diff --git a/configs/callbacks/csv_prediction_writer.yaml b/configs/callbacks/csv_prediction_writer.yaml
deleted file mode 100644
index b7fc6fb93940f0910938553caec31c02a3aeb60b..0000000000000000000000000000000000000000
--- a/configs/callbacks/csv_prediction_writer.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-csv_prediction_writer:
-  _target_: deepscreen.utils.lightning.CSVPredictionWriter
-  output_dir: ${paths.output_dir}
-  write_interval: batch
diff --git a/configs/callbacks/default.yaml b/configs/callbacks/default.yaml
deleted file mode 100644
index f94c639e898f22416a21af826e6453b99fbf01f1..0000000000000000000000000000000000000000
--- a/configs/callbacks/default.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-defaults:
-  - model_checkpoint
-  - early_stopping
-  - model_summary
-  - rich_progress_bar
diff --git a/configs/callbacks/early_stopping.yaml b/configs/callbacks/early_stopping.yaml
deleted file mode 100644
index 1d2bb37ad3f056b1fb6cff81f162f7222a3c5a3e..0000000000000000000000000000000000000000
--- a/configs/callbacks/early_stopping.yaml
+++ /dev/null
@@ -1,17 +0,0 @@
-# https://pytorch-lightning.readthedocs.io/en/latest/api/pytorch_lightning.callbacks.EarlyStopping.html
-
-# Monitor a metric and stop training when it stops improving.
-# Look at the above link for more detailed information.
-early_stopping:
-  _target_: lightning.pytorch.callbacks.EarlyStopping
-  monitor: ${oc.select:callbacks.model_checkpoint.monitor,"val/loss"} # quantity to be monitored, must be specified!!!
-  min_delta: 0. # minimum change in the monitored quantity to qualify as an improvement
-  patience: 50 # number of checks with no improvement after which training will be stopped
-  verbose: False # verbosity mode
-  mode: ${callbacks.model_checkpoint.mode} # "max" means higher metric value is better, can be also "min"
-  strict: True # whether to crash the training if monitor is not found in the validation metrics
-  check_finite: True # when set True, stops training when the monitor becomes NaN or infinite
-  stopping_threshold: null # stop training immediately once the monitored quantity reaches this threshold
-  divergence_threshold: null # stop training as soon as the monitored quantity becomes worse than this threshold
-  check_on_train_epoch_end: False # whether to run early stopping at the end of the training epoch
-  log_rank_zero_only: False  # logs the status of the early stopping callback only for rank 0 process
diff --git a/configs/callbacks/inference.yaml b/configs/callbacks/inference.yaml
deleted file mode 100644
index 22fe5db38092387f72718e3046e86f57663e8c00..0000000000000000000000000000000000000000
--- a/configs/callbacks/inference.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-defaults:
-  - model_summary
-  - rich_progress_bar
-
-model_summary:
-  max_depth: 2
diff --git a/configs/callbacks/model_checkpoint.yaml b/configs/callbacks/model_checkpoint.yaml
deleted file mode 100644
index f8e51b2bb6036ce4a0b1ce3dc47c2869514b2eeb..0000000000000000000000000000000000000000
--- a/configs/callbacks/model_checkpoint.yaml
+++ /dev/null
@@ -1,19 +0,0 @@
-# https://pytorch-lightning.readthedocs.io/en/latest/api/pytorch_lightning.callbacks.ModelCheckpoint.html
-
-# Save the model periodically by monitoring a quantity.
-# Look at the above link for more detailed information.
-model_checkpoint:
-  _target_: lightning.pytorch.callbacks.ModelCheckpoint
-  dirpath: ${paths.output_dir} # directory to save the model file
-  filename: "checkpoints/epoch_{epoch:03d}" # checkpoint filename
-  monitor: ${eval:'"val/loss" if ${data.train_val_test_split}[1] else "train/loss"'} # name of the logged metric which determines when model is improving
-  verbose: False # verbosity mode
-  save_last: True # additionally always save an exact copy of the last checkpoint to a file last.ckpt
-  save_top_k: 1 # save k best models (determined by above metric)
-  mode: "min" # "max" means higher metric value is better, can be also "min"
-  auto_insert_metric_name: False # when True, the checkpoints filenames will contain the metric name
-  save_weights_only: False # if True, then only the model’s weights will be saved
-  every_n_train_steps: null # number of training steps between checkpoints
-  train_time_interval: null # checkpoints are monitored at the specified time interval
-  every_n_epochs: null # number of epochs between checkpoints
-  save_on_train_epoch_end: null # whether to run checkpointing at the end of the training epoch or the end of validation
diff --git a/configs/callbacks/model_summary.yaml b/configs/callbacks/model_summary.yaml
deleted file mode 100644
index f854fd9fd17863a8c5930f482dc0d235cfc03698..0000000000000000000000000000000000000000
--- a/configs/callbacks/model_summary.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-# https://pytorch-lightning.readthedocs.io/en/latest/api/pytorch_lightning.callbacks.RichModelSummary.html
-
-# Generates a summary of all layers in a LightningModule with rich text formatting.
-# Look at the above link for more detailed information.
-model_summary:
-  _target_: lightning.pytorch.callbacks.RichModelSummary
-  max_depth: 2 # The maximum depth of layer nesting that the summary will include. `-1` for all modules `0` for none.
diff --git a/configs/callbacks/none.yaml b/configs/callbacks/none.yaml
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/configs/callbacks/rich_progress_bar.yaml b/configs/callbacks/rich_progress_bar.yaml
deleted file mode 100644
index 82d2f89d28be7511f2360e1b047656afeee16141..0000000000000000000000000000000000000000
--- a/configs/callbacks/rich_progress_bar.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-# https://pytorch-lightning.readthedocs.io/en/latest/api/pytorch_lightning.callbacks.RichProgressBar.html
-
-# Create a progress bar with rich text formatting.
-# Look at the above link for more detailed information.
-rich_progress_bar:
-  _target_: lightning.pytorch.callbacks.RichProgressBar
diff --git a/configs/data/collator/default.yaml b/configs/data/collator/default.yaml
deleted file mode 100644
index 514c0837c358aeb82d22ec2c34a7226d05580423..0000000000000000000000000000000000000000
--- a/configs/data/collator/default.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-_target_: deepscreen.data.utils.collator.collate_fn
-_partial_: true
-
-automatic_padding: false
-padding_value: 0.0
diff --git a/configs/data/collator/none.yaml b/configs/data/collator/none.yaml
deleted file mode 100644
index 29899b9fc6b0164c149e17b31e350be9135add49..0000000000000000000000000000000000000000
--- a/configs/data/collator/none.yaml
+++ /dev/null
@@ -1,2 +0,0 @@
-_target_: deepscreen.utils.passthrough
-_partial_: true
\ No newline at end of file
diff --git a/configs/data/drug_featurizer/ecfp.yaml b/configs/data/drug_featurizer/ecfp.yaml
deleted file mode 100644
index a341607f3f242e6f993bf758e7341b376f8b4ef3..0000000000000000000000000000000000000000
--- a/configs/data/drug_featurizer/ecfp.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-_target_: deepscreen.data.featurizers.fingerprint.smiles_to_fingerprint
-_partial_: true
-
-fingerprint: MorganFP
-nBits: 1024
-radius: 2
\ No newline at end of file
diff --git a/configs/data/drug_featurizer/fcs.yaml b/configs/data/drug_featurizer/fcs.yaml
deleted file mode 100644
index 77a0cdbec7168829ce846fa28543707a000d0c0d..0000000000000000000000000000000000000000
--- a/configs/data/drug_featurizer/fcs.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-_target_: deepscreen.data.featurizers.fcs.drug_to_embedding
-_partial_: true
-
-max_sequence_length: 205
\ No newline at end of file
diff --git a/configs/data/drug_featurizer/graph.yaml b/configs/data/drug_featurizer/graph.yaml
deleted file mode 100644
index d3d65a1fbec937c9484584d8f9f89bbc999539f9..0000000000000000000000000000000000000000
--- a/configs/data/drug_featurizer/graph.yaml
+++ /dev/null
@@ -1,2 +0,0 @@
-_target_: deepscreen.data.featurizers.graph.smiles_to_graph
-_partial_: true
\ No newline at end of file
diff --git a/configs/data/drug_featurizer/label.yaml b/configs/data/drug_featurizer/label.yaml
deleted file mode 100644
index 80ffe2fbdf7038953a8d94e4fa9def36196d66bb..0000000000000000000000000000000000000000
--- a/configs/data/drug_featurizer/label.yaml
+++ /dev/null
@@ -1,15 +0,0 @@
-#_target_: deepscreen.data.featurizers.categorical.smiles_to_label
-#_partial_: true
-#
-#max_sequence_length: 100
-##in_channels: 63
-
-_target_: deepscreen.data.featurizers.categorical.sequence_to_label
-_partial_: true
-charset: ['#', '%', ')', '(', '+', '-', '.', '1', '0', '3', '2', '5', '4',
-          '7', '6', '9', '8', '=', 'A', 'C', 'B', 'E', 'D', 'G', 'F', 'I',
-          'H', 'K', 'M', 'L', 'O', 'N', 'P', 'S', 'R', 'U', 'T', 'W', 'V',
-          'Y', '[', 'Z', ']', '_', 'a', 'c', 'b', 'e', 'd', 'g', 'f', 'i',
-          'h', 'm', 'l', 'o', 'n', 's', 'r', 'u', 't', 'y']
-
-max_sequence_length: 100
\ No newline at end of file
diff --git a/configs/data/drug_featurizer/mol_features.yaml b/configs/data/drug_featurizer/mol_features.yaml
deleted file mode 100644
index b0652eace74a5041d7bfa166152e347b9f009c64..0000000000000000000000000000000000000000
--- a/configs/data/drug_featurizer/mol_features.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-_target_: deepscreen.data.featurizers.graph.smiles_to_mol_features
-_partial_: true
-
-num_atom_feat: 34
diff --git a/configs/data/drug_featurizer/none.yaml b/configs/data/drug_featurizer/none.yaml
deleted file mode 100644
index 29899b9fc6b0164c149e17b31e350be9135add49..0000000000000000000000000000000000000000
--- a/configs/data/drug_featurizer/none.yaml
+++ /dev/null
@@ -1,2 +0,0 @@
-_target_: deepscreen.utils.passthrough
-_partial_: true
\ No newline at end of file
diff --git a/configs/data/drug_featurizer/onehot.yaml b/configs/data/drug_featurizer/onehot.yaml
deleted file mode 100644
index 827114b5c04984b2bbd78697dda712a109db3514..0000000000000000000000000000000000000000
--- a/configs/data/drug_featurizer/onehot.yaml
+++ /dev/null
@@ -1,15 +0,0 @@
-#_target_: deepscreen.data.featurizers.categorical.smiles_to_onehot
-#_partial_: true
-#
-#max_sequence_length: 100
-##in_channels: 63
-
-_target_: deepscreen.data.featurizers.categorical.sequence_to_onehot
-_partial_: true
-charset: ['#', '%', ')', '(', '+', '-', '.', '1', '0', '3', '2', '5', '4',
-          '7', '6', '9', '8', '=', 'A', 'C', 'B', 'E', 'D', 'G', 'F', 'I',
-          'H', 'K', 'M', 'L', 'O', 'N', 'P', 'S', 'R', 'U', 'T', 'W', 'V',
-          'Y', '[', 'Z', ']', '_', 'a', 'c', 'b', 'e', 'd', 'g', 'f', 'i',
-          'h', 'm', 'l', 'o', 'n', 's', 'r', 'u', 't', 'y']
-
-max_sequence_length: 100
\ No newline at end of file
diff --git a/configs/data/drug_featurizer/tokenizer.yaml b/configs/data/drug_featurizer/tokenizer.yaml
deleted file mode 100644
index 369aa42da9f2a5f3990dff0097afd0fe8cf5da55..0000000000000000000000000000000000000000
--- a/configs/data/drug_featurizer/tokenizer.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-_target_: deepscreen.data.featurizers.token.sequence_to_token_ids
-_partial_: true
-
-tokenizer:
-  _target_: deepscreen.data.featurizers.token.SmilesTokenizer
-  vocab_file: resources/vocabs/smiles.txt
diff --git a/configs/data/dti.yaml.bak b/configs/data/dti.yaml.bak
deleted file mode 100644
index 93682ed7b88a14ac5e7afecb4327aa50d51d29b8..0000000000000000000000000000000000000000
--- a/configs/data/dti.yaml.bak
+++ /dev/null
@@ -1,21 +0,0 @@
-_target_: deepscreen.data.dti_datamodule.DTIdatamodule
-
-defaults:
-  - _self_
-  - split: null
-  - drug_featurizer: null
-  - protein_featurizer: null
-
-task: ${task.task}
-n_class: ${oc.select:task.task.n_class,null}
-
-data_dir: ${paths.data_dir}
-dataset_name: null
-
-batch_size: 16
-train_val_test_split: [0.7, 0.1, 0.2]
-
-num_workers: 0
-pin_memory: false
-
-train: ${train}
\ No newline at end of file
diff --git a/configs/data/dti_data.yaml b/configs/data/dti_data.yaml
deleted file mode 100644
index 5b65659c15f8fac1a229e16586ffb226293b4f14..0000000000000000000000000000000000000000
--- a/configs/data/dti_data.yaml
+++ /dev/null
@@ -1,20 +0,0 @@
-_target_: deepscreen.data.dti.DTIDataModule
-
-defaults:
-  - split: null
-  - drug_featurizer: none  # ???
-  - protein_featurizer: none  # ???
-  - collator: default
-
-task: ${task.task}
-num_classes: ${task.num_classes}
-
-data_dir: ${paths.data_dir}
-data_file: null
-train_val_test_split: null
-
-batch_size: ???
