diff --git a/configs/callbacks/csv_prediction_writer.yaml b/configs/callbacks/csv_prediction_writer.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..b7fc6fb93940f0910938553caec31c02a3aeb60b
--- /dev/null
+++ b/configs/callbacks/csv_prediction_writer.yaml
@@ -0,0 +1,4 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..f94c639e898f22416a21af826e6453b99fbf01f1
--- /dev/null
+++ b/configs/callbacks/default.yaml
@@ -0,0 +1,5 @@
+defaults:
+  - model_checkpoint
+  - early_stopping
+  - model_summary
+  - rich_progress_bar
diff --git a/configs/callbacks/early_stopping.yaml b/configs/callbacks/early_stopping.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..1d2bb37ad3f056b1fb6cff81f162f7222a3c5a3e
--- /dev/null
+++ b/configs/callbacks/early_stopping.yaml
@@ -0,0 +1,17 @@
+# 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
new file mode 100644
index 0000000000000000000000000000000000000000..22fe5db38092387f72718e3046e86f57663e8c00
--- /dev/null
+++ b/configs/callbacks/inference.yaml
@@ -0,0 +1,6 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..f8e51b2bb6036ce4a0b1ce3dc47c2869514b2eeb
--- /dev/null
+++ b/configs/callbacks/model_checkpoint.yaml
@@ -0,0 +1,19 @@
+# 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
new file mode 100644
index 0000000000000000000000000000000000000000..f854fd9fd17863a8c5930f482dc0d235cfc03698
--- /dev/null
+++ b/configs/callbacks/model_summary.yaml
@@ -0,0 +1,7 @@
+# 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/callbacks/rich_progress_bar.yaml b/configs/callbacks/rich_progress_bar.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..82d2f89d28be7511f2360e1b047656afeee16141
--- /dev/null
+++ b/configs/callbacks/rich_progress_bar.yaml
@@ -0,0 +1,6 @@
+# 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/callbacks/tqdm_progress_bar.yaml b/configs/callbacks/tqdm_progress_bar.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..4f8653fcde6f4c1762dc82dbec824cd19ab097cf
--- /dev/null
+++ b/configs/callbacks/tqdm_progress_bar.yaml
@@ -0,0 +1,2 @@
+tqdm_progress_bar:
+  _target_: lightning.pytorch.callbacks.TQDMProgressBar
diff --git a/configs/data/collator/default.yaml b/configs/data/collator/default.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..514c0837c358aeb82d22ec2c34a7226d05580423
--- /dev/null
+++ b/configs/data/collator/default.yaml
@@ -0,0 +1,5 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..29899b9fc6b0164c149e17b31e350be9135add49
--- /dev/null
+++ b/configs/data/collator/none.yaml
@@ -0,0 +1,2 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..a341607f3f242e6f993bf758e7341b376f8b4ef3
--- /dev/null
+++ b/configs/data/drug_featurizer/ecfp.yaml
@@ -0,0 +1,6 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..77a0cdbec7168829ce846fa28543707a000d0c0d
--- /dev/null
+++ b/configs/data/drug_featurizer/fcs.yaml
@@ -0,0 +1,4 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..d3d65a1fbec937c9484584d8f9f89bbc999539f9
--- /dev/null
+++ b/configs/data/drug_featurizer/graph.yaml
@@ -0,0 +1,2 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..80ffe2fbdf7038953a8d94e4fa9def36196d66bb
--- /dev/null
+++ b/configs/data/drug_featurizer/label.yaml
@@ -0,0 +1,15 @@
+#_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
new file mode 100644
index 0000000000000000000000000000000000000000..b0652eace74a5041d7bfa166152e347b9f009c64
--- /dev/null
+++ b/configs/data/drug_featurizer/mol_features.yaml
@@ -0,0 +1,4 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..29899b9fc6b0164c149e17b31e350be9135add49
--- /dev/null
+++ b/configs/data/drug_featurizer/none.yaml
@@ -0,0 +1,2 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..827114b5c04984b2bbd78697dda712a109db3514
--- /dev/null
+++ b/configs/data/drug_featurizer/onehot.yaml
@@ -0,0 +1,15 @@
+#_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
new file mode 100644
index 0000000000000000000000000000000000000000..369aa42da9f2a5f3990dff0097afd0fe8cf5da55
--- /dev/null
+++ b/configs/data/drug_featurizer/tokenizer.yaml
