key] = stack
+        sanitized_encodings = [e for _, item in tokens_and_encodings for e in item]
+
+        # If returning overflowing tokens, we need to return a mapping
+        # from the batch idx to the original sample
+        if return_overflowing_tokens:
+            overflow_to_sample_mapping = []
+            for i, (toks, _) in enumerate(tokens_and_encodings):
+                overflow_to_sample_mapping += [i] * len(toks["input_ids"])
+            sanitized_tokens["overflow_to_sample_mapping"] = overflow_to_sample_mapping
+
+        for input_ids in sanitized_tokens["input_ids"]:
+            self._eventual_warn_about_too_long_sequence(input_ids, max_length, verbose)
+
+        # create the token boxes
+        token_boxes = []
+        for batch_index in range(len(sanitized_tokens["input_ids"])):
+            if return_overflowing_tokens:
+                original_index = sanitized_tokens["overflow_to_sample_mapping"][batch_index]
+            else:
+                original_index = batch_index
+            token_boxes_example = []
+            for id, sequence_id, word_id in zip(
+                sanitized_tokens["input_ids"][batch_index],
+                sanitized_encodings[batch_index].sequence_ids,
+                sanitized_encodings[batch_index].word_ids,
+            ):
+                if word_id is not None:
+                    if is_pair and sequence_id == 0:
+                        token_boxes_example.append(self.pad_token_box)
+                    else:
+                        token_boxes_example.append(boxes[original_index][word_id])
+                else:
+                    if id == self.cls_token_id:
+                        token_boxes_example.append(self.cls_token_box)
+                    elif id == self.sep_token_id:
+                        token_boxes_example.append(self.sep_token_box)
+                    elif id == self.pad_token_id:
+                        token_boxes_example.append(self.pad_token_box)
+                    else:
+                        raise ValueError("Id not recognized")
+            token_boxes.append(token_boxes_example)
+
+        sanitized_tokens["bbox"] = token_boxes
+
+        # optionally, create the labels
+        if word_labels is not None:
+            labels = []
+            for batch_index in range(len(sanitized_tokens["input_ids"])):
+                if return_overflowing_tokens:
+                    original_index = sanitized_tokens["overflow_to_sample_mapping"][batch_index]
+                else:
+                    original_index = batch_index
+                labels_example = []
+                for id, offset, word_id in zip(
+                    sanitized_tokens["input_ids"][batch_index],
+                    sanitized_tokens["offset_mapping"][batch_index],
+                    sanitized_encodings[batch_index].word_ids,
+                ):
+                    if word_id is not None:
+                        if self.only_label_first_subword:
+                            if offset[0] == 0:
+                                # Use the real label id for the first token of the word, and padding ids for the remaining tokens
+                                labels_example.append(word_labels[original_index][word_id])
+                            else:
+                                labels_example.append(self.pad_token_label)
+                        else:
+                            labels_example.append(word_labels[original_index][word_id])
+                    else:
+                        labels_example.append(self.pad_token_label)
+                labels.append(labels_example)
+
+            sanitized_tokens["labels"] = labels
+            # finally, remove offsets if the user didn't want them
+            if not return_offsets_mapping:
+                del sanitized_tokens["offset_mapping"]
+
+        return BatchEncoding(sanitized_tokens, sanitized_encodings, tensor_type=return_tensors)
+
+    def _encode_plus(
+        self,
+        text: Union[TextInput, PreTokenizedInput],
+        text_pair: Optional[PreTokenizedInput] = None,
+        boxes: Optional[List[List[int]]] = None,
+        word_labels: Optional[List[int]] = None,
+        add_special_tokens: bool = True,
+        padding_strategy: PaddingStrategy = PaddingStrategy.DO_NOT_PAD,
+        truncation_strategy: TruncationStrategy = TruncationStrategy.DO_NOT_TRUNCATE,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[bool] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+        **kwargs,
+    ) -> BatchEncoding:
+        # make it a batched input
+        # 2 options:
+        # 1) only text, in case text must be a list of str
+        # 2) text + text_pair, in which case text = str and text_pair a list of str
+        batched_input = [(text, text_pair)] if text_pair else [text]
+        batched_boxes = [boxes]
+        batched_word_labels = [word_labels] if word_labels is not None else None
+        batched_output = self._batch_encode_plus(
+            batched_input,
+            is_pair=bool(text_pair is not None),
+            boxes=batched_boxes,
+            word_labels=batched_word_labels,
+            add_special_tokens=add_special_tokens,
+            padding_strategy=padding_strategy,
+            truncation_strategy=truncation_strategy,
+            max_length=max_length,
+            stride=stride,
+            pad_to_multiple_of=pad_to_multiple_of,
+            return_tensors=return_tensors,
+            return_token_type_ids=return_token_type_ids,
+            return_attention_mask=return_attention_mask,
+            return_overflowing_tokens=return_overflowing_tokens,
+            return_special_tokens_mask=return_special_tokens_mask,
+            return_offsets_mapping=return_offsets_mapping,
+            return_length=return_length,
+            verbose=verbose,
+            **kwargs,
+        )
+
+        # Return tensor is None, then we can remove the leading batch axis
+        # Overflowing tokens are returned as a batch of output so we keep them in this case
+        if return_tensors is None and not return_overflowing_tokens:
+            batched_output = BatchEncoding(
+                {
+                    key: value[0] if len(value) > 0 and isinstance(value[0], list) else value
+                    for key, value in batched_output.items()
+                },
+                batched_output.encodings,
+            )
+
+        self._eventual_warn_about_too_long_sequence(batched_output["input_ids"], max_length, verbose)
+
+        return batched_output
+
+    def _pad(
+        self,
+        encoded_inputs: Union[Dict[str, EncodedInput], BatchEncoding],
+        max_length: Optional[int] = None,
+        padding_strategy: PaddingStrategy = PaddingStrategy.DO_NOT_PAD,
+        pad_to_multiple_of: Optional[int] = None,
+        return_attention_mask: Optional[bool] = None,
+    ) -> dict:
+        """
+        Pad encoded inputs (on left/right and up to predefined length or max length in the batch)
+
+        Args:
+            encoded_inputs:
+                Dictionary of tokenized inputs (`List[int]`) or batch of tokenized inputs (`List[List[int]]`).
+            max_length: maximum length of the returned list and optionally padding length (see below).
+                Will truncate by taking into account the special tokens.
+            padding_strategy: PaddingStrategy to use for padding.
+
+                - PaddingStrategy.LONGEST Pad to the longest sequence in the batch
+                - PaddingStrategy.MAX_LENGTH: Pad to the max length (default)
+                - PaddingStrategy.DO_NOT_PAD: Do not pad
+                The tokenizer padding sides are defined in self.padding_side:
+
+                    - 'left': pads on the left of the sequences
+                    - 'right': pads on the right of the sequences
+            pad_to_multiple_of: (optional) Integer if set will pad the sequence to a multiple of the provided value.
+                This is especially useful to enable the use of Tensor Core on NVIDIA hardware with compute capability
+                `>= 7.5` (Volta).
+            return_attention_mask:
+                (optional) Set to False to avoid returning attention mask (default: set to model specifics)
+        """
+        # Load from model defaults
+        if return_attention_mask is None:
+            return_attention_mask = "attention_mask" in self.model_input_names
+
+        required_input = encoded_inputs[self.model_input_names[0]]
+
+        if padding_strategy == PaddingStrategy.LONGEST:
+            max_length = len(required_input)
+
+        if max_length is not None and pad_to_multiple_of is not None and (max_length % pad_to_multiple_of != 0):
+            max_length = ((max_length // pad_to_multiple_of) + 1) * pad_to_multiple_of
+
+        needs_to_be_padded = padding_strategy != PaddingStrategy.DO_NOT_PAD and len(required_input) != max_length
+
+        # Initialize attention mask if not present.
+        if return_attention_mask and "attention_mask" not in encoded_inputs:
+            encoded_inputs["attention_mask"] = [1] * len(required_input)
+
+        if needs_to_be_padded:
+            difference = max_length - len(required_input)
+            if self.padding_side == "right":
+                if return_attention_mask:
+                    encoded_inputs["attention_mask"] = encoded_inputs["attention_mask"] + [0] * difference
+                if "token_type_ids" in encoded_inputs:
+                    encoded_inputs["token_type_ids"] = (
+                        encoded_inputs["token_type_ids"] + [self.pad_token_type_id] * difference
+                    )
+                if "bbox" in encoded_inputs:
+                    encoded_inputs["bbox"] = encoded_inputs["bbox"] + [self.pad_token_box] * difference
+                if "labels" in encoded_inputs:
+                    encoded_inputs["labels"] = encoded_inputs["labels"] + [self.pad_token_label] * difference
+                if "special_tokens_mask" in encoded_inputs:
+                    encoded_inputs["special_tokens_mask"] = encoded_inputs["special_tokens_mask"] + [1] * difference
+                encoded_inputs[self.model_input_names[0]] = required_input + [self.pad_token_id] * difference
+            elif self.padding_side == "left":
+                if return_attention_mask:
+                    encoded_inputs["attention_mask"] = [0] * difference + encoded_inputs["attention_mask"]
+                if "token_type_ids" in encoded_inputs:
+                    encoded_inputs["token_type_ids"] = [self.pad_token_type_id] * difference + encoded_inputs[
+                        "token_type_ids"
+                    ]
+                if "bbox" in encoded_inputs:
+                    encoded_inputs["bbox"] = [self.pad_token_box] * difference + encoded_inputs["bbox"]
+                if "labels" in encoded_inputs:
+                    encoded_inputs["labels"] = [self.pad_token_label] * difference + encoded_inputs["labels"]
+                if "special_tokens_mask" in encoded_inputs:
+                    encoded_inputs["special_tokens_mask"] = [1] * difference + encoded_inputs["special_tokens_mask"]
+                encoded_inputs[self.model_input_names[0]] = [self.pad_token_id] * difference + required_input
+            else:
+                raise ValueError("Invalid padding strategy:" + str(self.padding_side))
+
+        return encoded_inputs
+
+    def build_inputs_with_special_tokens(self, token_ids_0, token_ids_1=None):
+        """
+        Build model inputs from a sequence or a pair of sequence for sequence classification tasks by concatenating and
+        adding special tokens. A BERT sequence has the following format:
+
+        - single sequence: `[CLS] X [SEP]`
+        - pair of sequences: `[CLS] A [SEP] B [SEP]`
+
+        Args:
+            token_ids_0 (`List[int]`):
+                List of IDs to which the special tokens will be added.