-num_workers: 0
-pin_memory: false
-
-#train: ${train}
\ No newline at end of file
diff --git a/configs/data/protein_featurizer/fcs.yaml b/configs/data/protein_featurizer/fcs.yaml
deleted file mode 100644
index cbf1f380d2bd951a321971676cb20f7de5e17e7c..0000000000000000000000000000000000000000
--- a/configs/data/protein_featurizer/fcs.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-_target_: deepscreen.data.featurizers.fcs.protein_to_embedding
-_partial_: true
-
-max_sequence_length: 545
\ No newline at end of file
diff --git a/configs/data/protein_featurizer/label.yaml b/configs/data/protein_featurizer/label.yaml
deleted file mode 100644
index 1824297352e8d0706126486f1a00585e78c4f892..0000000000000000000000000000000000000000
--- a/configs/data/protein_featurizer/label.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-#_target_: deepscreen.data.featurizers.categorical.fasta_to_label
-#_partial_: true
-#
-#max_sequence_length: 1000
-##in_channels: 26
-
-_target_: deepscreen.data.featurizers.categorical.sequence_to_label
-_partial_: true
-charset: ['A', 'C', 'B', 'E', 'D', 'G', 'F', 'I', 'H', 'K', 'M', 'L', 'O',
-          'N', 'Q', 'P', 'S', 'R', 'U', 'T', 'W', 'V', 'Y', 'X', 'Z']
-
-max_sequence_length: 1000
\ No newline at end of file
diff --git a/configs/data/protein_featurizer/none.yaml b/configs/data/protein_featurizer/none.yaml
deleted file mode 100644
index 29899b9fc6b0164c149e17b31e350be9135add49..0000000000000000000000000000000000000000
--- a/configs/data/protein_featurizer/none.yaml
+++ /dev/null
@@ -1,2 +0,0 @@
-_target_: deepscreen.utils.passthrough
-_partial_: true
\ No newline at end of file
diff --git a/configs/data/protein_featurizer/onehot.yaml b/configs/data/protein_featurizer/onehot.yaml
deleted file mode 100644
index d44e8a5fcc0ac0cfd47e17fda8f302e73bcc359d..0000000000000000000000000000000000000000
--- a/configs/data/protein_featurizer/onehot.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-#_target_: deepscreen.data.featurizers.categorical.fasta_to_onehot
-#_partial_: true
-#
-#max_sequence_length: 1000
-##in_channels: 26
-
-_target_: deepscreen.data.featurizers.categorical.sequence_to_onehot
-_partial_: true
-charset: ['A', 'C', 'B', 'E', 'D', 'G', 'F', 'I', 'H', 'K', 'M', 'L', 'O',
-          'N', 'Q', 'P', 'S', 'R', 'U', 'T', 'W', 'V', 'Y', 'X', 'Z']
-
-max_sequence_length: 1000
\ No newline at end of file
diff --git a/configs/data/protein_featurizer/tokenizer.yaml b/configs/data/protein_featurizer/tokenizer.yaml
deleted file mode 100644
index 9e264020782f84719e5370dd3cfc10f44a7a236c..0000000000000000000000000000000000000000
--- a/configs/data/protein_featurizer/tokenizer.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-_target_: deepscreen.data.featurizers.token.sequence_to_token_ids
-_partial_: true
-
-tokenizer:
-  _target_: tape.TAPETokenizer.from_pretrained
-  vocab: iupac
diff --git a/configs/data/protein_featurizer/word2vec.yaml b/configs/data/protein_featurizer/word2vec.yaml
deleted file mode 100644
index 0d9f4761a374a05ce0f5b20cd80073632f0c030f..0000000000000000000000000000000000000000
--- a/configs/data/protein_featurizer/word2vec.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-_target_: deepscreen.data.featurizers.word.protein_to_word_embedding
-_partial_: true
-
-model:
-  _target_: gensim.models.Word2Vec.load
-  fname: ${paths.resource_dir}/models/word2vec_30.model
\ No newline at end of file
diff --git a/configs/data/split/cold_drug.yaml b/configs/data/split/cold_drug.yaml
deleted file mode 100644
index 3c0416a876682bb9759822d493e70a21ac0f28f6..0000000000000000000000000000000000000000
--- a/configs/data/split/cold_drug.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-_target_: deepscreen.data.utils.split.cold_start
-_partial_: true
-
-entity: drug
\ No newline at end of file
diff --git a/configs/data/split/cold_protein.yaml b/configs/data/split/cold_protein.yaml
deleted file mode 100644
index 7a3694841cc5cb00549d3563791a872781d0d775..0000000000000000000000000000000000000000
--- a/configs/data/split/cold_protein.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-_target_: deepscreen.data.utils.split.cold_start
-_partial_: true
-
-entity: protein
\ No newline at end of file
diff --git a/configs/data/split/none.yaml b/configs/data/split/none.yaml
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/configs/data/split/random.yaml b/configs/data/split/random.yaml
deleted file mode 100644
index e8c00c9b5b38f57fda3b03185a1e91dbefedff8c..0000000000000000000000000000000000000000
--- a/configs/data/split/random.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-#_target_: torch.utils.data.random_split
-#_partial_: true
-
-#generator:
-#  _target_: torch.Generator # will use global seed set by lightning.seed_everything or torch.manual_seed automatically
-
-_target_: deepscreen.data.utils.split.random_split
-_partial_: true
-
-seed: ${seed}
diff --git a/configs/data/transform/minmax.yaml b/configs/data/transform/minmax.yaml
deleted file mode 100644
index 3c4e68561d5768d6b1677900484c386ce3b8df7c..0000000000000000000000000000000000000000
--- a/configs/data/transform/minmax.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-_target_: deepscreen.data.utils.transform
-_partial_: true
-
-scaler:
-  _target_: sklearn.preprocessing.MinMaxScaler
diff --git a/configs/data/transform/none.yaml b/configs/data/transform/none.yaml
deleted file mode 100644
index 29899b9fc6b0164c149e17b31e350be9135add49..0000000000000000000000000000000000000000
--- a/configs/data/transform/none.yaml
+++ /dev/null
@@ -1,2 +0,0 @@
-_target_: deepscreen.utils.passthrough
-_partial_: true
\ No newline at end of file
diff --git a/configs/debug/advanced.yaml b/configs/debug/advanced.yaml
deleted file mode 100644
index 2c249cc45699de1d1d8f25aa7c873b127e3df6f9..0000000000000000000000000000000000000000
--- a/configs/debug/advanced.yaml
+++ /dev/null
@@ -1,25 +0,0 @@
-# @package _global_
-
-# advanced debug mode that enables callbacks, loggers and gpu during debugging
-job_name: "debug"
-
-extras:
-  ignore_warnings: False
-  enforce_tags: False
-
-hydra:
-  job_logging:
-    root:
-      level: DEBUG
-  verbose: True
-
-trainer:
-  max_epochs: 1
-  accelerator: gpu
-  devices: 1
-  detect_anomaly: true
-  deterministic: false
-
-data:
-  num_workers: 0
-  pin_memory: False
diff --git a/configs/debug/default.yaml b/configs/debug/default.yaml
deleted file mode 100644
index 84e7dc1e80b355c8ab075a28e65d8fae08127eea..0000000000000000000000000000000000000000
--- a/configs/debug/default.yaml
+++ /dev/null
@@ -1,35 +0,0 @@
-# @package _global_
-
-# default debugging setup, runs 1 full epoch
-# other debugging configs can inherit from this one
-
-# overwrite job name so debugging logs are stored in separate folder
-job_name: "debug"
-
-# disable callbacks and loggers during debugging
-callbacks: null
-logger: null
-
-extras:
-  ignore_warnings: False
-  enforce_tags: False
-
-# sets level of all command line loggers to 'DEBUG'
-# https://hydra.cc/docs/tutorials/basic/running_your_app/logging/
-hydra:
-  job_logging:
-    root:
-      level: DEBUG
-  # use this to also set hydra loggers to 'DEBUG'
-  verbose: True
-
-trainer:
-  max_epochs: 1
-  accelerator: cpu # debuggers don't like gpus
-  devices: 1 # debuggers don't like multiprocessing
-  detect_anomaly: true # raise exception if NaN or +/-inf is detected in any tensor
-  deterministic: false
-
-data:
-  num_workers: 0 # debuggers don't like multiprocessing
-  pin_memory: False # disable gpu memory pin
diff --git a/configs/debug/fdr.yaml b/configs/debug/fdr.yaml
deleted file mode 100644
index 111e2f35924bf77db6706867a5a381cb90e2e855..0000000000000000000000000000000000000000
--- a/configs/debug/fdr.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-# @package _global_
-
-# runs 1 train, 1 validation and 1 test step
-
-defaults:
-  - default
-
-trainer:
-  accelerator: gpu
-  fast_dev_run: true
-  detect_anomaly: true
diff --git a/configs/debug/fdr_advanced.yaml b/configs/debug/fdr_advanced.yaml
deleted file mode 100644
index 570718adfc2148760067ac799cdc3f4ae38f6c78..0000000000000000000000000000000000000000
--- a/configs/debug/fdr_advanced.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-# @package _global_
-
-# runs 1 train, 1 validation and 1 test step
-
-defaults:
-  - advanced
-
-trainer:
-  accelerator: gpu
-  fast_dev_run: true
-  detect_anomaly: true
\ No newline at end of file
diff --git a/configs/debug/limit.yaml b/configs/debug/limit.yaml
deleted file mode 100644
index 514d77fbd1475b03fff0372e3da3c2fa7ea7d190..0000000000000000000000000000000000000000
--- a/configs/debug/limit.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-# @package _global_
-
-# uses only 1% of the training data and 5% of validation/test data
-
-defaults:
-  - default
-
-trainer:
-  max_epochs: 3
-  limit_train_batches: 0.01
-  limit_val_batches: 0.05
-  limit_test_batches: 0.05
diff --git a/configs/debug/overfit.yaml b/configs/debug/overfit.yaml
deleted file mode 100644
index 9906586a67a12aa81ff69138f589a366dbe2222f..0000000000000000000000000000000000000000
--- a/configs/debug/overfit.yaml
+++ /dev/null
@@ -1,13 +0,0 @@
-# @package _global_
-
-# overfits to 3 batches
-
-defaults:
-  - default
-
-trainer:
-  max_epochs: 20
-  overfit_batches: 3
-
-# model ckpt and early stopping need to be disabled during overfitting
-callbacks: null
diff --git a/configs/debug/profiler.yaml b/configs/debug/profiler.yaml
deleted file mode 100644
index 2bd7da87ae23ed425ace99b09250a76a5634a3fb..0000000000000000000000000000000000000000
--- a/configs/debug/profiler.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-# @package _global_
-
-# runs with execution time profiling
-
-defaults:
-  - default
-
-trainer:
-  max_epochs: 1
-  profiler: "simple"
-  # profiler: "advanced"
-  # profiler: "pytorch"
diff --git a/configs/experiment/bindingdb.yaml b/configs/experiment/bindingdb.yaml
deleted file mode 100644
index e3e170d30a9bbdd3d0252b43979b2861aeb39ce1..0000000000000000000000000000000000000000
--- a/configs/experiment/bindingdb.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-# @package _global_
-defaults:
-  - dti_experiment
-  - override /task: binary
-
-data:
-  train_val_test_split: [dti_benchmark/random_split_update/bindingdb_train.csv,
-                         dti_benchmark/random_split_update/bindingdb_valid.csv,
-                         dti_benchmark/random_split_update/bindingdb_test.csv]
diff --git a/configs/experiment/chembl_random.yaml b/configs/experiment/chembl_random.yaml
deleted file mode 100644
index 01b9e8aca42b0925a22303d9f2c3f8c4f5998340..0000000000000000000000000000000000000000
--- a/configs/experiment/chembl_random.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-# @package _global_
-defaults:
-  - dti_experiment
-  - override /task: binary
-
-data:
-  train_val_test_split: [chembl_random_global_balance_1_train.csv,
-                         chembl_random_global_balance_1_valid.csv,
-                         chembl_random_global_balance_1_test.csv]
diff --git a/configs/experiment/chembl_rmfh_random.yaml b/configs/experiment/chembl_rmfh_random.yaml
deleted file mode 100644
index a15e8ebfac7db334dc82d22adae2181c1473d9c8..0000000000000000000000000000000000000000
--- a/configs/experiment/chembl_rmfh_random.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-# @package _global_
-defaults:
-  - dti_experiment
-  - override /task: binary
-
-data:
-  train_val_test_split: [chembl_rmFH_random_global_balance_1_train.csv,
-                         chembl_rmFH_random_global_balance_1_valid.csv,
-                         chembl_rmFH_random_global_balance_1_test.csv]
\ No newline at end of file
diff --git a/configs/experiment/davis.yaml b/configs/experiment/davis.yaml
deleted file mode 100644
index 95c628e21ba17d808363a8f89f36ad0513e6a1de..0000000000000000000000000000000000000000
--- a/configs/experiment/davis.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-# @package _global_
-defaults:
-  - dti_experiment
-  - override /task: binary
-
-data:
-  train_val_test_split: [dti_benchmark/random_split_update/davis_train.csv,
-                         dti_benchmark/random_split_update/davis_valid.csv,
-                         dti_benchmark/random_split_update/davis_test.csv]
diff --git a/configs/experiment/demo_bindingdb.yaml b/configs/experiment/demo_bindingdb.yaml
deleted file mode 100644
index 0ccc1bcdfd5a12025a0ff6aa591a6989f3db2982..0000000000000000000000000000000000000000
--- a/configs/experiment/demo_bindingdb.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-# @package _global_
-defaults:
-  - dti_experiment
-  - override /task: binary
-  - override /data/split: random
-
-data:
-  data_file: demo/binddb_ic50_demo.csv
-  train_val_test_split: [0.7, 0.1, 0.2]
diff --git a/configs/experiment/dti_experiment.yaml b/configs/experiment/dti_experiment.yaml
deleted file mode 100644
index df70106572153a3444128f46023e58cdb6001a04..0000000000000000000000000000000000000000
--- a/configs/experiment/dti_experiment.yaml
+++ /dev/null
@@ -1,19 +0,0 @@
-# @package _global_
-defaults:
-  - override /data: dti_data
-  - override /model: dti_model
-  - override /trainer: gpu
-
-seed: 12345
-
-trainer:
-  min_epochs: 1
-  max_epochs: 500
-  precision: 16-mixed
-
-callbacks:
-  early_stopping:
-    patience: 50
-
-data:
-  num_workers: 8
diff --git a/configs/experiment/example.yaml b/configs/experiment/example.yaml
deleted file mode 100644
index 03babeb44c0eec70b050e1f92534b6cd8de770d8..0000000000000000000000000000000000000000
--- a/configs/experiment/example.yaml
+++ /dev/null
@@ -1,35 +0,0 @@
-# @package _global_
-
-# to execute this experiment run:
-# python train.py experiment=example
-
-defaults:
-  - override /data: dti_data
-  - override /data/drug_featurizer: onehot
-  - override /data/protein_featurizer: onehot
-  - override /model: dti_model
-  - override /model/protein_encoder: cnn
-  - override /model/drug_encoder: cnn
-  - override /model/decoder: concat_mlp
-  - override /callbacks: default
-  - override /trainer: default
-
-# all parameters below will be merged with parameters from default configurations set above
-# this allows you to overwrite only specified parameters
-
-tags: ["dti"]
-
-seed: 12345
-
-data:
-  data_file: davis.csv
-  batch_size: 64
-
-model:
-  optimizer:
-    lr: 0.0001
-
-trainer:
-  min_epochs: 1
-  max_epochs: 100
-  accelerator: gpu
\ No newline at end of file
diff --git a/configs/experiment/ion_channels.yaml b/configs/experiment/ion_channels.yaml
deleted file mode 100644
index 261d7dac49ccb908a63719c01fd04374e4d21019..0000000000000000000000000000000000000000
--- a/configs/experiment/ion_channels.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-# @package _global_
-defaults:
-  - dti_experiment
-  - override /task: binary
-
-data:
-  train_val_test_split: [dti_benchmark/ChEMBL33/train/Ion_channels_train_data.csv,
-                         dti_benchmark/ChEMBL33/valid/Ion_channels_valid_data.csv,
-                         dti_benchmark/ChEMBL33/test/Ion_channels_both_unseen_test_data.csv]
diff --git a/configs/experiment/kiba.yaml b/configs/experiment/kiba.yaml
deleted file mode 100644
index f3a83942f41b75c800bf467690b88b8397955615..0000000000000000000000000000000000000000
--- a/configs/experiment/kiba.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-# @package _global_
-defaults:
-  - dti_experiment
-  - /task: binary
-
-data:
-  train_val_test_split: [dti_benchmark/random_split_update/kiba_train.csv,
-                         dti_benchmark/random_split_update/kiba_valid.csv,
-                         dti_benchmark/random_split_update/kiba_test.csv]
diff --git a/configs/experiment/kinase.yaml b/configs/experiment/kinase.yaml
deleted file mode 100644
index c7d129aca1c9d93934efbe61a243cf7603d30143..0000000000000000000000000000000000000000
--- a/configs/experiment/kinase.yaml
+++ /dev/null
@@ -1,13 +0,0 @@
-# @package _global_
-defaults:
-  - dti_experiment
-  - override /task: binary
-
-data:
-  train_val_test_split:
-    - dti_benchmark/ChEMBL33/train/kinase_train_data.csv
-    - null
-    - null
-#                         dti_benchmark/ChEMBL33/valid/kinase_valid_data.csv,
-#                         dti_benchmark/ChEMBL33/test/kinase_both_unseen_test_data.csv
-
diff --git a/configs/experiment/membrane_receptors.yaml b/configs/experiment/membrane_receptors.yaml
deleted file mode 100644
index a06d357351dba800c885d7d92e51a7a7ccffc474..0000000000000000000000000000000000000000
--- a/configs/experiment/membrane_receptors.yaml
+++ /dev/null
@@ -1,13 +0,0 @@
-# @package _global_
-defaults:
-  - dti_experiment
-  - override /task: binary
-
-data:
-  train_val_test_split:
-    - dti_benchmark/ChEMBL33/train/Membrane_receptor_train_data.csv
-    - null
-    - null
-#                         dti_benchmark/ChEMBL33/valid/Membrane_receptor_valid_data.csv,
-#                         dti_benchmark/ChEMBL33/test/Membrane_receptor_drug_repo_test_data.csv
-
diff --git a/configs/experiment/non_kinase_enzymes.yaml b/configs/experiment/non_kinase_enzymes.yaml
deleted file mode 100644
index 314eeb66a368dfcab29313a647e620ee5bcd7cd9..0000000000000000000000000000000000000000
--- a/configs/experiment/non_kinase_enzymes.yaml
+++ /dev/null
@@ -1,13 +0,0 @@
-# @package _global_
-defaults:
-  - dti_experiment
-  - override /task: binary
-
-data:
-  train_val_test_split:
-    - dti_benchmark/ChEMBL33/train/Non_kinase_enzyme_train_data.csv
-    - null
-    - null
-#                         dti_benchmark/ChEMBL33/valid/Non_kinase_enzyme_valid_data.csv,
-#                         dti_benchmark/ChEMBL33/test/Non_kinase_enzyme_both_unseen_test_data.csv
-
diff --git a/configs/experiment/nuclear_receptors.yaml b/configs/experiment/nuclear_receptors.yaml
deleted file mode 100644
index 2edf8a4dea610a9a7c2a9b73178f452888bb20c2..0000000000000000000000000000000000000000
--- a/configs/experiment/nuclear_receptors.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-# @package _global_
-defaults:
-  - dti_experiment
-  - override /task: binary
-
-data:
-  train_val_test_split: [dti_benchmark/ChEMBL33/train/Nuclear_receptors_train_data.csv,
-                         dti_benchmark/ChEMBL33/valid/Nuclear_receptors_valid_data.csv,
-                         dti_benchmark/ChEMBL33/test/Nuclear_receptors_both_unseen_test_data.csv]
diff --git a/configs/experiment/other_protein_targets.yaml b/configs/experiment/other_protein_targets.yaml
deleted file mode 100644
index ffe3f295621ee3ffc160521e88e2bdf547719190..0000000000000000000000000000000000000000
--- a/configs/experiment/other_protein_targets.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-# @package _global_
-defaults:
-  - dti_experiment
-  - override /task: binary
-
-data:
-  train_val_test_split: [dti_benchmark/ChEMBL33/train/Other_protein_targets_train_data.csv,
-                         dti_benchmark/ChEMBL33/valid/Other_protein_targets_valid_data.csv,
-                         dti_benchmark/ChEMBL33/test/Other_protein_targets_both_unseen_test_data.csv]
diff --git a/configs/extras/default.yaml b/configs/extras/default.yaml
deleted file mode 100644
index b9c6b622283a647fbc513166fc14f016cc3ed8a0..0000000000000000000000000000000000000000
--- a/configs/extras/default.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-# disable python warnings if they annoy you
-ignore_warnings: False
-
-# ask user for tags if none are provided in the config
-enforce_tags: True
-
-# pretty print config tree at the start of the run using Rich library
-print_config: True
diff --git a/configs/hydra/callbacks/csv_experiment_summary.yaml b/configs/hydra/callbacks/csv_experiment_summary.yaml
deleted file mode 100644
index 1b0d00b4f7c73dfdc02846e428fc6793133cc549..0000000000000000000000000000000000000000
--- a/configs/hydra/callbacks/csv_experiment_summary.yaml
+++ /dev/null
@@ -1,3 +0,0 @@
-csv_experiment_summary:
-  _target_: deepscreen.utils.hydra.CSVExperimentSummary
-  prefix: ['test/', 'epoch']
\ No newline at end of file
diff --git a/configs/hydra/callbacks/default.yaml b/configs/hydra/callbacks/default.yaml
deleted file mode 100644
index 3e7617d233fb7f325cdd03caf82bcc0e2ba6bf6d..0000000000000000000000000000000000000000
--- a/configs/hydra/callbacks/default.yaml
+++ /dev/null
@@ -1,2 +0,0 @@
-defaults:
-  - csv_experiment_summary
diff --git a/configs/hydra/default.yaml b/configs/hydra/default.yaml
deleted file mode 100644
index 8d76171f4585f3c26e6c249ba9d4e1617994b421..0000000000000000000000000000000000000000
--- a/configs/hydra/default.yaml
+++ /dev/null
@@ -1,27 +0,0 @@
-# https://hydra.cc/docs/configure_hydra/intro/
-
-# enable color logging
-defaults:
-  - override callbacks: default
-  - override hydra_logging: colorlog
-  - override job_logging: colorlog
-
-# output directory, generated dynamically on each run
-run:
-  dir: ${paths.log_dir}/${job_name}/runs/${now:%Y-%m-%d}_${now:%H-%M-%S-%f}_[${eval:'",".join(${tags})'}]
-sweep:
-  dir: ${paths.log_dir}/${job_name}/multiruns/${now:%Y-%m-%d}_${now:%H-%M-%S-%f}_[${eval:'",".join(${tags})'}]
-  # Sanitize override_dirname by replacing unsafe characters to avoid unintended subdirectory creation
-  subdir: ${sanitize_path:'${hydra:job.id}-${hydra:job.override_dirname}'}
-
-job_logging:
-  handlers:
-    file:
-      filename: ${hydra:runtime.output_dir}/${hydra.job.name}.log
-
-job:
-  config:
-    override_dirname:
-      kv_sep: '='
-      item_sep: ';'
-      exclude_keys: ['tags', 'sweep', 'data.data_file', 'data.train_val_test_split', 'ckpt_path', 'trainer']
diff --git a/configs/hydra/launcher/submitit_local_example.yaml b/configs/hydra/launcher/submitit_local_example.yaml
deleted file mode 100644
index 2f47752804b52ea1216d750ac3229d12e463aaff..0000000000000000000000000000000000000000
--- a/configs/hydra/launcher/submitit_local_example.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-# @package _global_
-defaults:
-  - submitit_local
-
-submitit_folder: ${hydra.sweep.dir}/.submitit/%j
-timeout_min: 60
-cpus_per_task: 1
-gpus_per_node: 1
-tasks_per_node: 8
-mem_gb: 16
-nodes: 1
-name: ${hydra.job.name}
diff --git a/configs/hydra/launcher/submitit_slurm_example.yaml b/configs/hydra/launcher/submitit_slurm_example.yaml
deleted file mode 100644
index 1dec61801ed47679ea6598ef2540965e110249c4..0000000000000000000000000000000000000000
--- a/configs/hydra/launcher/submitit_slurm_example.yaml
+++ /dev/null
@@ -1,31 +0,0 @@
-# @package _global_
-defaults:
-  - submitit_slurm
-
-hydra:
-  mode: "MULTIRUN"
-  launcher:
-    submitit_folder: ${hydra.sweep.dir}/.submitit/%j
-    timeout_min: null
-    cpus_per_task: null
-    gpus_per_node: null
-    tasks_per_node: 1
-    mem_gb: null
-    nodes: 1
-    name: ${hydra.job.name}
-    partition: null
-    qos: null
-    comment: null
-    constraint: null
-    exclude: null
-    gres: null
-    cpus_per_gpu: null
-    gpus_per_task: null
-    mem_per_gpu: null
-    mem_per_cpu: null
-    account: null
-    signal_delay_s: 120
-    max_num_timeout: 0
-    additional_parameters: {}
-    array_parallelism: 256
-    setup: null
diff --git a/configs/hydra/sweeper/optuna_hps.yaml b/configs/hydra/sweeper/optuna_hps.yaml
deleted file mode 100644
index 316cf24ab252557a08a5e82fa8c9c462b9835246..0000000000000000000000000000000000000000
--- a/configs/hydra/sweeper/optuna_hps.yaml
+++ /dev/null
@@ -1,44 +0,0 @@
-# @package _global_
-
-# example batch experiment of some experiment with Optuna:
-# python train.py -m sweep=optuna experiment=example
-
-defaults:
-  - optuna
-
-# choose metric which will be optimized by Optuna
-# make sure this is the correct name of some metric logged in lightning module!
-objective_metrics: ["val/auroc"]
-
-# here we define Optuna hyperparameter search
-# it optimizes for value returned from function with @hydra.main decorator
-# docs: https://hydra.cc/docs/next/plugins/optuna_sweeper
-hydra:
-  mode: "MULTIRUN" # set hydra to multirun by default if this config is attached
-  sweeper:
-    # storage URL to persist optimization results
-    # for example, you can use SQLite if you set 'sqlite:///example.db'
-    storage: null
-
-    # name of the study to persist optimization results
-    study_name: null
-
-    # number of parallel workers
-    n_jobs: 1
-
-    # 'minimize' or 'maximize' the objective
-    direction: minimize
-
-    # total number of runs that will be executed
-    n_trials: 20
-
-    # choose Optuna hyperparameter sampler
-    # you can choose bayesian sampler (tpe), random search (without optimization), grid sampler, and others
-    # docs: https://optuna.readthedocs.io/en/stable/reference/samplers.html
-    sampler:
-      _target_: optuna.samplers.TPESampler
-      seed: 12345
-      n_startup_trials: 10 # number of random sampling runs before optimization starts
-
-    # define hyperparameter search space
-    params: ???
diff --git a/configs/local/.gitkeep b/configs/local/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/configs/local/gpu3090.yaml b/configs/local/gpu3090.yaml
deleted file mode 100644
index 407f3e2b68c5f268b917310112398cdd607c51e6..0000000000000000000000000000000000000000
--- a/configs/local/gpu3090.yaml
+++ /dev/null
@@ -1,15 +0,0 @@
-# @package _global_
-defaults:
-  - override /hydra/launcher: submitit_slurm
-
-hydra:
-  launcher:
-    submitit_folder: ${hydra.sweep.dir}/.submitit
-    timeout_min: 6000
-    cpus_per_task: 8
-    gpus_per_task: 1
-    gres: gpu:1
-    partition: gpu3090
-    qos: gpu3090
-    additional_parameters: {}
-    array_parallelism: 256
diff --git a/configs/logger/comet.yaml b/configs/logger/comet.yaml
deleted file mode 100644
index ebe6c6f19bd172255e9f29148df10a4d2ec42c84..0000000000000000000000000000000000000000
--- a/configs/logger/comet.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-# https://www.comet.ml
-
-comet:
-  _target_: lightning.pytorch.loggers.comet.CometLogger
-  api_key: ${oc.env:COMET_API_TOKEN} # api key is loaded from environment variable
-  save_dir: "${paths.output_dir}"
-  project_name: "deepscreen"
-  rest_api_key: null
-  # experiment_name: ""
-  experiment_key: null # set to resume experiment
-  offline: False
-  prefix: ""
\ No newline at end of file
diff --git a/configs/logger/csv.yaml b/configs/logger/csv.yaml
deleted file mode 100644
index bf9af6fb5e70b1382a1421397b12ea677dd8926f..0000000000000000000000000000000000000000
--- a/configs/logger/csv.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-# csv logger built in lightning
-
-csv:
-  _target_: lightning.pytorch.loggers.csv_logs.CSVLogger
-  save_dir: "${paths.output_dir}"
-  name: "csv/"
-  prefix: ""
-  version: ""
diff --git a/configs/logger/default.yaml b/configs/logger/default.yaml
deleted file mode 100644
index bfdb2248689fcc8c5827c6c99c0d42bfad37b3c8..0000000000000000000000000000000000000000
--- a/configs/logger/default.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-defaults:
-  - csv
-#  - mlflow
-#  - wandb
-#  - comet
\ No newline at end of file
diff --git a/configs/logger/mlflow.yaml b/configs/logger/mlflow.yaml
deleted file mode 100644
index bed42abc9cd686d89137e236a009c2c9277f2608..0000000000000000000000000000000000000000
--- a/configs/logger/mlflow.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-# https://mlflow.org
-
-mlflow:
-  _target_: lightning.pytorch.loggers.mlflow.MLFlowLogger
-  # experiment_name: ""
-  # run_name: ""
-  tracking_uri: "file://${paths.output_dir}/mlflow/" # run `mlflow ui` command inside the `logs/mlflow/` dir to open the UI
-  tags: ${tags}
-  # save_dir: "./mlruns"
-  prefix: ""
-  artifact_location: null
-  # run_id: ""
\ No newline at end of file
diff --git a/configs/logger/multiple_loggers.yaml b/configs/logger/multiple_loggers.yaml
deleted file mode 100644
index 40d561d1b723cb314de4272210a96c4343dcace9..0000000000000000000000000000000000000000
--- a/configs/logger/multiple_loggers.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-# train with multiple loggers at once
-defaults:
-  - csv
-  - tensorboard
-#  - mlflow
-#  - wandb
\ No newline at end of file
diff --git a/configs/logger/neptune.yaml b/configs/logger/neptune.yaml
deleted file mode 100644
index 086e85fc59117f4a8035d0c1773e4c856fd7e995..0000000000000000000000000000000000000000
--- a/configs/logger/neptune.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-# https://neptune.ai
-
-neptune:
-  _target_: lightning.pytorch.loggers.neptune.NeptuneLogger
-  api_key: ${oc.env:NEPTUNE_API_TOKEN} # api key is loaded from environment variable
-  project: username/deepscreen
-  # name: ""
-  log_model_checkpoints: True
-  prefix: ""
\ No newline at end of file
diff --git a/configs/logger/tensorboard.yaml b/configs/logger/tensorboard.yaml
deleted file mode 100644
index f438664df015f88bd3cabffaa520da3ef98dc379..0000000000000000000000000000000000000000
--- a/configs/logger/tensorboard.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-# https://www.tensorflow.org/tensorboard/
-
-tensorboard:
-  _target_: lightning.pytorch.loggers.tensorboard.TensorBoardLogger
-  save_dir: "${paths.output_dir}/tensorboard/"
-  name: null
-  log_graph: False
-  default_hp_metric: True
-  prefix: ""
-  version: ""
diff --git a/configs/logger/wandb.yaml b/configs/logger/wandb.yaml
deleted file mode 100644
index 9ec9ba26d7673c20005d8e67e3bed2b647c80218..0000000000000000000000000000000000000000
--- a/configs/logger/wandb.yaml
+++ /dev/null
@@ -1,16 +0,0 @@
-# https://wandb.ai
-
-wandb:
-  _target_: lightning.pytorch.loggers.wandb.WandbLogger
-  # name: "" # name of the run (normally generated by wandb)
-  save_dir: "${paths.output_dir}"
-  offline: True
-  id: null # pass correct id to resume experiment!