@@ -0,0 +1,6 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..93682ed7b88a14ac5e7afecb4327aa50d51d29b8
--- /dev/null
+++ b/configs/data/dti.yaml.bak
@@ -0,0 +1,21 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..5b65659c15f8fac1a229e16586ffb226293b4f14
--- /dev/null
+++ b/configs/data/dti_data.yaml
@@ -0,0 +1,20 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..cbf1f380d2bd951a321971676cb20f7de5e17e7c
--- /dev/null
+++ b/configs/data/protein_featurizer/fcs.yaml
@@ -0,0 +1,4 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..1824297352e8d0706126486f1a00585e78c4f892
--- /dev/null
+++ b/configs/data/protein_featurizer/label.yaml
@@ -0,0 +1,12 @@
+#_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
new file mode 100644
index 0000000000000000000000000000000000000000..29899b9fc6b0164c149e17b31e350be9135add49
--- /dev/null
+++ b/configs/data/protein_featurizer/none.yaml
@@ -0,0 +1,2 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..d44e8a5fcc0ac0cfd47e17fda8f302e73bcc359d
--- /dev/null
+++ b/configs/data/protein_featurizer/onehot.yaml
@@ -0,0 +1,12 @@
+#_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
new file mode 100644
index 0000000000000000000000000000000000000000..9e264020782f84719e5370dd3cfc10f44a7a236c
--- /dev/null
+++ b/configs/data/protein_featurizer/tokenizer.yaml
@@ -0,0 +1,6 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..0d9f4761a374a05ce0f5b20cd80073632f0c030f
--- /dev/null
+++ b/configs/data/protein_featurizer/word2vec.yaml
@@ -0,0 +1,6 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..3c0416a876682bb9759822d493e70a21ac0f28f6
--- /dev/null
+++ b/configs/data/split/cold_drug.yaml
@@ -0,0 +1,4 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..7a3694841cc5cb00549d3563791a872781d0d775
--- /dev/null
+++ b/configs/data/split/cold_protein.yaml
@@ -0,0 +1,4 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/data/split/random.yaml b/configs/data/split/random.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..e8c00c9b5b38f57fda3b03185a1e91dbefedff8c
--- /dev/null
+++ b/configs/data/split/random.yaml
@@ -0,0 +1,10 @@
+#_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
new file mode 100644
index 0000000000000000000000000000000000000000..3c4e68561d5768d6b1677900484c386ce3b8df7c
--- /dev/null
+++ b/configs/data/transform/minmax.yaml
@@ -0,0 +1,5 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..29899b9fc6b0164c149e17b31e350be9135add49
--- /dev/null
+++ b/configs/data/transform/none.yaml
@@ -0,0 +1,2 @@
+_target_: deepscreen.utils.passthrough
+_partial_: true
\ No newline at end of file
diff --git a/configs/debug/advanced.yaml b/configs/debug/advanced.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..2c249cc45699de1d1d8f25aa7c873b127e3df6f9
--- /dev/null
+++ b/configs/debug/advanced.yaml
@@ -0,0 +1,25 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..84e7dc1e80b355c8ab075a28e65d8fae08127eea
--- /dev/null
+++ b/configs/debug/default.yaml
@@ -0,0 +1,35 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..111e2f35924bf77db6706867a5a381cb90e2e855
--- /dev/null
+++ b/configs/debug/fdr.yaml
@@ -0,0 +1,11 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..570718adfc2148760067ac799cdc3f4ae38f6c78
--- /dev/null
+++ b/configs/debug/fdr_advanced.yaml
@@ -0,0 +1,11 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..514d77fbd1475b03fff0372e3da3c2fa7ea7d190
--- /dev/null
+++ b/configs/debug/limit.yaml
@@ -0,0 +1,12 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..9906586a67a12aa81ff69138f589a366dbe2222f
--- /dev/null
+++ b/configs/debug/overfit.yaml
@@ -0,0 +1,13 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..2bd7da87ae23ed425ace99b09250a76a5634a3fb
--- /dev/null
+++ b/configs/debug/profiler.yaml
@@ -0,0 +1,12 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..e3e170d30a9bbdd3d0252b43979b2861aeb39ce1
--- /dev/null
+++ b/configs/experiment/bindingdb.yaml
@@ -0,0 +1,9 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..01b9e8aca42b0925a22303d9f2c3f8c4f5998340
--- /dev/null