+            token_ids_1 (`List[int]`, *optional*):
+                Optional second list of IDs for sequence pairs.
+
+        Returns:
+            `List[int]`: List of [input IDs](../glossary#input-ids) with the appropriate special tokens.
+        """
+        output = [self.cls_token_id] + token_ids_0 + [self.sep_token_id]
+
+        if token_ids_1:
+            output += token_ids_1 + [self.sep_token_id]
+
+        return output
+
+    def create_token_type_ids_from_sequences(
+        self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None
+    ) -> List[int]:
+        """
+        Create a mask from the two sequences passed to be used in a sequence-pair classification task. A BERT sequence
+        pair mask has the following format: :: 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 | first sequence | second
+        sequence | If `token_ids_1` is `None`, this method only returns the first portion of the mask (0s).
+
+        Args:
+            token_ids_0 (`List[int]`):
+                List of IDs.
+            token_ids_1 (`List[int]`, *optional*):
+                Optional second list of IDs for sequence pairs.
+
+        Returns:
+            `List[int]`: List of [token type IDs](../glossary#token-type-ids) according to the given sequence(s).
+        """
+        sep = [self.sep_token_id]
+        cls = [self.cls_token_id]
+        if token_ids_1 is None:
+            return len(cls + token_ids_0 + sep) * [0]
+        return len(cls + token_ids_0 + sep) * [0] + len(token_ids_1 + sep) * [1]
+
+    def save_vocabulary(self, save_directory: str, filename_prefix: Optional[str] = None) -> Tuple[str]:
+        files = self._tokenizer.model.save(save_directory, name=filename_prefix)
+        return tuple(files)

llmeval-env/lib/python3.10/site-packages/transformers/models/layoutlmv3/tokenization_layoutlmv3_fast.py

@@ -0,0 +1,837 @@
+# coding=utf-8
+# Copyright 2022 The HuggingFace Inc. team.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+Fast tokenization class for LayoutLMv3. It overwrites 2 methods of the slow tokenizer class, namely _batch_encode_plus
+and _encode_plus, in which the Rust tokenizer is used.
+"""
+
+import json
+from typing import Dict, List, Optional, Tuple, Union
+
+from tokenizers import pre_tokenizers, processors
+
+from ...tokenization_utils_base import (
+    BatchEncoding,
+    EncodedInput,
+    PaddingStrategy,
+    PreTokenizedInput,
+    TensorType,
+    TextInput,
+    TextInputPair,
+    TruncationStrategy,
+)
+from ...tokenization_utils_fast import PreTrainedTokenizerFast
+from ...utils import add_end_docstrings, logging
+from .tokenization_layoutlmv3 import (
+    LAYOUTLMV3_ENCODE_KWARGS_DOCSTRING,
+    LAYOUTLMV3_ENCODE_PLUS_ADDITIONAL_KWARGS_DOCSTRING,
+    LayoutLMv3Tokenizer,
+)
+
+
+logger = logging.get_logger(__name__)
+
+VOCAB_FILES_NAMES = {"vocab_file": "vocab.json", "merges_file": "merges.txt", "tokenizer_file": "tokenizer.json"}
+
+
+class LayoutLMv3TokenizerFast(PreTrainedTokenizerFast):
+    r"""
+    Construct a "fast" LayoutLMv3 tokenizer (backed by HuggingFace's *tokenizers* library). Based on BPE.
+
+    This tokenizer inherits from [`PreTrainedTokenizerFast`] which contains most of the main methods. Users should
+    refer to this superclass for more information regarding those methods.
+
+    Args:
+        vocab_file (`str`):
+            Path to the vocabulary file.
+        merges_file (`str`):
+            Path to the merges file.
+        errors (`str`, *optional*, defaults to `"replace"`):
+            Paradigm to follow when decoding bytes to UTF-8. See
+            [bytes.decode](https://docs.python.org/3/library/stdtypes.html#bytes.decode) for more information.
+        bos_token (`str`, *optional*, defaults to `"<s>"`):
+            The beginning of sequence token that was used during pretraining. Can be used a sequence classifier token.
+
+            <Tip>
+
+            When building a sequence using special tokens, this is not the token that is used for the beginning of
+            sequence. The token used is the `cls_token`.
+
+            </Tip>
+
+        eos_token (`str`, *optional*, defaults to `"</s>"`):
+            The end of sequence token.
+
+            <Tip>
+
+            When building a sequence using special tokens, this is not the token that is used for the end of sequence.
+            The token used is the `sep_token`.
+
+            </Tip>
+
+        sep_token (`str`, *optional*, defaults to `"</s>"`):
+            The separator token, which is used when building a sequence from multiple sequences, e.g. two sequences for
+            sequence classification or for a text and a question for question answering. It is also used as the last
+            token of a sequence built with special tokens.
+        cls_token (`str`, *optional*, defaults to `"<s>"`):
+            The classifier token which is used when doing sequence classification (classification of the whole sequence
+            instead of per-token classification). It is the first token of the sequence when built with special tokens.
+        unk_token (`str`, *optional*, defaults to `"<unk>"`):
+            The unknown token. A token that is not in the vocabulary cannot be converted to an ID and is set to be this
+            token instead.
+        pad_token (`str`, *optional*, defaults to `"<pad>"`):
+            The token used for padding, for example when batching sequences of different lengths.
+        mask_token (`str`, *optional*, defaults to `"<mask>"`):
+            The token used for masking values. This is the token used when training this model with masked language
+            modeling. This is the token which the model will try to predict.
+        add_prefix_space (`bool`, *optional*, defaults to `False`):
+            Whether or not to add an initial space to the input. This allows to treat the leading word just as any
+            other word. (RoBERTa tokenizer detect beginning of words by the preceding space).
+        trim_offsets (`bool`, *optional*, defaults to `True`):
+            Whether the post processing step should trim offsets to avoid including whitespaces.
+        cls_token_box (`List[int]`, *optional*, defaults to `[0, 0, 0, 0]`):
+            The bounding box to use for the special [CLS] token.
+        sep_token_box (`List[int]`, *optional*, defaults to `[0, 0, 0, 0]`):
+            The bounding box to use for the special [SEP] token.
+        pad_token_box (`List[int]`, *optional*, defaults to `[0, 0, 0, 0]`):
+            The bounding box to use for the special [PAD] token.
+        pad_token_label (`int`, *optional*, defaults to -100):
+            The label to use for padding tokens. Defaults to -100, which is the `ignore_index` of PyTorch's
+            CrossEntropyLoss.
+        only_label_first_subword (`bool`, *optional*, defaults to `True`):
+            Whether or not to only label the first subword, in case word labels are provided.
+    """
+
+    vocab_files_names = VOCAB_FILES_NAMES
+    model_input_names = ["input_ids", "attention_mask"]
+    slow_tokenizer_class = LayoutLMv3Tokenizer
+
+    def __init__(
+        self,
+        vocab_file=None,
+        merges_file=None,
+        tokenizer_file=None,
+        errors="replace",
+        bos_token="<s>",
+        eos_token="</s>",
+        sep_token="</s>",
+        cls_token="<s>",
+        unk_token="<unk>",
+        pad_token="<pad>",
+        mask_token="<mask>",
+        add_prefix_space=True,
+        trim_offsets=True,
+        cls_token_box=[0, 0, 0, 0],
+        sep_token_box=[0, 0, 0, 0],
+        pad_token_box=[0, 0, 0, 0],
+        pad_token_label=-100,
+        only_label_first_subword=True,
+        **kwargs,
+    ):
+        super().__init__(
+            vocab_file,
+            merges_file,
+            tokenizer_file=tokenizer_file,
+            errors=errors,
+            bos_token=bos_token,
+            eos_token=eos_token,
+            sep_token=sep_token,
+            cls_token=cls_token,
+            unk_token=unk_token,
+            pad_token=pad_token,
+            mask_token=mask_token,
+            add_prefix_space=add_prefix_space,
+            trim_offsets=trim_offsets,
+            cls_token_box=cls_token_box,
+            sep_token_box=sep_token_box,
+            pad_token_box=pad_token_box,
+            pad_token_label=pad_token_label,
+            only_label_first_subword=only_label_first_subword,
+            **kwargs,
+        )
+
+        pre_tok_state = json.loads(self.backend_tokenizer.pre_tokenizer.__getstate__())
+        if pre_tok_state.get("add_prefix_space", add_prefix_space) != add_prefix_space:
+            pre_tok_class = getattr(pre_tokenizers, pre_tok_state.pop("type"))
+            pre_tok_state["add_prefix_space"] = add_prefix_space
+            self.backend_tokenizer.pre_tokenizer = pre_tok_class(**pre_tok_state)
+
+        self.add_prefix_space = add_prefix_space
+
+        tokenizer_component = "post_processor"
+        tokenizer_component_instance = getattr(self.backend_tokenizer, tokenizer_component, None)
+        if tokenizer_component_instance:
+            state = json.loads(tokenizer_component_instance.__getstate__())
+
+            # The lists 'sep' and 'cls' must be cased in tuples for the object `post_processor_class`
+            if "sep" in state:
+                state["sep"] = tuple(state["sep"])
+            if "cls" in state:
+                state["cls"] = tuple(state["cls"])
+
+            changes_to_apply = False
+
+            if state.get("add_prefix_space", add_prefix_space) != add_prefix_space:
+                state["add_prefix_space"] = add_prefix_space
+                changes_to_apply = True
+
+            if state.get("trim_offsets", trim_offsets) != trim_offsets:
+                state["trim_offsets"] = trim_offsets
+                changes_to_apply = True
+
+            if changes_to_apply:
+                component_class = getattr(processors, state.pop("type"))
+                new_value = component_class(**state)
+                setattr(self.backend_tokenizer, tokenizer_component, new_value)
+
+        # additional properties
+        self.cls_token_box = cls_token_box
+        self.sep_token_box = sep_token_box
+        self.pad_token_box = pad_token_box
+        self.pad_token_label = pad_token_label
+        self.only_label_first_subword = only_label_first_subword
+
+    @add_end_docstrings(LAYOUTLMV3_ENCODE_KWARGS_DOCSTRING, LAYOUTLMV3_ENCODE_PLUS_ADDITIONAL_KWARGS_DOCSTRING)
+    # Copied from transformers.models.layoutlmv2.tokenization_layoutlmv2_fast.LayoutLMv2TokenizerFast.__call__
+    def __call__(
+        self,
+        text: Union[TextInput, PreTokenizedInput, List[TextInput], List[PreTokenizedInput]],
+        text_pair: Optional[Union[PreTokenizedInput, List[PreTokenizedInput]]] = None,
+        boxes: Union[List[List[int]], List[List[List[int]]]] = None,
+        word_labels: Optional[Union[List[int], List[List[int]]]] = None,
+        add_special_tokens: bool = True,
+        padding: Union[bool, str, PaddingStrategy] = False,
+        truncation: Union[bool, str, TruncationStrategy] = None,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[Union[str, TensorType]] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+        **kwargs,
+    ) -> BatchEncoding:
+        """
+        Main method to tokenize and prepare for the model one or several sequence(s) or one or several pair(s) of
+        sequences with word-level normalized bounding boxes and optional labels.