-  anonymous: null # enable anonymous logging
-  project: "deepscreen"
-  log_model: False # upload lightning ckpts
-  prefix: "" # a string to put at the beginning of metric keys
-  # entity: "" # set to name of your wandb team
-  group: ""
-  tags: ${tags}
-  job_type: ""
\ No newline at end of file
diff --git a/configs/model/dti_model.yaml b/configs/model/dti_model.yaml
deleted file mode 100644
index 72b1c9ee2b75a2f6ffce9a33b8d42cafd9cc67f0..0000000000000000000000000000000000000000
--- a/configs/model/dti_model.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-_target_: deepscreen.models.dti.DTILightningModule
-
-defaults:
-  - _self_
-  - optimizer: adam
-  - scheduler: default
-  - predictor: none
-  - metrics: dti_metrics
-
-out: ${task.out}
-loss: ${task.loss}
-activation: ${task.activation}
diff --git a/configs/model/loss/multitask_loss.yaml b/configs/model/loss/multitask_loss.yaml
deleted file mode 100644
index 6dfe6353808f3f91a42e151a34a3cae056e0fc7e..0000000000000000000000000000000000000000
--- a/configs/model/loss/multitask_loss.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-_target_: deepscreen.models.loss.multitask_loss.MultitaskLoss
-
-loss_fns:
-  - _target_: torch.nn.MSELoss
-  - _target_: torch.nn.CrossEntropyLoss
-    weight: null
-reduction: sum
\ No newline at end of file
diff --git a/configs/model/metrics/accuracy.yaml b/configs/model/metrics/accuracy.yaml
deleted file mode 100644
index 80a9d3f8a6837571b70d0cfb70ba7c6f59ee1c3e..0000000000000000000000000000000000000000
--- a/configs/model/metrics/accuracy.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-accuracy:
-  _target_: torchmetrics.Accuracy
-  task: ${task.task}
-  num_classes: ${task.num_classes}
\ No newline at end of file
diff --git a/configs/model/metrics/auprc.yaml b/configs/model/metrics/auprc.yaml
deleted file mode 100644
index b9de03c65fdeec91e8b39f38dd773d9956e2e8ce..0000000000000000000000000000000000000000
--- a/configs/model/metrics/auprc.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-auprc:
-  _target_: torchmetrics.AveragePrecision
-  task: ${task.task}
-  num_classes: ${task.num_classes}
\ No newline at end of file
diff --git a/configs/model/metrics/auroc.yaml b/configs/model/metrics/auroc.yaml
deleted file mode 100644
index a4bcdbbd885ae5ba05120e5568ca7d3a323f213f..0000000000000000000000000000000000000000
--- a/configs/model/metrics/auroc.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-auroc:
-  _target_: torchmetrics.AUROC
-  task: ${task.task}
-  num_classes: ${task.num_classes}
\ No newline at end of file
diff --git a/configs/model/metrics/bedroc.yaml b/configs/model/metrics/bedroc.yaml
deleted file mode 100644
index 86c68585882faefde5ee711dfe647d406a06dd09..0000000000000000000000000000000000000000
--- a/configs/model/metrics/bedroc.yaml
+++ /dev/null
@@ -1,3 +0,0 @@
-bedroc:
-  _target_: deepscreen.models.metrics.bedroc.BEDROC
-  alpha: 80.5
\ No newline at end of file
diff --git a/configs/model/metrics/concordance_index.yaml b/configs/model/metrics/concordance_index.yaml
deleted file mode 100644
index 634ea1906b5d0307e2e0342beec04c28e66af308..0000000000000000000000000000000000000000
--- a/configs/model/metrics/concordance_index.yaml
+++ /dev/null
@@ -1,2 +0,0 @@
-# FIXME: implement concordance index
-_target_:
\ No newline at end of file
diff --git a/configs/model/metrics/confusion_matrix.yaml b/configs/model/metrics/confusion_matrix.yaml
deleted file mode 100644
index d0be32b6b92a93e743d3926bf19fc3849c2e9260..0000000000000000000000000000000000000000
--- a/configs/model/metrics/confusion_matrix.yaml
+++ /dev/null
@@ -1 +0,0 @@
-_target_: torchmetrics.ConfusionMatrix
\ No newline at end of file
diff --git a/configs/model/metrics/dta_metrics.yaml b/configs/model/metrics/dta_metrics.yaml
deleted file mode 100644
index 2b0f108cb9df18dfcceae6af9fd94789685a54b2..0000000000000000000000000000000000000000
--- a/configs/model/metrics/dta_metrics.yaml
+++ /dev/null
@@ -1,2 +0,0 @@
-defaults:
-  - mean_squared_error
diff --git a/configs/model/metrics/dti_metrics.yaml b/configs/model/metrics/dti_metrics.yaml
deleted file mode 100644
index 93ca0c40a0d77ffb095ab91d52863667bf5746cc..0000000000000000000000000000000000000000
--- a/configs/model/metrics/dti_metrics.yaml
+++ /dev/null
@@ -1,14 +0,0 @@
-# train with many loggers at once
-
-defaults:
-  - auroc
-  - auprc
-  - specificity
-  - sensitivity
-  - precision
-  - recall
-  - f1_score
-# Common virtual screening metrics:
-#  - ef
-#  - bedroc
-#  - hit_rate
diff --git a/configs/model/metrics/ef.yaml b/configs/model/metrics/ef.yaml
deleted file mode 100644
index 82553b414da98c55508db9830d82b12af3db786d..0000000000000000000000000000000000000000
--- a/configs/model/metrics/ef.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-ef1:
-  _target_: deepscreen.models.metrics.ef.EF
-  alpha: 0.01
-
-ef5:
-  _target_: deepscreen.models.metrics.ef.EF
-  alpha: 0.05
\ No newline at end of file
diff --git a/configs/model/metrics/f1_score.yaml b/configs/model/metrics/f1_score.yaml
deleted file mode 100644
index abfb6e4ca37a9dad399aeb3b1244d958d542e238..0000000000000000000000000000000000000000
--- a/configs/model/metrics/f1_score.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-f1_score:
-  _target_: torchmetrics.F1Score
-  task: ${task.task}
-  num_classes: ${task.num_classes}
\ No newline at end of file
diff --git a/configs/model/metrics/hit_rate.yaml b/configs/model/metrics/hit_rate.yaml
deleted file mode 100644
index 70976774eb365fdf8b8c1f97bd3ad19d6cb64cb8..0000000000000000000000000000000000000000
--- a/configs/model/metrics/hit_rate.yaml
+++ /dev/null
@@ -1,3 +0,0 @@
-hit_rate:
-  _target_: deepscreen.models.metrics.hit_rate.HitRate
-  alpha: 0.05
diff --git a/configs/model/metrics/mean_squared_error.yaml b/configs/model/metrics/mean_squared_error.yaml
deleted file mode 100644
index 0d9a18c60d43210b16878ff479b1cfa3168788cf..0000000000000000000000000000000000000000
--- a/configs/model/metrics/mean_squared_error.yaml
+++ /dev/null
@@ -1,2 +0,0 @@
-mean_squared_error:
-  _target_: torchmetrics.MeanSquaredError
\ No newline at end of file
diff --git a/configs/model/metrics/prc.yaml b/configs/model/metrics/prc.yaml
deleted file mode 100644
index 75e3ee320d5b9a32a9acdb55d564fbacab975088..0000000000000000000000000000000000000000
--- a/configs/model/metrics/prc.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-prc:
-  _target_: torchmetrics.PrecisionRecallCurve
-  task: ${task.task}
-  num_classes: ${task.num_classes}
\ No newline at end of file
diff --git a/configs/model/metrics/precision.yaml b/configs/model/metrics/precision.yaml
deleted file mode 100644
index 4b8212b1999c10b627de5859e034260a39022608..0000000000000000000000000000000000000000
--- a/configs/model/metrics/precision.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-precision:
-  _target_: torchmetrics.Precision
-  task: ${task.task}
-  num_classes: ${task.num_classes}
diff --git a/configs/model/metrics/recall.yaml b/configs/model/metrics/recall.yaml
deleted file mode 100644
index eadad752ad1c4e1ac137580a289d4d32916ca975..0000000000000000000000000000000000000000
--- a/configs/model/metrics/recall.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-recall:
-  _target_: torchmetrics.Recall
-  task: ${task.task}
-  num_classes: ${task.num_classes}
\ No newline at end of file
diff --git a/configs/model/metrics/roc.yaml b/configs/model/metrics/roc.yaml
deleted file mode 100644
index 91968a6f42e3d399f39e587785eaddabda523a23..0000000000000000000000000000000000000000
--- a/configs/model/metrics/roc.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-roc:
-  _target_: torchmetrics.ROC
-  task: ${task.task}
-  num_classes: ${task.num_classes}
\ No newline at end of file
diff --git a/configs/model/metrics/sensitivity.yaml b/configs/model/metrics/sensitivity.yaml
deleted file mode 100644
index 49568b4512c2b75ebfce98d8ee03e2b1148966cc..0000000000000000000000000000000000000000
--- a/configs/model/metrics/sensitivity.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-sensitivity:
-  _target_: deepscreen.models.metrics.sensitivity.Sensitivity
-  task: ${task.task}
-  num_classes: ${task.num_classes}
\ No newline at end of file
diff --git a/configs/model/metrics/specificity.yaml b/configs/model/metrics/specificity.yaml
deleted file mode 100644
index 5b161be947876081ce9b6b070ed7201874f5cbc6..0000000000000000000000000000000000000000
--- a/configs/model/metrics/specificity.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-specificity:
-  _target_: torchmetrics.Specificity
-  task: ${task.task}
-  num_classes: ${task.num_classes}
\ No newline at end of file
diff --git a/configs/model/metrics/test_metrics.yaml b/configs/model/metrics/test_metrics.yaml
deleted file mode 100644
index 2ff2b80870d15e9863158e6dfbd17cf3dd9586c2..0000000000000000000000000000000000000000
--- a/configs/model/metrics/test_metrics.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-# train with many loggers at once
-
-defaults:
-  - auroc
-  - auprc
-  - roc
-  - prc
-# Common virtual screening metrics:
-#  - ef
-#  - bedroc
-#  - hit_rate
diff --git a/configs/model/optimizer/adam.yaml b/configs/model/optimizer/adam.yaml
deleted file mode 100644
index 67ab7f2cfeeb16daef186434fd4655afab56bf37..0000000000000000000000000000000000000000
--- a/configs/model/optimizer/adam.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-_target_: torch.optim.Adam
-_partial_: true
-
-lr: 0.0001
-weight_decay: 0.0
\ No newline at end of file
diff --git a/configs/model/optimizer/none.yaml b/configs/model/optimizer/none.yaml
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/configs/model/predictor/custom.yaml b/configs/model/predictor/custom.yaml
deleted file mode 100644
index d7a867b87888c03a7209b4b78bbdf2dadfff07a2..0000000000000000000000000000000000000000
--- a/configs/model/predictor/custom.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-_target_: deepscreen.models.predictors.custom.CustomPredictor
-
-defaults:
-  - drug_encoder: cnn
-  - protein_encoder: cnn
-  - decoder: concat_mlp
diff --git a/configs/model/predictor/decoder/concat_mlp.yaml b/configs/model/predictor/decoder/concat_mlp.yaml
deleted file mode 100644
index 17b92c9493a45d51b3463dc069a73295fc22eb4f..0000000000000000000000000000000000000000
--- a/configs/model/predictor/decoder/concat_mlp.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-_target_: deepscreen.models.components.mlp.ConcatMLP
-
-input_channels: ${eval:${model.drug_encoder.out_channels}+${model.protein_encoder.out_channels}}
-out_channels: 512
-hidden_channels: [1024,1024]
-dropout: 0.1
\ No newline at end of file
diff --git a/configs/model/predictor/decoder/mlp_deepdta.yaml b/configs/model/predictor/decoder/mlp_deepdta.yaml
deleted file mode 100644
index b6ee28076224a373a6879ece9296491dccfd280c..0000000000000000000000000000000000000000
--- a/configs/model/predictor/decoder/mlp_deepdta.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-_target_: deepscreen.models.components.mlp.MLP2
-
-input_channels: ${eval:${model.drug_encoder.out_channels}+${model.protein_encoder.out_channels}}
-out_channels: 1
-hidden_channels: [1024,1024,512]
-dropout: 0.1
\ No newline at end of file
diff --git a/configs/model/predictor/decoder/mlp_lazy.yaml b/configs/model/predictor/decoder/mlp_lazy.yaml
deleted file mode 100644
index 832863817e37fed6e5ef54eba4de99341310c4dc..0000000000000000000000000000000000000000
--- a/configs/model/predictor/decoder/mlp_lazy.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-_target_: deepscreen.models.components.mlp.LazyMLP
-
-out_channels: 1
-hidden_channels: [1024,1024,512]
-dropout: 0.1
\ No newline at end of file
diff --git a/configs/model/predictor/deep_dta.yaml b/configs/model/predictor/deep_dta.yaml
deleted file mode 100644
index 7f6cfc42a5e850554e0825d803f79575abdcdb1b..0000000000000000000000000000000000000000
--- a/configs/model/predictor/deep_dta.yaml
+++ /dev/null
@@ -1,15 +0,0 @@
-_target_: deepscreen.models.predictors.deep_dta.DeepDTA
-
-defaults:
-  - drug_encoder@drug_cnn: cnn
-  - protein_encoder@protein_cnn: cnn
-#  - /model/decoder@fc: concat_mlp
-
-num_features_drug: 63
-num_features_protein: 26
-embed_dim: 128
-
-drug_cnn:
-  in_channels: ${data.drug_featurizer.max_sequence_length}
-protein_cnn:
-  in_channels: ${data.protein_featurizer.max_sequence_length}
\ No newline at end of file
diff --git a/configs/model/predictor/drug_encoder/cnn.yaml b/configs/model/predictor/drug_encoder/cnn.yaml
deleted file mode 100644
index 453ef99dec6c2a5db821181e72eef24c9faab966..0000000000000000000000000000000000000000
--- a/configs/model/predictor/drug_encoder/cnn.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-_target_: deepscreen.models.components.cnn.CNN
-
-max_sequence_length: ${data.drug_featurizer.max_sequence_length}
-filters: [32, 64, 96]
-kernels: [4, 6, 8]
-in_channels: ${data.drug_featurizer.in_channels}
-out_channels: 256
-
-# TODO refactor the in_channels argument pipeline to be more reasonable
\ No newline at end of file
diff --git a/configs/model/predictor/drug_encoder/cnn_deepdta.yaml b/configs/model/predictor/drug_encoder/cnn_deepdta.yaml
deleted file mode 100644
index 97bf3a4870e224b2bc7a5eab946d38b57c279d26..0000000000000000000000000000000000000000
--- a/configs/model/predictor/drug_encoder/cnn_deepdta.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-_target_: deepscreen.models.components.cnn_deepdta.CNN_DeepDTA
-
-max_sequence_length: ${data.drug_featurizer.max_sequence_length}
-filters: [32, 64, 96]
-kernels: [4, 6, 8]
-in_channels: ${data.drug_featurizer.in_channels}
-out_channels: 128
\ No newline at end of file