+++ b/configs/experiment/chembl_random.yaml
@@ -0,0 +1,9 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..a15e8ebfac7db334dc82d22adae2181c1473d9c8
--- /dev/null
+++ b/configs/experiment/chembl_rmfh_random.yaml
@@ -0,0 +1,9 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..95c628e21ba17d808363a8f89f36ad0513e6a1de
--- /dev/null
+++ b/configs/experiment/davis.yaml
@@ -0,0 +1,9 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..0ccc1bcdfd5a12025a0ff6aa591a6989f3db2982
--- /dev/null
+++ b/configs/experiment/demo_bindingdb.yaml
@@ -0,0 +1,9 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..df70106572153a3444128f46023e58cdb6001a04
--- /dev/null
+++ b/configs/experiment/dti_experiment.yaml
@@ -0,0 +1,19 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..03babeb44c0eec70b050e1f92534b6cd8de770d8
--- /dev/null
+++ b/configs/experiment/example.yaml
@@ -0,0 +1,35 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..261d7dac49ccb908a63719c01fd04374e4d21019
--- /dev/null
+++ b/configs/experiment/ion_channels.yaml
@@ -0,0 +1,9 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..f3a83942f41b75c800bf467690b88b8397955615
--- /dev/null
+++ b/configs/experiment/kiba.yaml
@@ -0,0 +1,9 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..c7d129aca1c9d93934efbe61a243cf7603d30143
--- /dev/null
+++ b/configs/experiment/kinase.yaml
@@ -0,0 +1,13 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..a06d357351dba800c885d7d92e51a7a7ccffc474
--- /dev/null
+++ b/configs/experiment/membrane_receptors.yaml
@@ -0,0 +1,13 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..314eeb66a368dfcab29313a647e620ee5bcd7cd9
--- /dev/null
+++ b/configs/experiment/non_kinase_enzymes.yaml
@@ -0,0 +1,13 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..2edf8a4dea610a9a7c2a9b73178f452888bb20c2
--- /dev/null
+++ b/configs/experiment/nuclear_receptors.yaml
@@ -0,0 +1,9 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..ffe3f295621ee3ffc160521e88e2bdf547719190
--- /dev/null
+++ b/configs/experiment/other_protein_targets.yaml
@@ -0,0 +1,9 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..b9c6b622283a647fbc513166fc14f016cc3ed8a0
--- /dev/null
+++ b/configs/extras/default.yaml
@@ -0,0 +1,8 @@
+# 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
new file mode 100644
index 0000000000000000000000000000000000000000..1b0d00b4f7c73dfdc02846e428fc6793133cc549
--- /dev/null
+++ b/configs/hydra/callbacks/csv_experiment_summary.yaml
@@ -0,0 +1,3 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..3e7617d233fb7f325cdd03caf82bcc0e2ba6bf6d
--- /dev/null
+++ b/configs/hydra/callbacks/default.yaml
@@ -0,0 +1,2 @@
+defaults:
+  - csv_experiment_summary
diff --git a/configs/hydra/default.yaml b/configs/hydra/default.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..8d76171f4585f3c26e6c249ba9d4e1617994b421
--- /dev/null
+++ b/configs/hydra/default.yaml
@@ -0,0 +1,27 @@
+# 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
new file mode 100644
index 0000000000000000000000000000000000000000..2f47752804b52ea1216d750ac3229d12e463aaff
--- /dev/null
+++ b/configs/hydra/launcher/submitit_local_example.yaml
@@ -0,0 +1,12 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..1dec61801ed47679ea6598ef2540965e110249c4
--- /dev/null
+++ b/configs/hydra/launcher/submitit_slurm_example.yaml
@@ -0,0 +1,31 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..316cf24ab252557a08a5e82fa8c9c462b9835246
--- /dev/null
+++ b/configs/hydra/sweeper/optuna_hps.yaml
@@ -0,0 +1,44 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/local/slurm_example.yaml b/configs/local/slurm_example.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..5600310d09dc747aaba7616f3402c6de096ce918
--- /dev/null
+++ b/configs/local/slurm_example.yaml
@@ -0,0 +1,21 @@
+# @package _global_
+defaults:
+  - override /hydra/launcher: submitit_slurm
+
+hydra:
+  launcher:
+    submitit_folder: ${hydra.sweep.dir}/.submitit
+    name: "${hydra.job.name} ${eval:\"' '.join(${hydra.overrides.task}\")}"
+    timeout_min: 6000