+
+        Args:
+            text (`str`, `List[str]`, `List[List[str]]`):
+                The sequence or batch of sequences to be encoded. Each sequence can be a string, a list of strings
+                (words of a single example or questions of a batch of examples) or a list of list of strings (batch of
+                words).
+            text_pair (`List[str]`, `List[List[str]]`):
+                The sequence or batch of sequences to be encoded. Each sequence should be a list of strings
+                (pretokenized string).
+            boxes (`List[List[int]]`, `List[List[List[int]]]`):
+                Word-level bounding boxes. Each bounding box should be normalized to be on a 0-1000 scale.
+            word_labels (`List[int]`, `List[List[int]]`, *optional*):
+                Word-level integer labels (for token classification tasks such as FUNSD, CORD).
+        """
+
+        # Input type checking for clearer error
+        def _is_valid_text_input(t):
+            if isinstance(t, str):
+                # Strings are fine
+                return True
+            elif isinstance(t, (list, tuple)):
+                # List are fine as long as they are...
+                if len(t) == 0:
+                    # ... empty
+                    return True
+                elif isinstance(t[0], str):
+                    # ... list of strings
+                    return True
+                elif isinstance(t[0], (list, tuple)):
+                    # ... list with an empty list or with a list of strings
+                    return len(t[0]) == 0 or isinstance(t[0][0], str)
+                else:
+                    return False
+            else:
+                return False
+
+        if text_pair is not None:
+            # in case text + text_pair are provided, text = questions, text_pair = words
+            if not _is_valid_text_input(text):
+                raise ValueError("text input must of type `str` (single example) or `List[str]` (batch of examples). ")
+            if not isinstance(text_pair, (list, tuple)):
+                raise ValueError(
+                    "Words must be of type `List[str]` (single pretokenized example), "
+                    "or `List[List[str]]` (batch of pretokenized examples)."
+                )
+        else:
+            # in case only text is provided => must be words
+            if not isinstance(text, (list, tuple)):
+                raise ValueError(
+                    "Words must be of type `List[str]` (single pretokenized example), "
+                    "or `List[List[str]]` (batch of pretokenized examples)."
+                )
+
+        if text_pair is not None:
+            is_batched = isinstance(text, (list, tuple))
+        else:
+            is_batched = isinstance(text, (list, tuple)) and text and isinstance(text[0], (list, tuple))
+
+        words = text if text_pair is None else text_pair
+        if boxes is None:
+            raise ValueError("You must provide corresponding bounding boxes")
+        if is_batched:
+            if len(words) != len(boxes):
+                raise ValueError("You must provide words and boxes for an equal amount of examples")
+            for words_example, boxes_example in zip(words, boxes):
+                if len(words_example) != len(boxes_example):
+                    raise ValueError("You must provide as many words as there are bounding boxes")
+        else:
+            if len(words) != len(boxes):
+                raise ValueError("You must provide as many words as there are bounding boxes")
+
+        if is_batched:
+            if text_pair is not None and len(text) != len(text_pair):
+                raise ValueError(
+                    f"batch length of `text`: {len(text)} does not match batch length of `text_pair`:"
+                    f" {len(text_pair)}."
+                )
+            batch_text_or_text_pairs = list(zip(text, text_pair)) if text_pair is not None else text
+            is_pair = bool(text_pair is not None)
+            return self.batch_encode_plus(
+                batch_text_or_text_pairs=batch_text_or_text_pairs,
+                is_pair=is_pair,
+                boxes=boxes,
+                word_labels=word_labels,
+                add_special_tokens=add_special_tokens,
+                padding=padding,
+                truncation=truncation,
+                max_length=max_length,
+                stride=stride,
+                pad_to_multiple_of=pad_to_multiple_of,
+                return_tensors=return_tensors,
+                return_token_type_ids=return_token_type_ids,
+                return_attention_mask=return_attention_mask,
+                return_overflowing_tokens=return_overflowing_tokens,
+                return_special_tokens_mask=return_special_tokens_mask,
+                return_offsets_mapping=return_offsets_mapping,
+                return_length=return_length,
+                verbose=verbose,
+                **kwargs,
+            )
+        else:
+            return self.encode_plus(
+                text=text,
+                text_pair=text_pair,
+                boxes=boxes,
+                word_labels=word_labels,
+                add_special_tokens=add_special_tokens,
+                padding=padding,
+                truncation=truncation,
+                max_length=max_length,
+                stride=stride,
+                pad_to_multiple_of=pad_to_multiple_of,
+                return_tensors=return_tensors,
+                return_token_type_ids=return_token_type_ids,
+                return_attention_mask=return_attention_mask,
+                return_overflowing_tokens=return_overflowing_tokens,
+                return_special_tokens_mask=return_special_tokens_mask,
+                return_offsets_mapping=return_offsets_mapping,
+                return_length=return_length,
+                verbose=verbose,
+                **kwargs,
+            )
+
+    @add_end_docstrings(LAYOUTLMV3_ENCODE_KWARGS_DOCSTRING, LAYOUTLMV3_ENCODE_PLUS_ADDITIONAL_KWARGS_DOCSTRING)
+    # Copied from transformers.models.layoutlmv2.tokenization_layoutlmv2_fast.LayoutLMv2TokenizerFast.batch_encode_plus
+    def batch_encode_plus(
+        self,
+        batch_text_or_text_pairs: Union[
+            List[TextInput],
+            List[TextInputPair],
+            List[PreTokenizedInput],
+        ],
+        is_pair: bool = None,
+        boxes: Optional[List[List[List[int]]]] = None,
+        word_labels: Optional[Union[List[int], List[List[int]]]] = None,
+        add_special_tokens: bool = True,
+        padding: Union[bool, str, PaddingStrategy] = False,
+        truncation: Union[bool, str, TruncationStrategy] = None,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[Union[str, TensorType]] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+        **kwargs,
+    ) -> BatchEncoding:
+        # Backward compatibility for 'truncation_strategy', 'pad_to_max_length'
+        padding_strategy, truncation_strategy, max_length, kwargs = self._get_padding_truncation_strategies(
+            padding=padding,
+            truncation=truncation,
+            max_length=max_length,
+            pad_to_multiple_of=pad_to_multiple_of,
+            verbose=verbose,
+            **kwargs,
+        )
+
+        return self._batch_encode_plus(
+            batch_text_or_text_pairs=batch_text_or_text_pairs,
+            is_pair=is_pair,
+            boxes=boxes,
+            word_labels=word_labels,
+            add_special_tokens=add_special_tokens,
+            padding_strategy=padding_strategy,
+            truncation_strategy=truncation_strategy,
+            max_length=max_length,
+            stride=stride,
+            pad_to_multiple_of=pad_to_multiple_of,
+            return_tensors=return_tensors,
+            return_token_type_ids=return_token_type_ids,
+            return_attention_mask=return_attention_mask,
+            return_overflowing_tokens=return_overflowing_tokens,
+            return_special_tokens_mask=return_special_tokens_mask,
+            return_offsets_mapping=return_offsets_mapping,
+            return_length=return_length,
+            verbose=verbose,
+            **kwargs,
+        )
+
+    # Copied from transformers.models.layoutlmv2.tokenization_layoutlmv2_fast.LayoutLMv2TokenizerFast.tokenize
+    def tokenize(self, text: str, pair: Optional[str] = None, add_special_tokens: bool = False, **kwargs) -> List[str]:
+        batched_input = [(text, pair)] if pair else [text]
+        encodings = self._tokenizer.encode_batch(
+            batched_input, add_special_tokens=add_special_tokens, is_pretokenized=False, **kwargs
+        )
+
+        return encodings[0].tokens
+
+    @add_end_docstrings(LAYOUTLMV3_ENCODE_KWARGS_DOCSTRING, LAYOUTLMV3_ENCODE_PLUS_ADDITIONAL_KWARGS_DOCSTRING)
+    # Copied from transformers.models.layoutlmv2.tokenization_layoutlmv2_fast.LayoutLMv2TokenizerFast.encode_plus
+    def encode_plus(
+        self,
+        text: Union[TextInput, PreTokenizedInput],
+        text_pair: Optional[PreTokenizedInput] = None,
+        boxes: Optional[List[List[int]]] = None,
+        word_labels: Optional[List[int]] = None,
+        add_special_tokens: bool = True,
+        padding: Union[bool, str, PaddingStrategy] = False,
+        truncation: Union[bool, str, TruncationStrategy] = None,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[Union[str, TensorType]] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+        **kwargs,
+    ) -> BatchEncoding:
+        """
+        Tokenize and prepare for the model a sequence or a pair of sequences. .. warning:: This method is deprecated,
+        `__call__` should be used instead.
