evo_model.py

import torch
import torch.nn as nn
from transformers import PreTrainedModel, PretrainedConfig

class EvoTransformerConfig(PretrainedConfig):
    def __init__(self, hidden_size=384, num_layers=6, num_labels=2, **kwargs):
        super().__init__(**kwargs)
        self.hidden_size = hidden_size
        self.num_layers = num_layers
        self.num_labels = num_labels

class EvoTransformerForClassification(PreTrainedModel):
    config_class = EvoTransformerConfig

    def __init__(self, config):
        super().__init__(config)
        self.config = config
        self.embedding = nn.Embedding(30522, config.hidden_size)  # BERT vocab size
        self.layers = nn.ModuleList([
            nn.TransformerEncoderLayer(d_model=config.hidden_size, nhead=6, dim_feedforward=1024)
            for _ in range(config.num_layers)
        ])
        self.classifier = nn.Sequential(
            nn.Linear(config.hidden_size, 256),
            nn.ReLU(),
            nn.Linear(256, config.num_labels)
        )
        self.init_weights()

    def forward(self, input_ids, attention_mask=None, labels=None):
        x = self.embedding(input_ids)  # [batch, seq_len, hidden_size]
        x = x.transpose(0, 1)  # Transformer expects [seq_len, batch, hidden_size]
        for layer in self.layers:
            x = layer(x, src_key_padding_mask=(attention_mask == 0) if attention_mask is not None else None)
        x = x.mean(dim=0)  # mean pooling over seq_len
        logits = self.classifier(x)

        if labels is not None:
            loss = nn.functional.cross_entropy(logits, labels)
            return loss, logits
        return logits

    def save_pretrained(self, save_directory):
        import os, json
        os.makedirs(save_directory, exist_ok=True)
        torch.save(self.state_dict(), f"{save_directory}/pytorch_model.bin")
        with open(f"{save_directory}/config.json", "w") as f:
            f.write(self.config.to_json_string())

    @classmethod
    def from_pretrained(cls, load_directory):
        config_path = f"{load_directory}/config.json"
        model_path = f"{load_directory}/pytorch_model.bin"
        config = EvoTransformerConfig.from_json_file(config_path)
        model = cls(config)
        model.load_state_dict(torch.load(model_path, map_location="cpu"))
        return model