+    cpus_per_task: 4
+    gpus_per_task: 1
+    gres: gpu:1
+    partition: gpu3090
+    qos: gpu3090
+    additional_parameters:
+      error: ${hydra.launcher.submitit_folder}/%j_%t.log
+      output: ${hydra.launcher.submitit_folder}/%j_%t.log
+    array_parallelism: 256
+
+trainer:
+  precision: bf16
diff --git a/configs/logger/comet.yaml b/configs/logger/comet.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..ebe6c6f19bd172255e9f29148df10a4d2ec42c84
--- /dev/null
+++ b/configs/logger/comet.yaml
@@ -0,0 +1,12 @@
+# 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
new file mode 100644
index 0000000000000000000000000000000000000000..bf9af6fb5e70b1382a1421397b12ea677dd8926f
--- /dev/null
+++ b/configs/logger/csv.yaml
@@ -0,0 +1,8 @@
+# csv logger built in lightning
+
+csv:
+  _target_: lightning.pytorch.loggers.csv_logs.CSVLogger
+  save_dir: "${paths.output_dir}"
+  name: "csv/"
+  prefix: ""
+  version: ""
diff --git a/configs/logger/default.yaml b/configs/logger/default.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..bfdb2248689fcc8c5827c6c99c0d42bfad37b3c8
--- /dev/null
+++ b/configs/logger/default.yaml
@@ -0,0 +1,5 @@
+defaults:
+  - csv
+#  - mlflow
+#  - wandb
+#  - comet
\ No newline at end of file
diff --git a/configs/logger/mlflow.yaml b/configs/logger/mlflow.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..bed42abc9cd686d89137e236a009c2c9277f2608
--- /dev/null
+++ b/configs/logger/mlflow.yaml
@@ -0,0 +1,12 @@
+# https://mlflow.org
+
+mlflow:
+  _target_: lightning.pytorch.loggers.mlflow.MLFlowLogger
+  # experiment_name: ""
+  # run_name: ""
+  tracking_uri: "file://${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
new file mode 100644
index 0000000000000000000000000000000000000000..40d561d1b723cb314de4272210a96c4343dcace9
--- /dev/null
+++ b/configs/logger/multiple_loggers.yaml
@@ -0,0 +1,6 @@
+# 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
new file mode 100644
index 0000000000000000000000000000000000000000..086e85fc59117f4a8035d0c1773e4c856fd7e995
--- /dev/null
+++ b/configs/logger/neptune.yaml
@@ -0,0 +1,9 @@
+# https://neptune.ai
+
+neptune:
+  _target_: lightning.pytorch.loggers.neptune.NeptuneLogger
+  api_key: ${oc.env:NEPTUNE_API_TOKEN} # api key is loaded from environment variable
+  project: username/deepscreen
+  # name: ""
+  log_model_checkpoints: True
+  prefix: ""
\ No newline at end of file
diff --git a/configs/logger/tensorboard.yaml b/configs/logger/tensorboard.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..f438664df015f88bd3cabffaa520da3ef98dc379
--- /dev/null
+++ b/configs/logger/tensorboard.yaml
@@ -0,0 +1,10 @@
+# https://www.tensorflow.org/tensorboard/
+
+tensorboard:
+  _target_: lightning.pytorch.loggers.tensorboard.TensorBoardLogger
+  save_dir: "${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
new file mode 100644
index 0000000000000000000000000000000000000000..9ec9ba26d7673c20005d8e67e3bed2b647c80218
--- /dev/null
+++ b/configs/logger/wandb.yaml
@@ -0,0 +1,16 @@
+# 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
new file mode 100644
index 0000000000000000000000000000000000000000..72b1c9ee2b75a2f6ffce9a33b8d42cafd9cc67f0
--- /dev/null
+++ b/configs/model/dti_model.yaml
@@ -0,0 +1,12 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..6dfe6353808f3f91a42e151a34a3cae056e0fc7e
--- /dev/null
+++ b/configs/model/loss/multitask_loss.yaml
@@ -0,0 +1,7 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..80a9d3f8a6837571b70d0cfb70ba7c6f59ee1c3e
--- /dev/null
+++ b/configs/model/metrics/accuracy.yaml
@@ -0,0 +1,4 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..b9de03c65fdeec91e8b39f38dd773d9956e2e8ce
--- /dev/null
+++ b/configs/model/metrics/auprc.yaml
@@ -0,0 +1,4 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..a4bcdbbd885ae5ba05120e5568ca7d3a323f213f
--- /dev/null
+++ b/configs/model/metrics/auroc.yaml
@@ -0,0 +1,4 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..86c68585882faefde5ee711dfe647d406a06dd09
--- /dev/null
+++ b/configs/model/metrics/bedroc.yaml