diff --git a/configs/model/predictor/drug_encoder/gat.yaml b/configs/model/predictor/drug_encoder/gat.yaml
deleted file mode 100644
index 3b8dddd5ab5fac2b3cefff8191c01d3ab393c8a5..0000000000000000000000000000000000000000
--- a/configs/model/predictor/drug_encoder/gat.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-_target_: deepscreen.models.components.gat.GAT
-
-num_features: 78
-out_channels: 128
-dropout: 0.2
\ No newline at end of file
diff --git a/configs/model/predictor/drug_encoder/gcn.yaml b/configs/model/predictor/drug_encoder/gcn.yaml
deleted file mode 100644
index 5e2da337b324610297bd76b6783340d03bd681a8..0000000000000000000000000000000000000000
--- a/configs/model/predictor/drug_encoder/gcn.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-_target_: deepscreen.models.components.gcn.GCN
-
-num_features: 78
-out_channels: 128
-dropout: 0.2
\ No newline at end of file
diff --git a/configs/model/predictor/drug_encoder/gin.yaml b/configs/model/predictor/drug_encoder/gin.yaml
deleted file mode 100644
index caf5820c158ff7956b2440d25f7b5f901936f683..0000000000000000000000000000000000000000
--- a/configs/model/predictor/drug_encoder/gin.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-_target_: deepscreen.models.components.gin.GIN
-
-num_features: 78
-out_channels: 128
-dropout: 0.2
\ No newline at end of file
diff --git a/configs/model/predictor/drug_encoder/lstm.yaml b/configs/model/predictor/drug_encoder/lstm.yaml
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/configs/model/predictor/drug_encoder/transformer.yaml b/configs/model/predictor/drug_encoder/transformer.yaml
deleted file mode 100644
index 5eee1571675bcb2d2d539dbaa69ea0268c7b3908..0000000000000000000000000000000000000000
--- a/configs/model/predictor/drug_encoder/transformer.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-_target_: deepscreen.models.components.transformer
-
-input_dim: 1024
-emb_size: 128
-max_position_size: 50
-dropout: 0.1
-n_layer: 8
-intermediate_size: 512
-num_attention_heads: 8
-attention_probs_dropout: 0.1
-hidden_dropout: 0.1
\ No newline at end of file
diff --git a/configs/model/predictor/drug_vqa.yaml b/configs/model/predictor/drug_vqa.yaml
deleted file mode 100644
index 8ee31b6b3e5a62bec7998d3bdb4c4619ecd27e7f..0000000000000000000000000000000000000000
--- a/configs/model/predictor/drug_vqa.yaml
+++ /dev/null
@@ -1,15 +0,0 @@
-_target_: deepscreen.models.predictors.drug_vqa.DrugVQA
-
-conv_dim: 1
-lstm_hid_dim: 64
-d_a: 32
-r: 10
-n_chars_smi: 247
-n_chars_seq: 21
-dropout: 0.2
-in_channels: 8
-cnn_channels: 32
-cnn_layers: 4
-emb_dim: 30
-dense_hid: 64
-
diff --git a/configs/model/predictor/graph_dta.yaml b/configs/model/predictor/graph_dta.yaml
deleted file mode 100644
index 35bfdf8adc5ab69b780e81c828a195e48e8ec1a0..0000000000000000000000000000000000000000
--- a/configs/model/predictor/graph_dta.yaml
+++ /dev/null
@@ -1,16 +0,0 @@
-defaults:
-  - drug_encoder@gnn: gat
-  - _self_
-
-_target_: deepscreen.models.predictors.graph_dta.GraphDTA
-
-gnn:
-  num_features: 34
-  out_channels: 128
-  dropout: 0.2
-
-num_features_protein: 26
-n_filters: 32
-embed_dim: 128
-output_dim: 128
-dropout: 0.2
diff --git a/configs/model/predictor/hyper_attention_dti.yaml b/configs/model/predictor/hyper_attention_dti.yaml
deleted file mode 100644
index 87dde659688073d247953fce5ceef65a38786789..0000000000000000000000000000000000000000
--- a/configs/model/predictor/hyper_attention_dti.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-_target_: deepscreen.models.predictors.hyper_attention_dti.HyperAttentionDTI
-
-protein_kernel: [4,8,12]
-drug_kernel: [4,6,8]
-conv: 40
-char_dim: 64
-protein_max_len: ${data.protein_featurizer.max_sequence_length}
-drug_max_len: ${data.drug_featurizer.max_sequence_length}
\ No newline at end of file
diff --git a/configs/model/predictor/none.yaml b/configs/model/predictor/none.yaml
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/configs/model/predictor/protein_encoder/cnn.yaml b/configs/model/predictor/protein_encoder/cnn.yaml
deleted file mode 100644
index 9363e5e6130a5292d173b90eba8430c12edef3d1..0000000000000000000000000000000000000000
--- a/configs/model/predictor/protein_encoder/cnn.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-_target_: deepscreen.models.components.cnn.CNN
-
-max_sequence_length: ${data.protein_featurizer.max_sequence_length}
-filters: [32, 64, 96]
-kernels: [4, 8, 12]
-in_channels: ${data.protein_featurizer.in_channels}
-out_channels: 256
\ No newline at end of file
diff --git a/configs/model/predictor/protein_encoder/cnn_deepdta.yaml b/configs/model/predictor/protein_encoder/cnn_deepdta.yaml
deleted file mode 100644
index 8ac5f6d9064695cdfe2739946c1e55d55aa588d5..0000000000000000000000000000000000000000
--- a/configs/model/predictor/protein_encoder/cnn_deepdta.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-_target_: deepscreen.models.components.cnn_deepdta.CNN_DeepDTA
-
-max_sequence_length: ${data.protein_featurizer.max_sequence_length}
-filters: [32, 64, 96]
-kernels: [4, 8, 12]
-in_channels: ${data.protein_featurizer.in_channels}
-out_channels: 128
\ No newline at end of file
diff --git a/configs/model/predictor/protein_encoder/lstm.yaml b/configs/model/predictor/protein_encoder/lstm.yaml
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/configs/model/predictor/protein_encoder/tape_bert.yaml b/configs/model/predictor/protein_encoder/tape_bert.yaml
deleted file mode 100644
index 6a64b46c70850a5d796a19615ba553e69cb26a39..0000000000000000000000000000000000000000
--- a/configs/model/predictor/protein_encoder/tape_bert.yaml
+++ /dev/null
@@ -1,3 +0,0 @@
-_target_: tape.ProteinBertModel.from_pretrained
-
-pretrained_model_name_or_path: bert-base
\ No newline at end of file
diff --git a/configs/model/predictor/protein_encoder/transformer.yaml b/configs/model/predictor/protein_encoder/transformer.yaml
deleted file mode 100644
index 4fb7c9761bc098da84773f56bc949ce7c7d34c5f..0000000000000000000000000000000000000000
--- a/configs/model/predictor/protein_encoder/transformer.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-_target_: deepscreen.models.components.transformer
-
-input_dim: 8420
-emb_size: 64
-max_position_size: 545 50
-dropout: 0.1
-n_layer: 2
-intermediate_size: 256
-num_attention_heads: 4
-attention_probs_dropout: 0.1
-hidden_dropout: 0.1
-
diff --git a/configs/model/predictor/transformer_cpi.yaml b/configs/model/predictor/transformer_cpi.yaml
deleted file mode 100644
index c7d137ba108186e77e67878c4ad6ba40dbad52d3..0000000000000000000000000000000000000000
--- a/configs/model/predictor/transformer_cpi.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-_target_: deepscreen.models.predictors.transformer_cpi.TransformerCPI
-  
-protein_dim: 100
-atom_dim: 34
-hid_dim: 64
-n_layers: 3
-n_heads: 8
-pf_dim: 256
-dropout: 0.1
-kernel_size: 7
\ No newline at end of file
diff --git a/configs/model/predictor/transformer_cpi_2.yaml b/configs/model/predictor/transformer_cpi_2.yaml
deleted file mode 100644
index 2f9439a99c02720650635f2024acb36ef45b18fa..0000000000000000000000000000000000000000
--- a/configs/model/predictor/transformer_cpi_2.yaml
+++ /dev/null
@@ -1,14 +0,0 @@
-_target_: deepscreen.models.predictors.transformer_cpi_2.TransformerCPI2
-  
-encoder:
-  _target_: deepscreen.models.predictors.transformer_cpi_2.Encoder
-  # /model/protein_encoder@pretrain: tape_bert
-  n_layers: 3
-  pretrain:
-    _target_: tape.ProteinBertModel.from_pretrained
-    pretrained_model_name_or_path: bert-base
-
-decoder:
-  _target_: deepscreen.models.predictors.transformer_cpi_2.Decoder
-  n_layers: 3
-  dropout: 0.1
diff --git a/configs/model/scheduler/default.yaml b/configs/model/scheduler/default.yaml
deleted file mode 100644
index a319ea4099d233cec67de9477bbce25744368a91..0000000000000000000000000000000000000000
--- a/configs/model/scheduler/default.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-scheduler:
-  _target_: torch.optim.lr_scheduler.ReduceLROnPlateau
-  _partial_: true
-
-  mode: min
-  factor: 0.1
-  patience: 10
-
-monitor: ${oc.select:callbacks.model_checkpoint.monitor,"val/loss"}
-interval: "epoch"
-frequency: 1
\ No newline at end of file
diff --git a/configs/model/scheduler/none.yaml b/configs/model/scheduler/none.yaml
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/configs/model/scheduler/reduce_lr_on_plateau.yaml b/configs/model/scheduler/reduce_lr_on_plateau.yaml
deleted file mode 100644
index 221efd82d131473c6a51da966d153bb2ec85b69c..0000000000000000000000000000000000000000
--- a/configs/model/scheduler/reduce_lr_on_plateau.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-_target_: torch.optim.lr_scheduler.ReduceLROnPlateau
-_partial_: true
-
-mode: min
-factor: 0.1
-patience: 10
diff --git a/configs/paths/default.yaml b/configs/paths/default.yaml
deleted file mode 100644
index 862261ca7797da591715936cfd88a047c1722da3..0000000000000000000000000000000000000000
--- a/configs/paths/default.yaml
+++ /dev/null
@@ -1,19 +0,0 @@
-# path to root directory
-root_dir: .
-
-# path to data directory
-data_dir: ${paths.root_dir}/data
-
-# path to log directory
-log_dir: ${paths.root_dir}/logs
-
-# path to resource directory
-resource_dir: ${paths.root_dir}/resources
-
-# path to output directory, created dynamically by hydra
-# path generation pattern is specified in `configs/hydra/default.yaml`
-# use it to store all files generated during the run, like ckpts and metrics
-output_dir: ${hydra:runtime.output_dir}
-
-# path to working directory
-work_dir: ${hydra:runtime.cwd}
diff --git a/configs/predict.yaml b/configs/predict.yaml
deleted file mode 100644
index 2626280078af1ed4a3160e07f344afdef509f327..0000000000000000000000000000000000000000
--- a/configs/predict.yaml
+++ /dev/null
@@ -1,27 +0,0 @@
-# @package _global_
-
-defaults:
-  - model: dti_model # fixed for web server version
-  - task: null
-  - data: dti_data # fixed for web server version
-  - callbacks:
-    - model_summary
-    - rich_progress_bar
-    - csv_prediction_writer
-  - trainer: default
-  - paths: default
-  - extras: default
-  - hydra: default
-  - _self_
-  - preset: null
-  - experiment: null
-  - sweep: null
-  - debug: null
-  - optional local: default
-
-job_name: "predict"
-
-tags: ???
-
-# passing checkpoint path is necessary for prediction
-ckpt_path: ???
diff --git a/configs/preset/bacpi.yaml b/configs/preset/bacpi.yaml
deleted file mode 100644
index 9dbea130fd0f6b6fe07f009c340f33f6f8f6c558..0000000000000000000000000000000000000000
--- a/configs/preset/bacpi.yaml
+++ /dev/null
@@ -1,37 +0,0 @@
-# @package _global_
-model:
-  predictor:
-    _target_: deepscreen.models.predictors.bacpi.BACPI
-
-    n_atom: 20480
-    n_amino: 8448
-    comp_dim: 80
-    prot_dim: 80
-    latent_dim: 80
-    gat_dim: 50
-    num_head: 3
-    dropout: 0.1
-    alpha: 0.1
-    window: 5
-    layer_cnn: 3
-  optimizer:
-    lr: 5e-4
-
-data:
-  batch_size: 16
-
-  collator:
-    automatic_padding: True
-
-  drug_featurizer:
-    _target_: deepscreen.models.predictors.bacpi.drug_featurizer
-    _partial_: true
-    radius: 2
-
-  protein_featurizer:
-    _target_: deepscreen.models.predictors.bacpi.split_sequence
-    _partial_: true
-    ngram: 3
-#  collator:
-#    _target_: deepscreen.models.predictors.transformer_cpi_2.pack
-#    _partial_: true
diff --git a/configs/preset/coa_dti_pro.yaml b/configs/preset/coa_dti_pro.yaml
deleted file mode 100644
index 9ad501a6176a630b8edb97653607ef223946367d..0000000000000000000000000000000000000000
--- a/configs/preset/coa_dti_pro.yaml
+++ /dev/null
@@ -1,28 +0,0 @@
-# @package _global_
-defaults:
-  - override /data/protein_featurizer: none
-
-model:
-  predictor:
-    _target_: deepscreen.models.predictors.coa_dti_pro.CoaDTIPro
-
-    n_fingerprint: 20480
-    n_word: 26
-    dim: 512
-    layer_output: 3
-    layer_coa: 1
-    nhead: 8
-    dropout: 0.1
-    co_attention: 'inter'
-    gcn_pooling: False
-
-    esm_model_and_alphabet:
-      _target_: esm.pretrained.load_model_and_alphabet
-      model_name: resources/models/esm/esm1_t6_43M_UR50S.pt
-
-data:
-  drug_featurizer:
-    _target_: deepscreen.models.predictors.coa_dti_pro.drug_featurizer
-    _partial_: true
-    radius: 2
-  batch_size: 1
diff --git a/configs/preset/deep_conv_dti.yaml b/configs/preset/deep_conv_dti.yaml
deleted file mode 100644
index 025b151cf1539205f245feb41f9fd60f133c4497..0000000000000000000000000000000000000000
--- a/configs/preset/deep_conv_dti.yaml
+++ /dev/null
@@ -1,23 +0,0 @@
-# @package _global_
-defaults:
-  - override /data/drug_featurizer: ecfp
-  - override /data/protein_featurizer: label
-
-model:
-  predictor:
-    _target_: deepscreen.models.predictors.deep_conv_dti.DeepConvDTI
-
-    activation:
-      _target_: torch.nn.ELU
-
-    dropout: 0.0
-    drug_layers: [512, 128]
-    protein_windows: [10, 15, 20, 25, 30]
-    n_filters: 128
-    decay: 0.0001
-    convolution: true
-    protein_layers: [128,]
-    fc_layers: [128,]
-
-data:
-  batch_size: 512
diff --git a/configs/preset/deep_dta.yaml b/configs/preset/deep_dta.yaml
deleted file mode 100644
index f72d5c942226d88e798cb6a2fd6fef080df69053..0000000000000000000000000000000000000000
--- a/configs/preset/deep_dta.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-# @package _global_
-defaults:
-  - override /data/drug_featurizer: label
-  - override /data/protein_featurizer: label
-  - override /model/predictor: deep_dta
-
-data:
-  batch_size: 512
diff --git a/configs/preset/deep_dtaf.yaml b/configs/preset/deep_dtaf.yaml
deleted file mode 100644
index a2f2a8d143d28834b4c94e300c463bc776e23adf..0000000000000000000000000000000000000000
--- a/configs/preset/deep_dtaf.yaml
+++ /dev/null
@@ -1,19 +0,0 @@
-# @package _global_