+
+        Args:
+            text (`str`, `List[str]`, `List[List[str]]`):
+                The first sequence to be encoded. This can be a string, a list of strings or a list of list of strings.
+            text_pair (`List[str]` or `List[int]`, *optional*):
+                Optional second sequence to be encoded. This can be a list of strings (words of a single example) or a
+                list of list of strings (words of a batch of examples).
+        """
+
+        # Backward compatibility for 'truncation_strategy', 'pad_to_max_length'
+        padding_strategy, truncation_strategy, max_length, kwargs = self._get_padding_truncation_strategies(
+            padding=padding,
+            truncation=truncation,
+            max_length=max_length,
+            pad_to_multiple_of=pad_to_multiple_of,
+            verbose=verbose,
+            **kwargs,
+        )
+
+        return self._encode_plus(
+            text=text,
+            boxes=boxes,
+            text_pair=text_pair,
+            word_labels=word_labels,
+            add_special_tokens=add_special_tokens,
+            padding_strategy=padding_strategy,
+            truncation_strategy=truncation_strategy,
+            max_length=max_length,
+            stride=stride,
+            pad_to_multiple_of=pad_to_multiple_of,
+            return_tensors=return_tensors,
+            return_token_type_ids=return_token_type_ids,
+            return_attention_mask=return_attention_mask,
+            return_overflowing_tokens=return_overflowing_tokens,
+            return_special_tokens_mask=return_special_tokens_mask,
+            return_offsets_mapping=return_offsets_mapping,
+            return_length=return_length,
+            verbose=verbose,
+            **kwargs,
+        )
+
+    def _batch_encode_plus(
+        self,
+        batch_text_or_text_pairs: Union[
+            List[TextInput],
+            List[TextInputPair],
+            List[PreTokenizedInput],
+        ],
+        is_pair: bool = None,
+        boxes: Optional[List[List[List[int]]]] = None,
+        word_labels: Optional[List[List[int]]] = None,
+        add_special_tokens: bool = True,
+        padding_strategy: PaddingStrategy = PaddingStrategy.DO_NOT_PAD,
+        truncation_strategy: TruncationStrategy = TruncationStrategy.DO_NOT_TRUNCATE,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[str] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+    ) -> BatchEncoding:
+        if not isinstance(batch_text_or_text_pairs, list):
+            raise TypeError(f"batch_text_or_text_pairs has to be a list (got {type(batch_text_or_text_pairs)})")
+
+        # Set the truncation and padding strategy and restore the initial configuration
+        self.set_truncation_and_padding(
+            padding_strategy=padding_strategy,
+            truncation_strategy=truncation_strategy,
+            max_length=max_length,
+            stride=stride,
+            pad_to_multiple_of=pad_to_multiple_of,
+        )
+
+        if is_pair:
+            batch_text_or_text_pairs = [(text.split(), text_pair) for text, text_pair in batch_text_or_text_pairs]
+
+        encodings = self._tokenizer.encode_batch(
+            batch_text_or_text_pairs,
+            add_special_tokens=add_special_tokens,
+            is_pretokenized=True,  # we set this to True as LayoutLMv3 always expects pretokenized inputs
+        )
+
+        # Convert encoding to dict
+        # `Tokens` has type: Tuple[
+        #                       List[Dict[str, List[List[int]]]] or List[Dict[str, 2D-Tensor]],
+        #                       List[EncodingFast]
+        #                    ]
+        # with nested dimensions corresponding to batch, overflows, sequence length
+        tokens_and_encodings = [
+            self._convert_encoding(
+                encoding=encoding,
+                return_token_type_ids=return_token_type_ids,
+                return_attention_mask=return_attention_mask,
+                return_overflowing_tokens=return_overflowing_tokens,
+                return_special_tokens_mask=return_special_tokens_mask,
+                return_offsets_mapping=True
+                if word_labels is not None
+                else return_offsets_mapping,  # we use offsets to create the labels
+                return_length=return_length,
+                verbose=verbose,
+            )
+            for encoding in encodings
+        ]
+
+        # Convert the output to have dict[list] from list[dict] and remove the additional overflows dimension
+        # From (variable) shape (batch, overflows, sequence length) to ~ (batch * overflows, sequence length)
+        # (we say ~ because the number of overflow varies with the example in the batch)
+        #
+        # To match each overflowing sample with the original sample in the batch
+        # we add an overflow_to_sample_mapping array (see below)
+        sanitized_tokens = {}
+        for key in tokens_and_encodings[0][0].keys():
+            stack = [e for item, _ in tokens_and_encodings for e in item[key]]
+            sanitized_tokens[key] = stack
+        sanitized_encodings = [e for _, item in tokens_and_encodings for e in item]
+
+        # If returning overflowing tokens, we need to return a mapping
+        # from the batch idx to the original sample
+        if return_overflowing_tokens:
+            overflow_to_sample_mapping = []
+            for i, (toks, _) in enumerate(tokens_and_encodings):
+                overflow_to_sample_mapping += [i] * len(toks["input_ids"])
+            sanitized_tokens["overflow_to_sample_mapping"] = overflow_to_sample_mapping
+
+        for input_ids in sanitized_tokens["input_ids"]:
+            self._eventual_warn_about_too_long_sequence(input_ids, max_length, verbose)
+
+        # create the token boxes
+        token_boxes = []
+        for batch_index in range(len(sanitized_tokens["input_ids"])):
+            if return_overflowing_tokens:
+                original_index = sanitized_tokens["overflow_to_sample_mapping"][batch_index]
+            else:
+                original_index = batch_index
+            token_boxes_example = []
+            for id, sequence_id, word_id in zip(
+                sanitized_tokens["input_ids"][batch_index],
+                sanitized_encodings[batch_index].sequence_ids,
+                sanitized_encodings[batch_index].word_ids,
+            ):
+                if word_id is not None:
+                    if is_pair and sequence_id == 0:
+                        token_boxes_example.append(self.pad_token_box)
+                    else:
+                        token_boxes_example.append(boxes[original_index][word_id])
+                else:
+                    if id == self.cls_token_id:
+                        token_boxes_example.append(self.cls_token_box)
+                    elif id == self.sep_token_id:
+                        token_boxes_example.append(self.sep_token_box)
+                    elif id == self.pad_token_id:
+                        token_boxes_example.append(self.pad_token_box)
+                    else:
+                        raise ValueError("Id not recognized")
+            token_boxes.append(token_boxes_example)
+
+        sanitized_tokens["bbox"] = token_boxes
+
+        # optionally, create the labels
+        if word_labels is not None:
+            labels = []
+            for batch_index in range(len(sanitized_tokens["input_ids"])):
+                if return_overflowing_tokens:
+                    original_index = sanitized_tokens["overflow_to_sample_mapping"][batch_index]
+                else:
+                    original_index = batch_index
+                labels_example = []
+                previous_token_empty = False
+                for id, offset, word_id in zip(
+                    sanitized_tokens["input_ids"][batch_index],
+                    sanitized_tokens["offset_mapping"][batch_index],
+                    sanitized_encodings[batch_index].word_ids,
+                ):
+                    if word_id is not None:
+                        if self.only_label_first_subword:
+                            if offset[0] == 0 and not previous_token_empty:
+                                # Use the real label id for the first token of the word, and padding ids for the remaining tokens
+                                labels_example.append(word_labels[original_index][word_id])
+                            else:
+                                labels_example.append(self.pad_token_label)
+                            if offset == (0, 0):
+                                previous_token_empty = True
+                            else:
+                                previous_token_empty = False
+                        else:
+                            labels_example.append(word_labels[original_index][word_id])
+                    else:
+                        labels_example.append(self.pad_token_label)
+                labels.append(labels_example)
+
+            sanitized_tokens["labels"] = labels
+            # finally, remove offsets if the user didn't want them
+            if not return_offsets_mapping:
+                del sanitized_tokens["offset_mapping"]
+
+        return BatchEncoding(sanitized_tokens, sanitized_encodings, tensor_type=return_tensors)
+