@@ -0,0 +1,3 @@
+bedroc:
+  _target_: deepscreen.models.metrics.bedroc.BEDROC
+  alpha: 80.5
\ No newline at end of file
diff --git a/configs/model/metrics/ci.yaml b/configs/model/metrics/ci.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..634ea1906b5d0307e2e0342beec04c28e66af308
--- /dev/null
+++ b/configs/model/metrics/ci.yaml
@@ -0,0 +1,2 @@
+# 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
new file mode 100644
index 0000000000000000000000000000000000000000..d0be32b6b92a93e743d3926bf19fc3849c2e9260
--- /dev/null
+++ b/configs/model/metrics/confusion_matrix.yaml
@@ -0,0 +1 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..2b0f108cb9df18dfcceae6af9fd94789685a54b2
--- /dev/null
+++ b/configs/model/metrics/dta_metrics.yaml
@@ -0,0 +1,2 @@
+defaults:
+  - mean_squared_error
diff --git a/configs/model/metrics/dti_metrics.yaml b/configs/model/metrics/dti_metrics.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..93ca0c40a0d77ffb095ab91d52863667bf5746cc
--- /dev/null
+++ b/configs/model/metrics/dti_metrics.yaml
@@ -0,0 +1,14 @@
+# 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
new file mode 100644
index 0000000000000000000000000000000000000000..82553b414da98c55508db9830d82b12af3db786d
--- /dev/null
+++ b/configs/model/metrics/ef.yaml
@@ -0,0 +1,7 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..abfb6e4ca37a9dad399aeb3b1244d958d542e238
--- /dev/null
+++ b/configs/model/metrics/f1_score.yaml
@@ -0,0 +1,4 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..70976774eb365fdf8b8c1f97bd3ad19d6cb64cb8
--- /dev/null
+++ b/configs/model/metrics/hit_rate.yaml
@@ -0,0 +1,3 @@
+hit_rate:
+  _target_: deepscreen.models.metrics.hit_rate.HitRate
+  alpha: 0.05
diff --git a/configs/model/metrics/mse.yaml b/configs/model/metrics/mse.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..0d9a18c60d43210b16878ff479b1cfa3168788cf
--- /dev/null
+++ b/configs/model/metrics/mse.yaml
@@ -0,0 +1,2 @@
+mean_squared_error:
+  _target_: torchmetrics.MeanSquaredError
\ No newline at end of file
diff --git a/configs/model/metrics/pearson.yaml b/configs/model/metrics/pearson.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..918df0507b60ab7ce79635a3c9f5d4c210e0ff88
--- /dev/null
+++ b/configs/model/metrics/pearson.yaml
@@ -0,0 +1,2 @@
+Pearson:
+  _target_: torchmetrics.PearsonCorrCoef
\ No newline at end of file
diff --git a/configs/model/metrics/prc.yaml b/configs/model/metrics/prc.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..75e3ee320d5b9a32a9acdb55d564fbacab975088
--- /dev/null
+++ b/configs/model/metrics/prc.yaml
@@ -0,0 +1,4 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..4b8212b1999c10b627de5859e034260a39022608
--- /dev/null
+++ b/configs/model/metrics/precision.yaml
@@ -0,0 +1,4 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..eadad752ad1c4e1ac137580a289d4d32916ca975
--- /dev/null
+++ b/configs/model/metrics/recall.yaml
@@ -0,0 +1,4 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..91968a6f42e3d399f39e587785eaddabda523a23
--- /dev/null
+++ b/configs/model/metrics/roc.yaml
@@ -0,0 +1,4 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..49568b4512c2b75ebfce98d8ee03e2b1148966cc
--- /dev/null
+++ b/configs/model/metrics/sensitivity.yaml
@@ -0,0 +1,4 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..5b161be947876081ce9b6b070ed7201874f5cbc6
--- /dev/null
+++ b/configs/model/metrics/specificity.yaml
@@ -0,0 +1,4 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..2ff2b80870d15e9863158e6dfbd17cf3dd9586c2
--- /dev/null
+++ b/configs/model/metrics/test_metrics.yaml
@@ -0,0 +1,11 @@
+# train with many loggers at once
+
+defaults:
+  - auroc
+  - auprc
+  - roc
+  - prc
+# Common virtual screening metrics:
+#  - ef
+#  - bedroc
+#  - hit_rate
diff --git a/configs/model/metrics/ww_dti_metrics.yaml b/configs/model/metrics/ww_dti_metrics.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..c2685e108dfa2476c8eb67ef7f41d41dd9910390
--- /dev/null
+++ b/configs/model/metrics/ww_dti_metrics.yaml
@@ -0,0 +1,193 @@