-defaults:
-  - override /data/drug_featurizer: label
-  - override /data/protein_featurizer: label
-  - override /model/predictor: deep_dta
-
-data:
-  drug_featurizer:
-    charset: {'Z', 'Y', 'H', '[', 'O', ']', '5', 'M', 'K', '.', '9', 'e',
-               '(', 'l', 'U', 'V', 'L', 'B', 'y', 'm', 'd', 'h', 'T', 'A',
-               'W', 'b', 'i', 'D', 'R', '8', '/', 's', '#', 'u', '+', '@',
-               'n', '%', 'F', 'r', 't', 'I', 'S', '6', 'P', 'G', 'f', ')',
-               '-', '\\', 'C', 'E', 'o', '3', '2', '1', '=', 'g', 'c', 'N',
-               '7', '4', 'a', '0']
-  batch_size: 512
-
-model:
-  predictor:
-    smi_charset_len: ${eval:'len(${data.protein_featurizer.charset})+1'}
diff --git a/configs/preset/drug_ban.yaml b/configs/preset/drug_ban.yaml
deleted file mode 100644
index 537c9d79276383542e956ff4ef27178c4c358fc4..0000000000000000000000000000000000000000
--- a/configs/preset/drug_ban.yaml
+++ /dev/null
@@ -1,28 +0,0 @@
-# @package _global_
-defaults:
-  - override /data/protein_featurizer: label
-
-model:
-  predictor:
-    _target_: deepscreen.models.predictors.drug_ban.DrugBAN
-
-    drug_in_feats: 75
-    drug_embedding: 128
-    drug_hidden_feats: [128, 128, 128]
-    drug_padding: True
-    protein_emb_dim: 128
-    num_filters: [128, 128, 128]
-    kernel_size: [3, 6, 9]
-    protein_padding: True
-    mlp_in_dim: 256
-    mlp_hidden_dim: 512
-    mlp_out_dim: 128
-    ban_heads: 2
-
-data:
-  drug_featurizer:
-    _target_: deepscreen.models.predictors.drug_ban.drug_featurizer
-    _partial_: true
-    max_drug_nodes: 330
-
-  batch_size: 512
diff --git a/configs/preset/drug_vqa.yaml b/configs/preset/drug_vqa.yaml
deleted file mode 100644
index 26361c45c25c936a1d9c9b28942343ba7a96a127..0000000000000000000000000000000000000000
--- a/configs/preset/drug_vqa.yaml
+++ /dev/null
@@ -1,21 +0,0 @@
-# @package _global_
-defaults:
-  - override /data/drug_featurizer: tokenizer
-  - override /data/protein_featurizer: label
-  - override /model/predictor: drug_vqa
-
-model:
-  loss:
-    _target_: deepscreen.models.loss.multitask_loss.MultitaskWeightedLoss
-    loss_fns:
-      - ${task.loss}
-      - _target_: deepscreen.models.predictors.drug_vqa.AttentionL2Regularization
-    weights: [1, 0.001]
-
-data:
-  batch_size: 512
-  drug_featurizer:
-    tokenizer:
-      _target_: deepscreen.data.featurizers.token.SmilesTokenizer
-      vocab_file: resources/vocabs/drug_vqa/combinedVoc-wholeFour.voc
-      regex_pattern: '(\[[^\[\]]{1,10}\])'
\ No newline at end of file
diff --git a/configs/preset/graph_dta.yaml b/configs/preset/graph_dta.yaml
deleted file mode 100644
index 159cb4e619f252663dccda18294600602674e01d..0000000000000000000000000000000000000000
--- a/configs/preset/graph_dta.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-# @package _global_
-defaults:
-  - override /data/drug_featurizer: graph
-  - override /data/protein_featurizer: label
-  - override /model/predictor: graph_dta
-
-data:
-  batch_size: 512
\ No newline at end of file
diff --git a/configs/preset/hyper_attention_dti.yaml b/configs/preset/hyper_attention_dti.yaml
deleted file mode 100644
index ae63593517d0ce34310ba3f0dbf1201f66e7e3a5..0000000000000000000000000000000000000000
--- a/configs/preset/hyper_attention_dti.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-# @package _global_
-defaults:
-  - override /data/drug_featurizer: label
-  - override /data/protein_featurizer: label
-  - override /model/predictor: hyper_attention_dti
-
-data:
-  batch_size: 32
\ No newline at end of file
diff --git a/configs/preset/m_graph_dta.yaml b/configs/preset/m_graph_dta.yaml
deleted file mode 100644
index 8609b499b94168c7c5da2b5779b310be5c769020..0000000000000000000000000000000000000000
--- a/configs/preset/m_graph_dta.yaml
+++ /dev/null
@@ -1,22 +0,0 @@
-# @package _global_
-defaults:
-  - override /data/drug_featurizer: graph
-  - override /data/protein_featurizer: label
-
-model:
-  predictor:
-    _target_: deepscreen.models.predictors.m_graph_dta.MGraphDTA
-    block_num: 3
-    vocab_protein_size: ${eval:'len(${data.protein_featurizer.charset})+1'}
-    embedding_size: 128
-    filter_num: 32
-
-data:
-  drug_featurizer:
-    atom_features:
-      _target_: deepscreen.models.predictors.m_graph_dta.atom_features
-      _partial_: true
-  batch_size: 512
-
-trainer:
-  precision: 'bf16'
\ No newline at end of file
diff --git a/configs/preset/mol_trans.yaml b/configs/preset/mol_trans.yaml
deleted file mode 100644
index ed7fcf5ce9d43b0e047b9720cb544faf707fb64f..0000000000000000000000000000000000000000
--- a/configs/preset/mol_trans.yaml
+++ /dev/null
@@ -1,39 +0,0 @@
-# @package _global_
-defaults:
-  - override /data/drug_featurizer: fcs
-  - override /data/protein_featurizer: fcs
-
-data:
-  batch_size: 16
-  drug_featurizer:
-    max_sequence_length: 205
-  protein_featurizer:
-    max_sequence_length: 545
-
-model:
-  predictor:
-    _target_: deepscreen.models.predictors.mol_trans.MolTrans
-
-    input_dim_drug: 23532
-    input_dim_target: 16693
-    max_drug_seq: ${data.drug_featurizer.max_sequence_length}
-    max_protein_seq: ${data.protein_featurizer.max_sequence_length}
-    emb_size: 384
-    dropout_rate: 0.1
-
-    # DenseNet
-    scale_down_ratio: 0.25
-    growth_rate: 20
-    transition_rate: 0.5
-    num_dense_blocks: 4
-    kernal_dense_size: 3
-
-    # Encoder
-    intermediate_size: 1536
-    num_attention_heads: 12
-    attention_probs_dropout_prob: 0.1
-    hidden_dropout_prob: 0.1
-    #flatten_dim: 293412
-
-  optimizer:
-    lr: 1e-6
\ No newline at end of file
diff --git a/configs/preset/monn.yaml b/configs/preset/monn.yaml
deleted file mode 100644
index 117031aaf9f51f3f935c0a679af40883474b7880..0000000000000000000000000000000000000000
--- a/configs/preset/monn.yaml
+++ /dev/null
@@ -1,17 +0,0 @@
-# @package _global_
-defaults:
-  - dti_experiment
-  # TODO MONN featurizers not fully implemented yet
-  - override /data/drug_featurizer: label
-  - override /data/protein_featurizer: label
-  - override /model/predictor: monn
-  - override /task: binary
-  - _self_
-
-model:
-  loss:
-    _target_: deepscreen.models.loss.multitask_loss.MultitaskWeightedLoss
-    loss_fns:
-      - _target_: ${model.loss}
-      - _target_: deepscreen.models.predictors.monn.MaskedBCELoss
-    weights: [1, 0.1]
diff --git a/configs/preset/transformer_cpi_2.yaml b/configs/preset/transformer_cpi_2.yaml
deleted file mode 100644
index e1c224f88a6de1266ee4d836c15ff5e88b06f119..0000000000000000000000000000000000000000
--- a/configs/preset/transformer_cpi_2.yaml
+++ /dev/null
@@ -1,35 +0,0 @@
-# @package _global_
-defaults:
-  - override /data/drug_featurizer: mol_features
-  - override /data/protein_featurizer: tokenizer
-
-model:
-  predictor:
-    _target_: deepscreen.models.predictors.transformer_cpi_2.TransformerCPI2
-
-    encoder:
-      _target_: deepscreen.models.predictors.transformer_cpi_2.Encoder
-      # /model/protein_encoder@pretrain: tape_bert
-      n_layers: 3
-      pretrain:
-        _target_: tape.ProteinBertModel.from_pretrained
-        pretrained_model_name_or_path: resources/models/tape/bert-base/ # bert-base
-
-    decoder:
-      _target_: deepscreen.models.predictors.transformer_cpi_2.Decoder
-      n_layers: 3
-      dropout: 0.1
-
-data:
-  batch_size: 16
-  collator:
-    automatic_padding: True
-
-  protein_featurizer:
-    tokenizer:
-      _target_: tape.TAPETokenizer.from_pretrained
-      vocab: iupac
-
-#  collator:
-#    _target_: deepscreen.models.predictors.transformer_cpi_2.pack
-#    _partial_: true
diff --git a/configs/sweep/chembl33_benchmark.yaml b/configs/sweep/chembl33_benchmark.yaml
deleted file mode 100644
index b18bcbb0656411aa393181a5bfd79663d144dc59..0000000000000000000000000000000000000000
--- a/configs/sweep/chembl33_benchmark.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-# @package _global_
-tags: ['sweep', 'benchmark']
-hydra:
-  sweeper:
-    params:
-      experiment: kinase,membrane_receptors,non_kinase_enzymes #,ion_channels,nuclear_receptors,other_protein_targets
\ No newline at end of file
diff --git a/configs/sweep/ddp_multirun.yaml b/configs/sweep/ddp_multirun.yaml
deleted file mode 100644
index fbf6641a20019ae41cf8d231d01433b2562a9c77..0000000000000000000000000000000000000000
--- a/configs/sweep/ddp_multirun.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-# @package _global_
-hydra:
-  sweeper:
-    params:
-      preset: graph_dta,deep_dta # drug_vqa,mol_trans,hyper_attention_dti,transformer_cpi_2
-      experiment: kiba,davis,bindingdb
\ No newline at end of file
diff --git a/configs/sweep/dti_benchmark.yaml b/configs/sweep/dti_benchmark.yaml
deleted file mode 100644
index b404a86d52131cbde1d7b877be92a80d8000d5b8..0000000000000000000000000000000000000000
--- a/configs/sweep/dti_benchmark.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-# @package _global_
-tags: ['sweep', 'benchmark']
-hydra:
-  sweeper:
-    params:
-      preset: transformer_cpi_2 #graph_dta,deep_dta #,mol_trans,hyper_attention_dti,m_graph_dta
-      experiment: other_protein_targets
-
diff --git a/configs/sweep/example_multirun.yaml b/configs/sweep/example_multirun.yaml
deleted file mode 100644
index b2d7edad480a88165ca51475c7fd076110d2fef0..0000000000000000000000000000000000000000
--- a/configs/sweep/example_multirun.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-# @package _global_
-hydra:
-  sweeper:
-    params:
-      preset: graph_dta,deep_dta
-      experiment: chembl_random
diff --git a/configs/sweep/example_multirun_test.yaml b/configs/sweep/example_multirun_test.yaml
deleted file mode 100644
index a609000341c88314547dfe300ec59e059c0d9825..0000000000000000000000000000000000000000
--- a/configs/sweep/example_multirun_test.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-# @package _global_
-hydra:
-  sweeper:
-    params:
-#      ckpt_path: "'C:/Users/libok/Documents/GitHub/DeepScreen/logs/train/runs/2023-11-07_23-21-55-442205_[debug]/checkpoints/epoch_000.ckpt','C:/Users/libok/Documents/GitHub/DeepScreen/logs/train/runs/2023-11-07_19-46-08-740035_[debug]/checkpoints/epoch_000.ckpt'"
-      data.data_file: dti_benchmark/random_split_update/davis_reserved_test.csv,dti_benchmark/random_split_update/kiba_reserved_test.csv
-      ckpt_path: "'C:/Users/libok/Documents/GitHub/DeepScreen/logs/test/multiruns/2023-11-10_10-31-15-339335_[multirun,test,dev]/metrics_summary.csv'"
\ No newline at end of file
diff --git a/configs/sweep/example_submitit.yaml b/configs/sweep/example_submitit.yaml
deleted file mode 100644
index 510522a9cb855b9afd2ac3ebd6a0f50baea93459..0000000000000000000000000000000000000000
--- a/configs/sweep/example_submitit.yaml
+++ /dev/null
@@ -1,17 +0,0 @@
-# @package _global_
-defaults:
-  - basic
-  - override /hydra/launcher: submitit_local
-
-hydra:
-  sweeper:
-    params:
-      preset: graph_dta,deep_dta
-      experiment: chembl_random
-  launcher:
-    timeout_min: 60
-    cpus_per_task: 1
-    gpus_per_node: 1
-    tasks_per_node: 4
-    mem_gb: 32
-    nodes: 1
\ No newline at end of file
diff --git a/configs/sweep/experiment_summary.csv b/configs/sweep/experiment_summary.csv
deleted file mode 100644
index 73e924007e4c3936dadc918f7cece50574336c3e..0000000000000000000000000000000000000000
--- a/configs/sweep/experiment_summary.csv
+++ /dev/null
@@ -1,21 +0,0 @@
-test/loss,test/auprc,test/auroc,test/f1_score,test/precision,test/recall,test/sensitivity,test/specificity,ckpt_path,job_status,preset,experiment,sweep,tags,model.optimizer.lr,local,data.batch_size
-0.1525115370750427,0.735183835029602,0.9363504648208618,0.661261260509491,0.7816826701164246,0.5729898810386658,0.5729898810386658,0.984080135822296,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_14-53-13-645337_[benchmark,ddta,gdta]/experiment=kiba;preset=deep_dta;sweep=slurm_test;tags=[benchmark,ddta,gdta]/checkpoints/epoch_041.ckpt",COMPLETED,deep_dta,kiba,slurm_test,"[benchmark,ddta,gdta]",,,
-0.193635880947113,0.4078962802886963,0.8581838607788086,0.3916666805744171,0.5371428728103638,0.3081967234611511,0.3081967234611511,0.9788622260093688,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_14-53-13-645337_[benchmark,ddta,gdta]/experiment=davis;preset=deep_dta;sweep=slurm_test;tags=[benchmark,ddta,gdta]/checkpoints/epoch_008.ckpt",COMPLETED,deep_dta,davis,slurm_test,"[benchmark,ddta,gdta]",,,
-0.5104637742042542,0.7619075775146484,0.8163812756538391,0.6808292269706726,0.6954700350761414,0.6667922139167786,0.6667922139167786,0.789406955242157,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_14-53-13-645337_[benchmark,ddta,gdta]/experiment=bindingdb;preset=deep_dta;sweep=slurm_test;tags=[benchmark,ddta,gdta]/checkpoints/epoch_003.ckpt",COMPLETED,deep_dta,bindingdb,slurm_test,"[benchmark,ddta,gdta]",,,
-0.2221491634845733,0.3560383319854736,0.78690105676651,0.2659846544265747,0.604651153087616,0.1704917997121811,0.1704917997121811,0.9911273717880248,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_14-53-13-645337_[benchmark,ddta,gdta]/experiment=davis;preset=graph_dta;sweep=slurm_test;tags=[benchmark,ddta,gdta]/checkpoints/epoch_054.ckpt",COMPLETED,graph_dta,davis,slurm_test,"[benchmark,ddta,gdta]",,,
-0.2281630784273147,0.4483628869056701,0.8383051156997681,0.2730720639228821,0.7176079750061035,0.1686182618141174,0.1686182618141174,0.9933990836143494,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_14-53-13-645337_[benchmark,ddta,gdta]/experiment=kiba;preset=graph_dta;sweep=slurm_test;tags=[benchmark,ddta,gdta]/checkpoints/epoch_065.ckpt",COMPLETED,graph_dta,kiba,slurm_test,"[benchmark,ddta,gdta]",,,