+    # Copied from transformers.models.layoutlmv2.tokenization_layoutlmv2_fast.LayoutLMv2TokenizerFast._encode_plus
+    def _encode_plus(
+        self,
+        text: Union[TextInput, PreTokenizedInput],
+        text_pair: Optional[PreTokenizedInput] = None,
+        boxes: Optional[List[List[int]]] = None,
+        word_labels: Optional[List[int]] = None,
+        add_special_tokens: bool = True,
+        padding_strategy: PaddingStrategy = PaddingStrategy.DO_NOT_PAD,
+        truncation_strategy: TruncationStrategy = TruncationStrategy.DO_NOT_TRUNCATE,
+        max_length: Optional[int] = None,
+        stride: int = 0,
+        pad_to_multiple_of: Optional[int] = None,
+        return_tensors: Optional[bool] = None,
+        return_token_type_ids: Optional[bool] = None,
+        return_attention_mask: Optional[bool] = None,
+        return_overflowing_tokens: bool = False,
+        return_special_tokens_mask: bool = False,
+        return_offsets_mapping: bool = False,
+        return_length: bool = False,
+        verbose: bool = True,
+        **kwargs,
+    ) -> BatchEncoding:
+        # make it a batched input
+        # 2 options:
+        # 1) only text, in case text must be a list of str
+        # 2) text + text_pair, in which case text = str and text_pair a list of str
+        batched_input = [(text, text_pair)] if text_pair else [text]
+        batched_boxes = [boxes]
+        batched_word_labels = [word_labels] if word_labels is not None else None
+        batched_output = self._batch_encode_plus(
+            batched_input,
+            is_pair=bool(text_pair is not None),
+            boxes=batched_boxes,
+            word_labels=batched_word_labels,
+            add_special_tokens=add_special_tokens,
+            padding_strategy=padding_strategy,
+            truncation_strategy=truncation_strategy,
+            max_length=max_length,
+            stride=stride,
+            pad_to_multiple_of=pad_to_multiple_of,
+            return_tensors=return_tensors,
+            return_token_type_ids=return_token_type_ids,
+            return_attention_mask=return_attention_mask,
+            return_overflowing_tokens=return_overflowing_tokens,
+            return_special_tokens_mask=return_special_tokens_mask,
+            return_offsets_mapping=return_offsets_mapping,
+            return_length=return_length,
+            verbose=verbose,
+            **kwargs,
+        )
+
+        # Return tensor is None, then we can remove the leading batch axis
+        # Overflowing tokens are returned as a batch of output so we keep them in this case
+        if return_tensors is None and not return_overflowing_tokens:
+            batched_output = BatchEncoding(
+                {
+                    key: value[0] if len(value) > 0 and isinstance(value[0], list) else value
+                    for key, value in batched_output.items()
+                },
+                batched_output.encodings,
+            )
+
+        self._eventual_warn_about_too_long_sequence(batched_output["input_ids"], max_length, verbose)
+
+        return batched_output
+
+    # Copied from transformers.models.layoutlmv2.tokenization_layoutlmv2_fast.LayoutLMv2TokenizerFast._pad
+    def _pad(
+        self,
+        encoded_inputs: Union[Dict[str, EncodedInput], BatchEncoding],
+        max_length: Optional[int] = None,
+        padding_strategy: PaddingStrategy = PaddingStrategy.DO_NOT_PAD,
+        pad_to_multiple_of: Optional[int] = None,
+        return_attention_mask: Optional[bool] = None,
+    ) -> dict:
+        """
+        Pad encoded inputs (on left/right and up to predefined length or max length in the batch)
+
+        Args:
+            encoded_inputs:
+                Dictionary of tokenized inputs (`List[int]`) or batch of tokenized inputs (`List[List[int]]`).
+            max_length: maximum length of the returned list and optionally padding length (see below).
+                Will truncate by taking into account the special tokens.
+            padding_strategy: PaddingStrategy to use for padding.
+
+                - PaddingStrategy.LONGEST Pad to the longest sequence in the batch
+                - PaddingStrategy.MAX_LENGTH: Pad to the max length (default)
+                - PaddingStrategy.DO_NOT_PAD: Do not pad
+                The tokenizer padding sides are defined in self.padding_side:
+
+                    - 'left': pads on the left of the sequences
+                    - 'right': pads on the right of the sequences
+            pad_to_multiple_of: (optional) Integer if set will pad the sequence to a multiple of the provided value.
+                This is especially useful to enable the use of Tensor Core on NVIDIA hardware with compute capability
+                `>= 7.5` (Volta).
+            return_attention_mask:
+                (optional) Set to False to avoid returning attention mask (default: set to model specifics)
+        """
+        # Load from model defaults
+        if return_attention_mask is None:
+            return_attention_mask = "attention_mask" in self.model_input_names
+
+        required_input = encoded_inputs[self.model_input_names[0]]
+
+        if padding_strategy == PaddingStrategy.LONGEST:
+            max_length = len(required_input)
+
+        if max_length is not None and pad_to_multiple_of is not None and (max_length % pad_to_multiple_of != 0):
+            max_length = ((max_length // pad_to_multiple_of) + 1) * pad_to_multiple_of
+
+        needs_to_be_padded = padding_strategy != PaddingStrategy.DO_NOT_PAD and len(required_input) != max_length
+
+        # Initialize attention mask if not present.
+        if return_attention_mask and "attention_mask" not in encoded_inputs:
+            encoded_inputs["attention_mask"] = [1] * len(required_input)
+
+        if needs_to_be_padded:
+            difference = max_length - len(required_input)
+            if self.padding_side == "right":
+                if return_attention_mask:
+                    encoded_inputs["attention_mask"] = encoded_inputs["attention_mask"] + [0] * difference
+                if "token_type_ids" in encoded_inputs:
+                    encoded_inputs["token_type_ids"] = (
+                        encoded_inputs["token_type_ids"] + [self.pad_token_type_id] * difference
+                    )
+                if "bbox" in encoded_inputs:
+                    encoded_inputs["bbox"] = encoded_inputs["bbox"] + [self.pad_token_box] * difference
+                if "labels" in encoded_inputs:
+                    encoded_inputs["labels"] = encoded_inputs["labels"] + [self.pad_token_label] * difference
+                if "special_tokens_mask" in encoded_inputs:
+                    encoded_inputs["special_tokens_mask"] = encoded_inputs["special_tokens_mask"] + [1] * difference
+                encoded_inputs[self.model_input_names[0]] = required_input + [self.pad_token_id] * difference
+            elif self.padding_side == "left":
+                if return_attention_mask:
+                    encoded_inputs["attention_mask"] = [0] * difference + encoded_inputs["attention_mask"]
+                if "token_type_ids" in encoded_inputs:
+                    encoded_inputs["token_type_ids"] = [self.pad_token_type_id] * difference + encoded_inputs[
+                        "token_type_ids"
+                    ]
+                if "bbox" in encoded_inputs:
+                    encoded_inputs["bbox"] = [self.pad_token_box] * difference + encoded_inputs["bbox"]
+                if "labels" in encoded_inputs:
+                    encoded_inputs["labels"] = [self.pad_token_label] * difference + encoded_inputs["labels"]
+                if "special_tokens_mask" in encoded_inputs:
+                    encoded_inputs["special_tokens_mask"] = [1] * difference + encoded_inputs["special_tokens_mask"]
+                encoded_inputs[self.model_input_names[0]] = [self.pad_token_id] * difference + required_input
+            else:
+                raise ValueError("Invalid padding strategy:" + str(self.padding_side))
+
+        return encoded_inputs
+
+    # Copied from transformers.models.layoutlmv2.tokenization_layoutlmv2_fast.LayoutLMv2TokenizerFast.save_vocabulary
+    def save_vocabulary(self, save_directory: str, filename_prefix: Optional[str] = None) -> Tuple[str]:
+        files = self._tokenizer.model.save(save_directory, name=filename_prefix)
+        return tuple(files)
+
+    def build_inputs_with_special_tokens(self, token_ids_0, token_ids_1=None):
+        output = [self.bos_token_id] + token_ids_0 + [self.eos_token_id]
+        if token_ids_1 is None:
+            return output
+
+        return output + [self.eos_token_id] + token_ids_1 + [self.eos_token_id]
+
+    def create_token_type_ids_from_sequences(
+        self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None
+    ) -> List[int]:
+        """
+        Args:
+        Create a mask from the two sequences passed to be used in a sequence-pair classification task. RoBERTa does not:
+        make use of token type ids, therefore a list of zeros is returned.
+            token_ids_0 (`List[int]`):
+                List of IDs.
+            token_ids_1 (`List[int]`, *optional*):
+                Optional second list of IDs for sequence pairs.
+        Returns:
+            `List[int]`: List of zeros.