-0.4569543302059173,0.828099250793457,0.8623664379119873,0.7299983501434326,0.7756586670875549,0.6894148588180542,0.6894148588180542,0.8561919927597046,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_14-53-13-645337_[benchmark,ddta,gdta]/experiment=bindingdb;preset=graph_dta;sweep=slurm_test;tags=[benchmark,ddta,gdta]/checkpoints/epoch_034.ckpt",COMPLETED,graph_dta,bindingdb,slurm_test,"[benchmark,ddta,gdta]",,,
-0.1881016194820404,0.5213174819946289,0.8876519203186035,0.5207100510597229,0.6534653306007385,0.4327868819236755,0.4327868819236755,0.9817327857017516,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_18-08-40-028557_[sweep,benchmark]/experiment=davis;preset=hyper_attention_dti;sweep=slurm_test/checkpoints/epoch_017.ckpt",COMPLETED,hyper_attention_dti,davis,slurm_test,,,,
-0.144176036119461,0.7704265117645264,0.9501243829727172,0.6897732019424438,0.7632575631141663,0.6291959285736084,0.6291959285736084,0.980585515499115,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_18-08-40-028557_[sweep,benchmark]/experiment=kiba;preset=hyper_attention_dti;sweep=slurm_test/checkpoints/epoch_014.ckpt",COMPLETED,hyper_attention_dti,kiba,slurm_test,,,,
-0.3445079922676086,0.915877878665924,0.934882640838623,0.8371888399124146,0.8385065793991089,0.8358752131462097,0.8358752131462097,0.8838841319084167,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_18-08-40-028557_[sweep,benchmark]/experiment=bindingdb;preset=hyper_attention_dti;sweep=slurm_test/checkpoints/epoch_017.ckpt",COMPLETED,hyper_attention_dti,bindingdb,slurm_test,,,,
-0.3915603458881378,0.3016493022441864,0.7910888195037842,0.085626907646656,0.6363636255264282,0.0459016375243663,0.0459016375243663,0.9979122877120972,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-20_18-50-02-680654_[mol_trans,benchmark]/experiment=davis;preset=mol_trans;sweep=slurm_test/checkpoints/epoch_000.ckpt",COMPLETED,mol_trans,davis,slurm_test,,,,
-0.1662539541721344,0.7397991418838501,0.9369943141937256,0.6784178614616394,0.7550238966941833,0.6159250736236572,0.6159250736236572,0.9801195859909058,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-20_18-50-02-680654_[mol_trans,benchmark]/experiment=kiba;preset=mol_trans;sweep=slurm_test/checkpoints/epoch_008.ckpt",COMPLETED,mol_trans,kiba,slurm_test,,,,
-0.2160931378602981,0.3230183720588684,0.796424388885498,0.3271028101444244,0.5691056847572327,0.2295081913471222,0.2295081913471222,0.9861690998077391,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-20_20-20-11-193061_[tcpi2,kiba,davis]/experiment=davis;model.optimizer.lr=1e-06;preset=transformer_cpi_2;sweep=slurm_test;tags=[tcpi2,kiba,davis]/checkpoints/epoch_023.ckpt",COMPLETED,transformer_cpi_2,davis,slurm_test,"[tcpi2,kiba,davis]",1e-06,,
-0.2221459150314331,0.5159928798675537,0.8539965152740479,0.4716618657112121,0.612983763217926,0.3832943141460418,0.3832943141460418,0.9759260416030884,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-20_20-20-11-193061_[tcpi2,kiba,davis]/experiment=kiba;model.optimizer.lr=1e-06;preset=transformer_cpi_2;sweep=slurm_test;tags=[tcpi2,kiba,davis]/checkpoints/epoch_077.ckpt",COMPLETED,transformer_cpi_2,kiba,slurm_test,"[tcpi2,kiba,davis]",1e-06,,
-0.1689525544643402,0.5410239696502686,0.9028607606887816,0.4678111672401428,0.6770186424255371,0.3573770523071289,0.3573770523071289,0.986430048942566,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-20_21-25-54-050914_[deep_conv_dti,benchmark]/experiment=davis;local=gpu3090;preset=deep_conv_dti;tags=[deep_conv_dti,benchmark]/checkpoints/epoch_012.ckpt",COMPLETED,deep_conv_dti,davis,,"[deep_conv_dti,benchmark]",,gpu3090,
-0.1273866593837738,0.8186066746711731,0.95548677444458,0.7409326434135437,0.8289855122566223,0.6697892546653748,0.6697892546653748,0.9862545728683472,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-20_21-25-54-050914_[deep_conv_dti,benchmark]/experiment=kiba;local=gpu3090;preset=deep_conv_dti;tags=[deep_conv_dti,benchmark]/checkpoints/epoch_026.ckpt",COMPLETED,deep_conv_dti,kiba,,"[deep_conv_dti,benchmark]",,gpu3090,
-0.3221746683120727,0.9174473285675048,0.9374850988388062,0.8440826535224915,0.8421315550804138,0.846042811870575,0.846042811870575,0.8856043219566345,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-20_21-25-54-050914_[deep_conv_dti,benchmark]/experiment=bindingdb;local=gpu3090;preset=deep_conv_dti;tags=[deep_conv_dti,benchmark]/checkpoints/epoch_008.ckpt",COMPLETED,deep_conv_dti,bindingdb,,"[deep_conv_dti,benchmark]",,gpu3090,
-0.3808988630771637,0.9017271995544434,0.92254638671875,0.8203105330467224,0.818312406539917,0.822318434715271,0.822318434715271,0.8683114647865295,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-23_23-21-02-704802_[mol_trans,bindingdb]/experiment=bindingdb;local=gpu3090;preset=mol_trans;tags=[mol_trans,bindingdb]/checkpoints/epoch_064.ckpt",COMPLETED,mol_trans,bindingdb,,"[mol_trans,bindingdb]",,gpu3090,
-0.202189102768898,0.3614169955253601,0.8401678204536438,0.330232560634613,0.5680000185966492,0.2327868789434433,0.2327868789434433,0.9859081506729126,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-23_23-27-18-387556_[m_graph_dta,benchmark]/experiment=davis;local=gpu3090;preset=m_graph_dta;tags=[m_graph_dta,benchmark]/checkpoints/epoch_094.ckpt",COMPLETED,m_graph_dta,davis,,"[m_graph_dta,benchmark]",,gpu3090,
-0.1921116858720779,0.6082723736763,0.8893994092941284,0.4803767800331116,0.7285714149475098,0.3583138287067413,0.3583138287067413,0.9867205023765564,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-23_23-27-18-387556_[m_graph_dta,benchmark]/experiment=kiba;local=gpu3090;preset=m_graph_dta;tags=[m_graph_dta,benchmark]/checkpoints/epoch_246.ckpt",COMPLETED,m_graph_dta,kiba,,"[m_graph_dta,benchmark]",,gpu3090,
-0.6574236750602722,0.5444095730781555,0.6328268051147461,0.483252614736557,0.5203881859779358,0.4510641098022461,0.4510641098022461,0.7001991868019104,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-11-06_14-16-25-154180_[benchmark,tcpi2,bindingdb]/data.batch_size=32;experiment=bindingdb;preset=transformer_cpi_2;tags=[benchmark,tcpi2,bindingdb]/checkpoints/epoch_017.ckpt",COMPLETED,transformer_cpi_2,bindingdb,,"[benchmark,tcpi2,bindingdb]",,,32.0
diff --git a/configs/sweep/experiment_summary_bindingdb.csv b/configs/sweep/experiment_summary_bindingdb.csv
deleted file mode 100644
index b2a3ee1ab0192c82662c03cf59ed07bda14b1862..0000000000000000000000000000000000000000
--- a/configs/sweep/experiment_summary_bindingdb.csv
+++ /dev/null
@@ -1,7 +0,0 @@
-test/loss,test/auprc,test/auroc,test/f1_score,test/precision,test/recall,test/sensitivity,test/specificity,ckpt_path,job_status,preset,experiment,sweep,tags,model.optimizer.lr,local,data.batch_size
-0.5104637742042542,0.7619075775146484,0.8163812756538391,0.6808292269706726,0.6954700350761414,0.6667922139167786,0.6667922139167786,0.789406955242157,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_14-53-13-645337_[benchmark,ddta,gdta]/experiment=bindingdb;preset=deep_dta;sweep=slurm_test;tags=[benchmark,ddta,gdta]/checkpoints/epoch_003.ckpt",COMPLETED,deep_dta,bindingdb,slurm_test,"[benchmark,ddta,gdta]",,,
-0.4569543302059173,0.828099250793457,0.8623664379119873,0.7299983501434326,0.7756586670875549,0.6894148588180542,0.6894148588180542,0.8561919927597046,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_14-53-13-645337_[benchmark,ddta,gdta]/experiment=bindingdb;preset=graph_dta;sweep=slurm_test;tags=[benchmark,ddta,gdta]/checkpoints/epoch_034.ckpt",COMPLETED,graph_dta,bindingdb,slurm_test,"[benchmark,ddta,gdta]",,,
-0.3445079922676086,0.915877878665924,0.934882640838623,0.8371888399124146,0.8385065793991089,0.8358752131462097,0.8358752131462097,0.8838841319084167,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_18-08-40-028557_[sweep,benchmark]/experiment=bindingdb;preset=hyper_attention_dti;sweep=slurm_test/checkpoints/epoch_017.ckpt",COMPLETED,hyper_attention_dti,bindingdb,slurm_test,,,,
-0.3221746683120727,0.9174473285675048,0.9374850988388062,0.8440826535224915,0.8421315550804138,0.846042811870575,0.846042811870575,0.8856043219566345,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-20_21-25-54-050914_[deep_conv_dti,benchmark]/experiment=bindingdb;local=gpu3090;preset=deep_conv_dti;tags=[deep_conv_dti,benchmark]/checkpoints/epoch_008.ckpt",COMPLETED,deep_conv_dti,bindingdb,,"[deep_conv_dti,benchmark]",,gpu3090,
-0.3808988630771637,0.9017271995544434,0.92254638671875,0.8203105330467224,0.818312406539917,0.822318434715271,0.822318434715271,0.8683114647865295,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-23_23-21-02-704802_[mol_trans,bindingdb]/experiment=bindingdb;local=gpu3090;preset=mol_trans;tags=[mol_trans,bindingdb]/checkpoints/epoch_064.ckpt",COMPLETED,mol_trans,bindingdb,,"[mol_trans,bindingdb]",,gpu3090,
-0.6574236750602722,0.5444095730781555,0.6328268051147461,0.483252614736557,0.5203881859779358,0.4510641098022461,0.4510641098022461,0.7001991868019104,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-11-06_14-16-25-154180_[benchmark,tcpi2,bindingdb]/data.batch_size=32;experiment=bindingdb;preset=transformer_cpi_2;tags=[benchmark,tcpi2,bindingdb]/checkpoints/epoch_017.ckpt",COMPLETED,transformer_cpi_2,bindingdb,,"[benchmark,tcpi2,bindingdb]",,,32.0
diff --git a/configs/sweep/experiment_summary_davis.csv b/configs/sweep/experiment_summary_davis.csv
deleted file mode 100644
index 1cc9af384ea7c91cdc510d734862bbe56edc3f43..0000000000000000000000000000000000000000
--- a/configs/sweep/experiment_summary_davis.csv
+++ /dev/null
@@ -1,8 +0,0 @@
-test/loss,test/auprc,test/auroc,test/f1_score,test/precision,test/recall,test/sensitivity,test/specificity,ckpt_path,job_status,preset,experiment,sweep,tags,model.optimizer.lr,local,data.batch_size
-0.193635880947113,0.4078962802886963,0.8581838607788086,0.3916666805744171,0.5371428728103638,0.3081967234611511,0.3081967234611511,0.9788622260093688,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_14-53-13-645337_[benchmark,ddta,gdta]/experiment=davis;preset=deep_dta;sweep=slurm_test;tags=[benchmark,ddta,gdta]/checkpoints/epoch_008.ckpt",COMPLETED,deep_dta,davis,slurm_test,"[benchmark,ddta,gdta]",,,
-0.2221491634845733,0.3560383319854736,0.78690105676651,0.2659846544265747,0.604651153087616,0.1704917997121811,0.1704917997121811,0.9911273717880248,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_14-53-13-645337_[benchmark,ddta,gdta]/experiment=davis;preset=graph_dta;sweep=slurm_test;tags=[benchmark,ddta,gdta]/checkpoints/epoch_054.ckpt",COMPLETED,graph_dta,davis,slurm_test,"[benchmark,ddta,gdta]",,,
-0.1881016194820404,0.5213174819946289,0.8876519203186035,0.5207100510597229,0.6534653306007385,0.4327868819236755,0.4327868819236755,0.9817327857017516,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_18-08-40-028557_[sweep,benchmark]/experiment=davis;preset=hyper_attention_dti;sweep=slurm_test/checkpoints/epoch_017.ckpt",COMPLETED,hyper_attention_dti,davis,slurm_test,,,,
-0.3915603458881378,0.3016493022441864,0.7910888195037842,0.085626907646656,0.6363636255264282,0.0459016375243663,0.0459016375243663,0.9979122877120972,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-20_18-50-02-680654_[mol_trans,benchmark]/experiment=davis;preset=mol_trans;sweep=slurm_test/checkpoints/epoch_000.ckpt",COMPLETED,mol_trans,davis,slurm_test,,,,
-0.2160931378602981,0.3230183720588684,0.796424388885498,0.3271028101444244,0.5691056847572327,0.2295081913471222,0.2295081913471222,0.9861690998077391,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-20_20-20-11-193061_[tcpi2,kiba,davis]/experiment=davis;model.optimizer.lr=1e-06;preset=transformer_cpi_2;sweep=slurm_test;tags=[tcpi2,kiba,davis]/checkpoints/epoch_023.ckpt",COMPLETED,transformer_cpi_2,davis,slurm_test,"[tcpi2,kiba,davis]",1e-06,,
-0.1689525544643402,0.5410239696502686,0.9028607606887816,0.4678111672401428,0.6770186424255371,0.3573770523071289,0.3573770523071289,0.986430048942566,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-20_21-25-54-050914_[deep_conv_dti,benchmark]/experiment=davis;local=gpu3090;preset=deep_conv_dti;tags=[deep_conv_dti,benchmark]/checkpoints/epoch_012.ckpt",COMPLETED,deep_conv_dti,davis,,"[deep_conv_dti,benchmark]",,gpu3090,
-0.202189102768898,0.3614169955253601,0.8401678204536438,0.330232560634613,0.5680000185966492,0.2327868789434433,0.2327868789434433,0.9859081506729126,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-23_23-27-18-387556_[m_graph_dta,benchmark]/experiment=davis;local=gpu3090;preset=m_graph_dta;tags=[m_graph_dta,benchmark]/checkpoints/epoch_094.ckpt",COMPLETED,m_graph_dta,davis,,"[m_graph_dta,benchmark]",,gpu3090,
diff --git a/configs/sweep/experiment_summary_kiba.csv b/configs/sweep/experiment_summary_kiba.csv
deleted file mode 100644
index fea61408c0c735bb75f05494db511650a4beff79..0000000000000000000000000000000000000000
--- a/configs/sweep/experiment_summary_kiba.csv
+++ /dev/null
@@ -1,8 +0,0 @@
-test/loss,test/auprc,test/auroc,test/f1_score,test/precision,test/recall,test/sensitivity,test/specificity,ckpt_path,job_status,preset,experiment,sweep,tags,model.optimizer.lr,local,data.batch_size
-0.1525115370750427,0.735183835029602,0.9363504648208618,0.661261260509491,0.7816826701164246,0.5729898810386658,0.5729898810386658,0.984080135822296,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_14-53-13-645337_[benchmark,ddta,gdta]/experiment=kiba;preset=deep_dta;sweep=slurm_test;tags=[benchmark,ddta,gdta]/checkpoints/epoch_041.ckpt",COMPLETED,deep_dta,kiba,slurm_test,"[benchmark,ddta,gdta]",,,
-0.2281630784273147,0.4483628869056701,0.8383051156997681,0.2730720639228821,0.7176079750061035,0.1686182618141174,0.1686182618141174,0.9933990836143494,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_14-53-13-645337_[benchmark,ddta,gdta]/experiment=kiba;preset=graph_dta;sweep=slurm_test;tags=[benchmark,ddta,gdta]/checkpoints/epoch_065.ckpt",COMPLETED,graph_dta,kiba,slurm_test,"[benchmark,ddta,gdta]",,,