+        """
+        sep = [self.sep_token_id]
+        cls = [self.cls_token_id]
+
+        if token_ids_1 is None:
+            return len(cls + token_ids_0 + sep) * [0]
+        return len(cls + token_ids_0 + sep + sep + token_ids_1 + sep) * [0]

llmeval-env/lib/python3.10/site-packages/transformers/models/mbart50/__init__.py

@@ -0,0 +1,58 @@
+# Copyright 2020 The HuggingFace Team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+from typing import TYPE_CHECKING
+
+from ...utils import OptionalDependencyNotAvailable, _LazyModule, is_sentencepiece_available, is_tokenizers_available
+
+
+_import_structure = {}
+
+try:
+    if not is_sentencepiece_available():
+        raise OptionalDependencyNotAvailable()
+except OptionalDependencyNotAvailable:
+    pass
+else:
+    _import_structure["tokenization_mbart50"] = ["MBart50Tokenizer"]
+
+try:
+    if not is_tokenizers_available():
+        raise OptionalDependencyNotAvailable()
+except OptionalDependencyNotAvailable:
+    pass
+else:
+    _import_structure["tokenization_mbart50_fast"] = ["MBart50TokenizerFast"]
+
+
+if TYPE_CHECKING:
+    try:
+        if not is_sentencepiece_available():
+            raise OptionalDependencyNotAvailable()
+    except OptionalDependencyNotAvailable:
+        pass
+    else:
+        from .tokenization_mbart50 import MBart50Tokenizer
+
+    try:
+        if not is_tokenizers_available():
+            raise OptionalDependencyNotAvailable()
+    except OptionalDependencyNotAvailable:
+        pass
+    else:
+        from .tokenization_mbart50_fast import MBart50TokenizerFast
+
+else:
+    import sys
+
+    sys.modules[__name__] = _LazyModule(__name__, globals()["__file__"], _import_structure, module_spec=__spec__)

llmeval-env/lib/python3.10/site-packages/transformers/models/mbart50/tokenization_mbart50.py

@@ -0,0 +1,354 @@
+# coding=utf-8
+# Copyright 2021 The Facebook AI Research Team Authors and The HuggingFace Inc. team.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import os
+from shutil import copyfile
+from typing import Any, Dict, List, Optional, Tuple
+
+import sentencepiece as spm
+
+from ...tokenization_utils import AddedToken, BatchEncoding, PreTrainedTokenizer
+from ...utils import logging
+
+
+logger = logging.get_logger(__name__)
+
+SPIECE_UNDERLINE = "▁"
+
+VOCAB_FILES_NAMES = {"vocab_file": "sentencepiece.bpe.model"}
+
+
+FAIRSEQ_LANGUAGE_CODES = ["ar_AR", "cs_CZ", "de_DE", "en_XX", "es_XX", "et_EE", "fi_FI", "fr_XX", "gu_IN", "hi_IN", "it_IT", "ja_XX", "kk_KZ", "ko_KR", "lt_LT", "lv_LV", "my_MM", "ne_NP", "nl_XX", "ro_RO", "ru_RU", "si_LK", "tr_TR", "vi_VN", "zh_CN", "af_ZA", "az_AZ", "bn_IN", "fa_IR", "he_IL", "hr_HR", "id_ID", "ka_GE", "km_KH", "mk_MK", "ml_IN", "mn_MN", "mr_IN", "pl_PL", "ps_AF", "pt_XX", "sv_SE", "sw_KE", "ta_IN", "te_IN", "th_TH", "tl_XX", "uk_UA", "ur_PK", "xh_ZA", "gl_ES", "sl_SI"]  # fmt: skip
+
+
+class MBart50Tokenizer(PreTrainedTokenizer):
+    """
+    Construct a MBart50 tokenizer. Based on [SentencePiece](https://github.com/google/sentencepiece).
+
+    This tokenizer inherits from [`PreTrainedTokenizer`] which contains most of the main methods. Users should refer to
+    this superclass for more information regarding those methods.
+
+    Args:
+        vocab_file (`str`):
+            Path to the vocabulary file.
+        src_lang (`str`, *optional*):
+            A string representing the source language.
+        tgt_lang (`str`, *optional*):
+            A string representing the target language.
+        eos_token (`str`, *optional*, defaults to `"</s>"`):
+            The end of sequence token.
+        sep_token (`str`, *optional*, defaults to `"</s>"`):
+            The separator token, which is used when building a sequence from multiple sequences, e.g. two sequences for
+            sequence classification or for a text and a question for question answering. It is also used as the last
+            token of a sequence built with special tokens.
+        cls_token (`str`, *optional*, defaults to `"<s>"`):
+            The classifier token which is used when doing sequence classification (classification of the whole sequence
+            instead of per-token classification). It is the first token of the sequence when built with special tokens.
+        unk_token (`str`, *optional*, defaults to `"<unk>"`):
+            The unknown token. A token that is not in the vocabulary cannot be converted to an ID and is set to be this
+            token instead.
+        pad_token (`str`, *optional*, defaults to `"<pad>"`):
+            The token used for padding, for example when batching sequences of different lengths.
+        mask_token (`str`, *optional*, defaults to `"<mask>"`):
+            The token used for masking values. This is the token used when training this model with masked language
+            modeling. This is the token which the model will try to predict.
+        sp_model_kwargs (`dict`, *optional*):
+            Will be passed to the `SentencePieceProcessor.__init__()` method. The [Python wrapper for
+            SentencePiece](https://github.com/google/sentencepiece/tree/master/python) can be used, among other things,
+            to set:
+
+            - `enable_sampling`: Enable subword regularization.
+            - `nbest_size`: Sampling parameters for unigram. Invalid for BPE-Dropout.
+
+              - `nbest_size = {0,1}`: No sampling is performed.
+              - `nbest_size > 1`: samples from the nbest_size results.
+              - `nbest_size < 0`: assuming that nbest_size is infinite and samples from the all hypothesis (lattice)
+                using forward-filtering-and-backward-sampling algorithm.
+
+            - `alpha`: Smoothing parameter for unigram sampling, and dropout probability of merge operations for
+              BPE-dropout.
+
+    Examples:
+
+    ```python
+    >>> from transformers import MBart50Tokenizer
+
+    >>> tokenizer = MBart50Tokenizer.from_pretrained("facebook/mbart-large-50", src_lang="en_XX", tgt_lang="ro_RO")
+    >>> src_text = " UN Chief Says There Is No Military Solution in Syria"
+    >>> tgt_text = "Şeful ONU declară că nu există o soluţie militară în Siria"
+    >>> model_inputs = tokenizer(src_text, text_target=tgt_text, return_tensors="pt")
+    >>> # model(**model_inputs) should work
+    ```"""
+
+    vocab_files_names = VOCAB_FILES_NAMES
+    model_input_names = ["input_ids", "attention_mask"]
+
+    prefix_tokens: List[int] = []
+    suffix_tokens: List[int] = []
+
+    def __init__(
+        self,
+        vocab_file,
+        src_lang=None,
+        tgt_lang=None,
+        eos_token="</s>",
+        sep_token="</s>",
+        cls_token="<s>",
+        unk_token="<unk>",
+        pad_token="<pad>",
+        mask_token="<mask>",
+        sp_model_kwargs: Optional[Dict[str, Any]] = None,
+        **kwargs,
+    ) -> None:
+        # Mask token behave like a normal word, i.e. include the space before it
+        mask_token = AddedToken(mask_token, lstrip=True, rstrip=False) if isinstance(mask_token, str) else mask_token
+
+        self.sp_model_kwargs = {} if sp_model_kwargs is None else sp_model_kwargs
+
+        kwargs["additional_special_tokens"] = kwargs.get("additional_special_tokens", []) or []
+        kwargs["additional_special_tokens"] += [
+            code for code in FAIRSEQ_LANGUAGE_CODES if code not in kwargs["additional_special_tokens"]
+        ]
+
+        self.sp_model = spm.SentencePieceProcessor(**self.sp_model_kwargs)
+        self.sp_model.Load(str(vocab_file))
+        self.vocab_file = vocab_file
+
+        # Original fairseq vocab and spm vocab must be "aligned":
+        # Vocab    |    0    |    1    |   2    |    3    |  4  |  5  |  6  |   7   |   8   |  9
+        # -------- | ------- | ------- | ------ | ------- | --- | --- | --- | ----- | ----- | ----
+        # fairseq  | '<s>'   | '<pad>' | '</s>' | '<unk>' | ',' | '.' | '▁' | 's'   | '▁de' | '-'
+        # spm      | '<unk>' | '<s>'   | '</s>' | ','     | '.' | '▁' | 's' | '▁de' | '-'   | '▁a'
+
+        # Mimic fairseq token-to-id alignment for the first 4 token
+        self.fairseq_tokens_to_ids = {"<s>": 0, "<pad>": 1, "</s>": 2, "<unk>": 3}
+
+        # The first "real" token "," has position 4 in the original fairseq vocab and position 3 in the spm vocab
+        self.fairseq_offset = 1
+
+        self.sp_model_size = len(self.sp_model)
+        self.lang_code_to_id = {
+            code: self.sp_model_size + i + self.fairseq_offset for i, code in enumerate(FAIRSEQ_LANGUAGE_CODES)
+        }
+        self.id_to_lang_code = {v: k for k, v in self.lang_code_to_id.items()}
+        self.fairseq_tokens_to_ids["<mask>"] = len(self.sp_model) + len(self.lang_code_to_id) + self.fairseq_offset
+
+        self.fairseq_tokens_to_ids.update(self.lang_code_to_id)
+        self.fairseq_ids_to_tokens = {v: k for k, v in self.fairseq_tokens_to_ids.items()}
+
+        super().__init__(
+            src_lang=src_lang,
+            tgt_lang=tgt_lang,
+            eos_token=eos_token,
+            unk_token=unk_token,
+            sep_token=sep_token,
+            cls_token=cls_token,
+            pad_token=pad_token,
+            mask_token=mask_token,
+            sp_model_kwargs=self.sp_model_kwargs,
+            **kwargs,
+        )
+
+        self._src_lang = src_lang if src_lang is not None else "en_XX"
+        self.cur_lang_code_id = self.lang_code_to_id[self._src_lang]
+        self.tgt_lang = tgt_lang
+        self.set_src_lang_special_tokens(self._src_lang)
+
+    @property
+    def vocab_size(self) -> int:
+        return len(self.sp_model) + len(self.lang_code_to_id) + self.fairseq_offset + 1  # Plus 1 for the mask token
+
+    @property
+    def src_lang(self) -> str:
+        return self._src_lang
+
+    @src_lang.setter
+    def src_lang(self, new_src_lang: str) -> None:
+        self._src_lang = new_src_lang
+        self.set_src_lang_special_tokens(self._src_lang)
+
+    def __getstate__(self) -> Dict:
+        state = self.__dict__.copy()
+        state["sp_model"] = None
+        return state
+
+    def __setstate__(self, d: Dict) -> None:
+        self.__dict__ = d
+
+        # for backward compatibility
+        if not hasattr(self, "sp_model_kwargs"):
+            self.sp_model_kwargs = {}
+
+        self.sp_model = spm.SentencePieceProcessor(**self.sp_model_kwargs)
+        self.sp_model.Load(self.vocab_file)
+
+    def get_vocab(self) -> Dict:
+        vocab = {self.convert_ids_to_tokens(i): i for i in range(self.vocab_size)}
+        vocab.update(self.added_tokens_encoder)
+        return vocab
+
+    def _tokenize(self, text: str) -> List[str]:
+        return self.sp_model.encode(text, out_type=str)
+
+    def _convert_token_to_id(self, token: str) -> int:
+        """Converts a token (str) in an id using the vocab."""
+        if token in self.fairseq_tokens_to_ids:
+            return self.fairseq_tokens_to_ids[token]
+        spm_id = self.sp_model.PieceToId(token)
+
+        # Need to return unknown token if the SP model returned 0
+        return spm_id + self.fairseq_offset if spm_id else self.unk_token_id
+
+    def _convert_id_to_token(self, index: int) -> str:
+        """Converts an index (integer) in a token (str) using the vocab."""
+        if index in self.fairseq_ids_to_tokens:
+            return self.fairseq_ids_to_tokens[index]
+        return self.sp_model.IdToPiece(index - self.fairseq_offset)
+
+    # Copied from transformers.models.albert.tokenization_albert.AlbertTokenizer.convert_tokens_to_string
+    def convert_tokens_to_string(self, tokens):
+        """Converts a sequence of tokens (string) in a single string."""
+        current_sub_tokens = []
+        out_string = ""
+        prev_is_special = False
+        for token in tokens:
+            # make sure that special tokens are not decoded using sentencepiece model
+            if token in self.all_special_tokens:
+                if not prev_is_special:
+                    out_string += " "
+                out_string += self.sp_model.decode(current_sub_tokens) + token
+                prev_is_special = True
+                current_sub_tokens = []
+            else:
+                current_sub_tokens.append(token)
+                prev_is_special = False
+        out_string += self.sp_model.decode(current_sub_tokens)
+        return out_string.strip()
+
+    def save_vocabulary(self, save_directory: str, filename_prefix: Optional[str] = None) -> Tuple[str]:
+        if not os.path.isdir(save_directory):
+            logger.error(f"Vocabulary path ({save_directory}) should be a directory")
+            return
+        out_vocab_file = os.path.join(
+            save_directory, (filename_prefix + "-" if filename_prefix else "") + VOCAB_FILES_NAMES["vocab_file"]
+        )
+
+        if os.path.abspath(self.vocab_file) != os.path.abspath(out_vocab_file) and os.path.isfile(self.vocab_file):
+            copyfile(self.vocab_file, out_vocab_file)
+        elif not os.path.isfile(self.vocab_file):
+            with open(out_vocab_file, "wb") as fi:
+                content_spiece_model = self.sp_model.serialized_model_proto()
+                fi.write(content_spiece_model)
+
+        return (out_vocab_file,)
+
+    def get_special_tokens_mask(
+        self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None, already_has_special_tokens: bool = False
+    ) -> List[int]:
+        """
+        Retrieve sequence ids from a token list that has no special tokens added. This method is called when adding
+        special tokens using the tokenizer `prepare_for_model` method.
+
+        Args:
+            token_ids_0 (`List[int]`):
+                List of IDs.
+            token_ids_1 (`List[int]`, *optional*):
+                Optional second list of IDs for sequence pairs.
+            already_has_special_tokens (`bool`, *optional*, defaults to `False`):
+                Whether or not the token list is already formatted with special tokens for the model.
+
+        Returns:
+            `List[int]`: A list of integers in the range [0, 1]: 1 for a special token, 0 for a sequence token.
+        """
+
+        if already_has_special_tokens:
+            return super().get_special_tokens_mask(
+                token_ids_0=token_ids_0, token_ids_1=token_ids_1, already_has_special_tokens=True
+            )
+
+        prefix_ones = [1] * len(self.prefix_tokens)
+        suffix_ones = [1] * len(self.suffix_tokens)
+        if token_ids_1 is None:
+            return prefix_ones + ([0] * len(token_ids_0)) + suffix_ones
+        return prefix_ones + ([0] * len(token_ids_0)) + ([0] * len(token_ids_1)) + suffix_ones
+
+    def build_inputs_with_special_tokens(
+        self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None
+    ) -> List[int]:
+        """
+        Build model inputs from a sequence or a pair of sequence for sequence classification tasks by concatenating and
+        adding special tokens. An MBART-50 sequence has the following format, where `X` represents the sequence:
+
+        - `input_ids` (for encoder) `[src_lang_code] X [eos]`
+        - `labels`: (for decoder) `[tgt_lang_code] X [eos]`
+
+        BOS is never used. Pairs of sequences are not the expected use case, but they will be handled without a
+        separator.
+
+        Args:
+            token_ids_0 (`List[int]`):
+                List of IDs to which the special tokens will be added.
+            token_ids_1 (`List[int]`, *optional*):
+                Optional second list of IDs for sequence pairs.
+
+        Returns:
+            `List[int]`: List of [input IDs](../glossary#input-ids) with the appropriate special tokens.
+        """
+        if token_ids_1 is None:
+            return self.prefix_tokens + token_ids_0 + self.suffix_tokens
+        # We don't expect to process pairs, but leave the pair logic for API consistency
+        return self.prefix_tokens + token_ids_0 + token_ids_1 + self.suffix_tokens
+
+    def _build_translation_inputs(
+        self, raw_inputs, return_tensors: str, src_lang: Optional[str], tgt_lang: Optional[str], **extra_kwargs
+    ):
+        """Used by translation pipeline, to prepare inputs for the generate function"""
+        if src_lang is None or tgt_lang is None:
+            raise ValueError("Translation requires a `src_lang` and a `tgt_lang` for this model")
+        self.src_lang = src_lang
+        inputs = self(raw_inputs, add_special_tokens=True, return_tensors=return_tensors, **extra_kwargs)
+        tgt_lang_id = self.convert_tokens_to_ids(tgt_lang)
+        inputs["forced_bos_token_id"] = tgt_lang_id
+        return inputs
+
+    def prepare_seq2seq_batch(
+        self,
+        src_texts: List[str],
+        src_lang: str = "en_XX",
+        tgt_texts: Optional[List[str]] = None,
+        tgt_lang: str = "ro_RO",
+        **kwargs,
+    ) -> BatchEncoding:
+        self.src_lang = src_lang
+        self.tgt_lang = tgt_lang
+        return super().prepare_seq2seq_batch(src_texts, tgt_texts, **kwargs)
+
+    def _switch_to_input_mode(self):
+        return self.set_src_lang_special_tokens(self.src_lang)
+
+    def _switch_to_target_mode(self):
+        return self.set_tgt_lang_special_tokens(self.tgt_lang)
+
+    def set_src_lang_special_tokens(self, src_lang: str) -> None:
+        """Reset the special tokens to the source lang setting. prefix=[src_lang_code] and suffix=[eos]."""
+        self.cur_lang_code_id = self.lang_code_to_id[src_lang]
+        self.prefix_tokens = [self.cur_lang_code_id]
+        self.suffix_tokens = [self.eos_token_id]
+
+    def set_tgt_lang_special_tokens(self, tgt_lang: str) -> None:
+        """Reset the special tokens to the target language setting. prefix=[tgt_lang_code] and suffix=[eos]."""
+        self.cur_lang_code_id = self.lang_code_to_id[tgt_lang]
+        self.prefix_tokens = [self.cur_lang_code_id]
+        self.suffix_tokens = [self.eos_token_id]

llmeval-env/lib/python3.10/site-packages/transformers/models/mbart50/tokenization_mbart50_fast.py

@@ -0,0 +1,259 @@
+# coding=utf-8
+# Copyright 2021 The Facebook AI Research Team Authors and The HuggingFace Inc. team.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import os
+from shutil import copyfile
+from typing import List, Optional, Tuple
+
+from tokenizers import processors
+
+from ...tokenization_utils import AddedToken, BatchEncoding
+from ...tokenization_utils_fast import PreTrainedTokenizerFast
+from ...utils import is_sentencepiece_available, logging
+
+
+if is_sentencepiece_available():
+    from .tokenization_mbart50 import MBart50Tokenizer
+else:
+    MBart50Tokenizer = None
+
+
+logger = logging.get_logger(__name__)
+
+VOCAB_FILES_NAMES = {"vocab_file": "sentencepiece.bpe.model", "tokenizer_file": "tokenizer.json"}
+
+
+FAIRSEQ_LANGUAGE_CODES = ["ar_AR", "cs_CZ", "de_DE", "en_XX", "es_XX", "et_EE", "fi_FI", "fr_XX", "gu_IN", "hi_IN", "it_IT", "ja_XX", "kk_KZ", "ko_KR", "lt_LT", "lv_LV", "my_MM", "ne_NP", "nl_XX", "ro_RO", "ru_RU", "si_LK", "tr_TR", "vi_VN", "zh_CN", "af_ZA", "az_AZ", "bn_IN", "fa_IR", "he_IL", "hr_HR", "id_ID", "ka_GE", "km_KH", "mk_MK", "ml_IN", "mn_MN", "mr_IN", "pl_PL", "ps_AF", "pt_XX", "sv_SE", "sw_KE", "ta_IN", "te_IN", "th_TH", "tl_XX", "uk_UA", "ur_PK", "xh_ZA", "gl_ES", "sl_SI"]  # fmt: skip
+
+
+class MBart50TokenizerFast(PreTrainedTokenizerFast):
+    """
+    Construct a "fast" MBART tokenizer for mBART-50 (backed by HuggingFace's *tokenizers* library). Based on
+    [BPE](https://huggingface.co/docs/tokenizers/python/latest/components.html?highlight=BPE#models).
+
+    This tokenizer inherits from [`PreTrainedTokenizerFast`] which contains most of the main methods. Users should
+    refer to this superclass for more information regarding those methods.