-0.144176036119461,0.7704265117645264,0.9501243829727172,0.6897732019424438,0.7632575631141663,0.6291959285736084,0.6291959285736084,0.980585515499115,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_18-08-40-028557_[sweep,benchmark]/experiment=kiba;preset=hyper_attention_dti;sweep=slurm_test/checkpoints/epoch_014.ckpt",COMPLETED,hyper_attention_dti,kiba,slurm_test,,,,
-0.1662539541721344,0.7397991418838501,0.9369943141937256,0.6784178614616394,0.7550238966941833,0.6159250736236572,0.6159250736236572,0.9801195859909058,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-20_18-50-02-680654_[mol_trans,benchmark]/experiment=kiba;preset=mol_trans;sweep=slurm_test/checkpoints/epoch_008.ckpt",COMPLETED,mol_trans,kiba,slurm_test,,,,
-0.2221459150314331,0.5159928798675537,0.8539965152740479,0.4716618657112121,0.612983763217926,0.3832943141460418,0.3832943141460418,0.9759260416030884,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-20_20-20-11-193061_[tcpi2,kiba,davis]/experiment=kiba;model.optimizer.lr=1e-06;preset=transformer_cpi_2;sweep=slurm_test;tags=[tcpi2,kiba,davis]/checkpoints/epoch_077.ckpt",COMPLETED,transformer_cpi_2,kiba,slurm_test,"[tcpi2,kiba,davis]",1e-06,,
-0.1273866593837738,0.8186066746711731,0.95548677444458,0.7409326434135437,0.8289855122566223,0.6697892546653748,0.6697892546653748,0.9862545728683472,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-20_21-25-54-050914_[deep_conv_dti,benchmark]/experiment=kiba;local=gpu3090;preset=deep_conv_dti;tags=[deep_conv_dti,benchmark]/checkpoints/epoch_026.ckpt",COMPLETED,deep_conv_dti,kiba,,"[deep_conv_dti,benchmark]",,gpu3090,
-0.1921116858720779,0.6082723736763,0.8893994092941284,0.4803767800331116,0.7285714149475098,0.3583138287067413,0.3583138287067413,0.9867205023765564,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-23_23-27-18-387556_[m_graph_dta,benchmark]/experiment=kiba;local=gpu3090;preset=m_graph_dta;tags=[m_graph_dta,benchmark]/checkpoints/epoch_246.ckpt",COMPLETED,m_graph_dta,kiba,,"[m_graph_dta,benchmark]",,gpu3090,
diff --git a/configs/sweep/experiment_summary_test.csv b/configs/sweep/experiment_summary_test.csv
deleted file mode 100644
index a1ce0b60c2e5c9e1cd678cc7a7a8867a2472d15f..0000000000000000000000000000000000000000
--- a/configs/sweep/experiment_summary_test.csv
+++ /dev/null
@@ -1,4 +0,0 @@
-test/loss,test/auprc,test/auroc,test/f1_score,test/precision,test/recall,test/sensitivity,test/specificity,ckpt_path,job_status,preset,experiment,sweep,tags,model.optimizer.lr,local,data.batch_size
-0.193635880947113,0.4078962802886963,0.8581838607788086,0.3916666805744171,0.5371428728103638,0.3081967234611511,0.3081967234611511,0.9788622260093688,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_14-53-13-645337_[benchmark,ddta,gdta]/experiment=davis;preset=deep_dta;sweep=slurm_test;tags=[benchmark,ddta,gdta]/checkpoints/epoch_008.ckpt",COMPLETED,deep_dta,davis,slurm_test,"[benchmark,ddta,gdta]",,,
-0.2221491634845733,0.3560383319854736,0.78690105676651,0.2659846544265747,0.604651153087616,0.1704917997121811,0.1704917997121811,0.9911273717880248,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_14-53-13-645337_[benchmark,ddta,gdta]/experiment=davis;preset=graph_dta;sweep=slurm_test;tags=[benchmark,ddta,gdta]/checkpoints/epoch_054.ckpt",COMPLETED,graph_dta,davis,slurm_test,"[benchmark,ddta,gdta]",,,
-0.1689525544643402,0.5410239696502686,0.9028607606887816,0.4678111672401428,0.6770186424255371,0.3573770523071289,0.3573770523071289,0.986430048942566,"/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-20_21-25-54-050914_[deep_conv_dti,benchmark]/experiment=davis;local=gpu3090;preset=deep_conv_dti;tags=[deep_conv_dti,benchmark]/checkpoints/epoch_012.ckpt",COMPLETED,deep_conv_dti,davis,,"[deep_conv_dti,benchmark]",,gpu3090,
diff --git a/configs/sweep/midterm_benchmark.yaml b/configs/sweep/midterm_benchmark.yaml
deleted file mode 100644
index 17c6fbef87d5df1a6b3a5362a3332f710c30031b..0000000000000000000000000000000000000000
--- a/configs/sweep/midterm_benchmark.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-# @package _global_
-tags: ['midterm', 'benchmark']
-hydra:
-  sweeper:
-    params:
-      experiment: kinase,membrane_receptors,non_kinase_enzymes #,ion_channels,nuclear_receptors,other_protein_targets
\ No newline at end of file
diff --git a/configs/sweep/multi_test.yaml b/configs/sweep/multi_test.yaml
deleted file mode 100644
index 8fe120a7805b77823572d7ed83ab168ec685c939..0000000000000000000000000000000000000000
--- a/configs/sweep/multi_test.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-# @package _global_
-hydra:
-  sweeper:
-    params:
-#      ckpt_path: "'C:/Users/libok/Documents/GitHub/DeepScreen/logs/train/runs/2023-11-07_23-21-55-442205_[debug]/checkpoints/epoch_000.ckpt','C:/Users/libok/Documents/GitHub/DeepScreen/logs/train/runs/2023-11-07_19-46-08-740035_[debug]/checkpoints/epoch_000.ckpt'"
-      data.data_file: dti_benchmark/random_split_update/bindingdb_reserved_test.csv
-#      ckpt_path: "'/gpfs/work/pha/daiyunhuang/WavyWaffle/logs/train/multiruns/2023-10-16_14-53-13-645337_[benchmark,ddta,gdta]/metrics_summary.csv'"
-#      ckpt_path: "/gpfs/work/pha/daiyunhuang/WavyWaffle/configs/sweep/experiment_summary_bindingdb.csv"
diff --git a/configs/sweep/slurm_test.yaml b/configs/sweep/slurm_test.yaml
deleted file mode 100644
index 530ab519eed0ffe86445f2960c667e4484097459..0000000000000000000000000000000000000000
--- a/configs/sweep/slurm_test.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-# @package _global_
-tags: ['sweep', 'benchmark']
-hydra:
-  sweeper:
-    params:
-      preset: graph_dta,deep_dta,drug_vqa, mol_trans,hyper_attention_dti,transformer_cpi_2
-      experiment: kiba,davis,bindingdb
-
diff --git a/configs/task/binary.yaml b/configs/task/binary.yaml
deleted file mode 100644
index 31eafe56289ebcb591ddd4254a943015c0d3e429..0000000000000000000000000000000000000000
--- a/configs/task/binary.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-task: binary
-num_classes: null
-
-out:
-  _target_: torch.nn.LazyLinear
-  out_features: 1
-
-loss:
-  _target_: torch.nn.BCEWithLogitsLoss
-
-activation:
-  _target_: torch.nn.Sigmoid
\ No newline at end of file
diff --git a/configs/task/multiclass.yaml b/configs/task/multiclass.yaml
deleted file mode 100644
index 686e9f9b96c98839ec4bdad32351d29aca026618..0000000000000000000000000000000000000000
--- a/configs/task/multiclass.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-task: multiclass
-num_classes: 3
-
-out:
-  _target_: torch.nn.LazyLinear
-  out_features: ${num_classes}
-
-loss:
-  _target_: torch.nn.CrossEntropyLoss
-
-activation:
-  _target_: torch.nn.Softmax
\ No newline at end of file
diff --git a/configs/task/regression.yaml b/configs/task/regression.yaml
deleted file mode 100644
index 0de6eeb0179fcf63608df8a62719a5f6792baf1d..0000000000000000000000000000000000000000
--- a/configs/task/regression.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-task: regression
-num_classes: null
-
-out:
-  _target_: torch.nn.LazyLinear
-  out_features: 1
-
-loss:
-  _target_: torch.nn.MSELoss
-
-activation:
-  _target_: torch.nn.Identity
\ No newline at end of file
diff --git a/configs/test.yaml b/configs/test.yaml
deleted file mode 100644
index cc96bf8ed23b5f342b1bd2e49d39a31e401a5db4..0000000000000000000000000000000000000000
--- a/configs/test.yaml
+++ /dev/null
@@ -1,33 +0,0 @@
-# @package _global_
-defaults:
-  - model: dti_model # fixed for web server version
-  - task: null
-  - data: dti_data # fixed for web server version
-  - callbacks:
-      - model_summary
-      - rich_progress_bar
-  - logger: csv
-  - trainer: default
-  - paths: default
-  - extras: default
-  - hydra: default
-#  - hydra/callbacks:
-#      - csv_metrics_summary
-  - _self_
-  - preset: null
-  - experiment: null
-  - sweep: null
-  - debug: null
-  - optional local: default
-
-
-job_name: "test"
-
-tags: ???
-
-# passing checkpoint path is necessary for evaluation
-ckpt_path: ???
-
-model:
-  optimizer: null
-  scheduler: null
\ No newline at end of file
diff --git a/configs/train.yaml b/configs/train.yaml
deleted file mode 100644
index 8ccc566f93ae5ce7d80ebe65e215b6df3877c533..0000000000000000000000000000000000000000
--- a/configs/train.yaml
+++ /dev/null
@@ -1,53 +0,0 @@
-# @package _global_
-
-# specify here default configuration
-# order of defaults determines the order in which configs override each other
-defaults:
-  - model: dti_model # fixed for web server version
-  - task: null
-  - data: dti_data # fixed for web server version
-  - callbacks: default
-  - logger: multiple_loggers # set logger here or use command line (e.g. `python train.py logger=tensorboard`)
-  - trainer: default
-  - paths: default
-  - extras: default
-  - hydra: default
-
-  - _self_
-
-  - preset: null
-  # Experiment configs allow for version control of specific hyperparameters
-  # e.g. the best hyperparameters for given model and data
-  - experiment: null
-  # Sweeping config, for batch experiments, hyperparameter optimization, etc.
-  - sweep: null
-  # Debugging config (enable through command line, e.g. `python train.py debug=default)
-  - debug: null
-
-  - optional local: default
-
-# job name, determines output directory path
-job_name: "train"
-
-# tags to help you identify your experiments
-# you can overwrite this in experiment configs
-# overwrite from command line with `python train.py tags="[first_tag, second_tag]"`
-tags: ???
-
-# evaluate on test set, using best model weights achieved during training
-# lightning chooses best weights based on the metric specified in checkpoint callback
-# test: True
-
-# compile model for faster training with PyTorch 2.0+
-compile: False
-
-# simply provide checkpoint path to resume training
-ckpt_path: null
-
-# seed for random number generators in torch, numpy and python.random
-seed: 12345
-
-trainer:
-  check_val_every_n_epoch: 1
-  limit_val_batches: ${eval:'1.0 if ${data.train_val_test_split}[1] else 0'}
-  num_sanity_val_steps: ${eval:'2 if ${data.train_val_test_split}[1] else 0'}
diff --git a/configs/trainer/cpu.yaml b/configs/trainer/cpu.yaml
deleted file mode 100644
index b7d6767e60c956567555980654f15e7bb673a41f..0000000000000000000000000000000000000000
--- a/configs/trainer/cpu.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-defaults:
-  - default
-
-accelerator: cpu
-devices: 1
diff --git a/configs/trainer/ddp.yaml b/configs/trainer/ddp.yaml
deleted file mode 100644
index 3c9778447171ba5f5282e1087aa61be2b4763622..0000000000000000000000000000000000000000
--- a/configs/trainer/ddp.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-defaults:
-  - default
-
-strategy: ddp
-
-accelerator: gpu
-devices: 4
-num_nodes: 1
-sync_batchnorm: True
-precision: 16-mixed
diff --git a/configs/trainer/ddp_sim.yaml b/configs/trainer/ddp_sim.yaml
deleted file mode 100644
index 8404419e5c295654967d0dfb73a7366e75be2f1f..0000000000000000000000000000000000000000
--- a/configs/trainer/ddp_sim.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-defaults:
-  - default
-
-# simulate DDP on CPU, useful for debugging
-accelerator: cpu
-devices: 2
-strategy: ddp_spawn
diff --git a/configs/trainer/default.yaml b/configs/trainer/default.yaml
deleted file mode 100644
index 5a00b4536dec28a739772e2cc798ab46b2dc2824..0000000000000000000000000000000000000000
--- a/configs/trainer/default.yaml
+++ /dev/null
@@ -1,18 +0,0 @@
-_target_: lightning.Trainer
-
-default_root_dir: ${paths.output_dir}
-
-min_epochs: 1
-max_epochs: 50
-
-precision: 32
-
-gradient_clip_val: 0.5
-gradient_clip_algorithm: norm
-
-# deterministic algorithms might make training slower but offers more reproducibility than only setting seeds
-# True: use deterministic always, throwing an error on an operation that doesn't support deterministic
-# warn: use deterministic when possible, throwing warnings on operations that don’t support deterministic
-deterministic: warn
-
-inference_mode: True
\ No newline at end of file
diff --git a/configs/trainer/gpu.yaml b/configs/trainer/gpu.yaml
deleted file mode 100644
index f9dc7f73609b2b2fe595d84288a3b556d8d3356c..0000000000000000000000000000000000000000
--- a/configs/trainer/gpu.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-defaults:
-  - default
-
-accelerator: gpu
-devices: 1
-precision: 16-mixed
\ No newline at end of file
diff --git a/configs/trainer/mps.yaml b/configs/trainer/mps.yaml
deleted file mode 100644
index 1ecf6d5cc3a34ca127c5510f4a18e989561e38e4..0000000000000000000000000000000000000000
--- a/configs/trainer/mps.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-defaults:
-  - default
-
-accelerator: mps
-devices: 1
diff --git a/configs/webserver_inference.yaml b/configs/webserver_inference.yaml
deleted file mode 100644
index 194b8b81dff65bdbfe260c106e09bd7d5eaa0e42..0000000000000000000000000000000000000000
--- a/configs/webserver_inference.yaml
+++ /dev/null
@@ -1,27 +0,0 @@
-# @package _global_
-defaults:
-  - model: dti_model # fixed for web server version
-  - task: null
-  - data: dti_data # fixed for web server version
-  - callbacks: null
-  - trainer: default
-  - paths: default
-  - extras: null
-  - hydra: null
-  - _self_
-  - preset: null
-  - experiment: null
-  - sweep: null
-  - debug: null
-  - optional local: default
-
-job_name: "webserver_inference"
-
-tags: null
-
-# passing checkpoint path is necessary for prediction
-ckpt_path: ???
-
-paths:
-  output_dir: null
-  work_dir: null
\ No newline at end of file