+
+    Args:
+        vocab_file (`str`):
+            Path to the vocabulary file.
+        src_lang (`str`, *optional*):
+            A string representing the source language.
+        tgt_lang (`str`, *optional*):
+            A string representing the target language.
+        eos_token (`str`, *optional*, defaults to `"</s>"`):
+            The end of sequence token.
+        sep_token (`str`, *optional*, defaults to `"</s>"`):
+            The separator token, which is used when building a sequence from multiple sequences, e.g. two sequences for
+            sequence classification or for a text and a question for question answering. It is also used as the last
+            token of a sequence built with special tokens.
+        cls_token (`str`, *optional*, defaults to `"<s>"`):
+            The classifier token which is used when doing sequence classification (classification of the whole sequence
+            instead of per-token classification). It is the first token of the sequence when built with special tokens.
+        unk_token (`str`, *optional*, defaults to `"<unk>"`):
+            The unknown token. A token that is not in the vocabulary cannot be converted to an ID and is set to be this
+            token instead.
+        pad_token (`str`, *optional*, defaults to `"<pad>"`):
+            The token used for padding, for example when batching sequences of different lengths.
+        mask_token (`str`, *optional*, defaults to `"<mask>"`):
+            The token used for masking values. This is the token used when training this model with masked language
+            modeling. This is the token which the model will try to predict.
+
+    Examples:
+
+    ```python
+    >>> from transformers import MBart50TokenizerFast
+
+    >>> tokenizer = MBart50TokenizerFast.from_pretrained("facebook/mbart-large-50", src_lang="en_XX", tgt_lang="ro_RO")
+    >>> src_text = " UN Chief Says There Is No Military Solution in Syria"
+    >>> tgt_text = "Şeful ONU declară că nu există o soluţie militară în Siria"
+    >>> model_inputs = tokenizer(src_text, text_target=tgt_text, return_tensors="pt")
+    >>> # model(**model_inputs) should work
+    ```"""
+
+    vocab_files_names = VOCAB_FILES_NAMES
+    model_input_names = ["input_ids", "attention_mask"]
+    slow_tokenizer_class = MBart50Tokenizer
+
+    prefix_tokens: List[int] = []
+    suffix_tokens: List[int] = []
+
+    def __init__(
+        self,
+        vocab_file=None,
+        src_lang=None,
+        tgt_lang=None,
+        tokenizer_file=None,
+        eos_token="</s>",
+        sep_token="</s>",
+        cls_token="<s>",
+        unk_token="<unk>",
+        pad_token="<pad>",
+        mask_token="<mask>",
+        **kwargs,
+    ):
+        # Mask token behave like a normal word, i.e. include the space before it
+        mask_token = AddedToken(mask_token, lstrip=True, rstrip=False) if isinstance(mask_token, str) else mask_token
+
+        kwargs["additional_special_tokens"] = kwargs.get("additional_special_tokens", []) or []
+        kwargs["additional_special_tokens"] += [
+            code for code in FAIRSEQ_LANGUAGE_CODES if code not in kwargs["additional_special_tokens"]
+        ]
+
+        super().__init__(
+            vocab_file,
+            src_lang=src_lang,
+            tgt_lang=tgt_lang,
+            tokenizer_file=tokenizer_file,
+            eos_token=eos_token,
+            sep_token=sep_token,
+            cls_token=cls_token,
+            unk_token=unk_token,
+            pad_token=pad_token,
+            mask_token=mask_token,
+            **kwargs,
+        )
+
+        self.vocab_file = vocab_file
+
+        self.lang_code_to_id = {
+            lang_code: self.convert_tokens_to_ids(lang_code) for lang_code in FAIRSEQ_LANGUAGE_CODES
+        }
+
+        self._src_lang = src_lang if src_lang is not None else "en_XX"
+        self.tgt_lang = tgt_lang
+        self.cur_lang_code_id = self.lang_code_to_id[self._src_lang]
+        self.set_src_lang_special_tokens(self._src_lang)
+
+    @property
+    def can_save_slow_tokenizer(self) -> bool:
+        return os.path.isfile(self.vocab_file) if self.vocab_file else False
+
+    @property
+    def src_lang(self) -> str:
+        return self._src_lang
+
+    @src_lang.setter
+    def src_lang(self, new_src_lang: str) -> None:
+        self._src_lang = new_src_lang
+        self.set_src_lang_special_tokens(self._src_lang)
+
+    def build_inputs_with_special_tokens(
+        self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None
+    ) -> List[int]:
+        """
+        Build model inputs from a sequence or a pair of sequence for sequence classification tasks by concatenating and
+        adding special tokens. The special tokens depend on calling set_lang.
+
+        An MBART-50 sequence has the following format, where `X` represents the sequence:
+
+        - `input_ids` (for encoder) `[src_lang_code] X [eos]`
+        - `labels`: (for decoder) `[tgt_lang_code] X [eos]`
+
+        BOS is never used. Pairs of sequences are not the expected use case, but they will be handled without a
+        separator.
+
+        Args:
+            token_ids_0 (`List[int]`):
+                List of IDs to which the special tokens will be added.
+            token_ids_1 (`List[int]`, *optional*):
+                Optional second list of IDs for sequence pairs.
+
+        Returns:
+            `List[int]`: list of [input IDs](../glossary#input-ids) with the appropriate special tokens.
+        """
+        if token_ids_1 is None:
+            return self.prefix_tokens + token_ids_0 + self.suffix_tokens
+        # We don't expect to process pairs, but leave the pair logic for API consistency
+        return self.prefix_tokens + token_ids_0 + token_ids_1 + self.suffix_tokens
+
+    def prepare_seq2seq_batch(
+        self,
+        src_texts: List[str],
+        src_lang: str = "en_XX",
+        tgt_texts: Optional[List[str]] = None,
+        tgt_lang: str = "ro_RO",
+        **kwargs,
+    ) -> BatchEncoding:
+        self.src_lang = src_lang
+        self.tgt_lang = tgt_lang
+        return super().prepare_seq2seq_batch(src_texts, tgt_texts, **kwargs)
+
+    def _switch_to_input_mode(self):
+        return self.set_src_lang_special_tokens(self.src_lang)
+
+    def _switch_to_target_mode(self):
+        return self.set_tgt_lang_special_tokens(self.tgt_lang)
+
+    def set_src_lang_special_tokens(self, src_lang: str) -> None:
+        """Reset the special tokens to the source lang setting. prefix=[src_lang_code] and suffix=[eos]."""
+        self.cur_lang_code_id = self.convert_tokens_to_ids(src_lang)
+        self.prefix_tokens = [self.cur_lang_code_id]
+        self.suffix_tokens = [self.eos_token_id]
+
+        prefix_tokens_str = self.convert_ids_to_tokens(self.prefix_tokens)
+        suffix_tokens_str = self.convert_ids_to_tokens(self.suffix_tokens)
+
+        self._tokenizer.post_processor = processors.TemplateProcessing(
+            single=prefix_tokens_str + ["$A"] + suffix_tokens_str,
+            pair=prefix_tokens_str + ["$A", "$B"] + suffix_tokens_str,
+            special_tokens=list(zip(prefix_tokens_str + suffix_tokens_str, self.prefix_tokens + self.suffix_tokens)),
+        )
+
+    def set_tgt_lang_special_tokens(self, tgt_lang: str) -> None:
+        """Reset the special tokens to the target language setting. prefix=[src_lang_code] and suffix=[eos]."""
+        self.cur_lang_code_id = self.convert_tokens_to_ids(tgt_lang)
+        self.prefix_tokens = [self.cur_lang_code_id]
+        self.suffix_tokens = [self.eos_token_id]
+
+        prefix_tokens_str = self.convert_ids_to_tokens(self.prefix_tokens)
+        suffix_tokens_str = self.convert_ids_to_tokens(self.suffix_tokens)
+
+        self._tokenizer.post_processor = processors.TemplateProcessing(
+            single=prefix_tokens_str + ["$A"] + suffix_tokens_str,
+            pair=prefix_tokens_str + ["$A", "$B"] + suffix_tokens_str,
+            special_tokens=list(zip(prefix_tokens_str + suffix_tokens_str, self.prefix_tokens + self.suffix_tokens)),
+        )
+
+    def _build_translation_inputs(
+        self, raw_inputs, return_tensors: str, src_lang: Optional[str], tgt_lang: Optional[str], **extra_kwargs
+    ):
+        """Used by translation pipeline, to prepare inputs for the generate function"""
+        if src_lang is None or tgt_lang is None:
+            raise ValueError("Translation requires a `src_lang` and a `tgt_lang` for this model")
+        self.src_lang = src_lang
+        inputs = self(raw_inputs, add_special_tokens=True, return_tensors=return_tensors, **extra_kwargs)
+        tgt_lang_id = self.convert_tokens_to_ids(tgt_lang)
+        inputs["forced_bos_token_id"] = tgt_lang_id
+        return inputs
+
+    def save_vocabulary(self, save_directory: str, filename_prefix: Optional[str] = None) -> Tuple[str]:
+        if not self.can_save_slow_tokenizer:
+            raise ValueError(
+                "Your fast tokenizer does not have the necessary information to save the vocabulary for a slow "
+                "tokenizer."
+            )
+
+        if not os.path.isdir(save_directory):
+            logger.error(f"Vocabulary path ({save_directory}) should be a directory")
+            return
+        out_vocab_file = os.path.join(
+            save_directory, (filename_prefix + "-" if filename_prefix else "") + VOCAB_FILES_NAMES["vocab_file"]
+        )
+
+        if os.path.abspath(self.vocab_file) != os.path.abspath(out_vocab_file):
+            copyfile(self.vocab_file, out_vocab_file)
+
+        return (out_vocab_file,)