+defaults:
+  - auroc
+  - auprc
+
+Accuracy0_5:
+  _target_: torchmetrics.Accuracy
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.5
+
+Accuracy0_8:
+  _target_: torchmetrics.Accuracy
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.8
+
+Accuracy0_85:
+  _target_: torchmetrics.Accuracy
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.85
+
+Accuracy0_9:
+  _target_: torchmetrics.Accuracy
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.9
+
+Accuracy0_95:
+  _target_: torchmetrics.Accuracy
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.95
+
+
+
+Sensitivity0_5:
+  _target_: deepscreen.models.metrics.sensitivity.Sensitivity
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.5
+
+Sensitivity0_8:
+  _target_: deepscreen.models.metrics.sensitivity.Sensitivity
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.8
+
+Sensitivity0_85:
+  _target_: deepscreen.models.metrics.sensitivity.Sensitivity
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.85
+
+Sensitivity0_9:
+  _target_: deepscreen.models.metrics.sensitivity.Sensitivity
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.9
+
+Sensitivity0_95:
+  _target_: deepscreen.models.metrics.sensitivity.Sensitivity
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.95
+
+
+
+Specificity0_5:
+  _target_: torchmetrics.Specificity
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.5
+
+Specificity0_8:
+  _target_: torchmetrics.Specificity
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.8
+
+Specificity0_85:
+  _target_: torchmetrics.Specificity
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.85
+
+Specificity0_9:
+  _target_: torchmetrics.Specificity
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.9
+
+Specificity0_95:
+  _target_: torchmetrics.Specificity
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.95
+  
+
+
+Precision0_5:
+  _target_: torchmetrics.Precision
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.5
+
+Precision0_8:
+  _target_: torchmetrics.Precision
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.8
+
+Precision0_85:
+  _target_: torchmetrics.Precision
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.85
+
+Precision0_9:
+  _target_: torchmetrics.Precision
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.9
+
+Precision0_95:
+  _target_: torchmetrics.Precision
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.95
+  
+  
+
+Recall0_5:
+  _target_: torchmetrics.Recall
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.5
+
+Recall0_8:
+  _target_: torchmetrics.Recall
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.8
+
+Recall0_85:
+  _target_: torchmetrics.Recall
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.85
+
+Recall0_9:
+  _target_: torchmetrics.Recall
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.9
+
+Recall0_95:
+  _target_: torchmetrics.Recall
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.95
+  
+
+
+F1Score0_5:
+  _target_: torchmetrics.F1Score
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.5
+
+F1Score0_8:
+  _target_: torchmetrics.F1Score
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.8
+
+F1Score0_85:
+  _target_: torchmetrics.F1Score
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.85
+
+F1Score0_9:
+  _target_: torchmetrics.F1Score
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.9
+
+F1Score0_95:
+  _target_: torchmetrics.F1Score
+  task: ${task.task}
+  num_classes: ${task.num_classes}
+  threshold: 0.95
\ No newline at end of file
diff --git a/configs/model/optimizer/adam.yaml b/configs/model/optimizer/adam.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..67ab7f2cfeeb16daef186434fd4655afab56bf37
--- /dev/null
+++ b/configs/model/optimizer/adam.yaml
@@ -0,0 +1,5 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/model/predictor/custom.yaml b/configs/model/predictor/custom.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..d7a867b87888c03a7209b4b78bbdf2dadfff07a2
--- /dev/null
+++ b/configs/model/predictor/custom.yaml
@@ -0,0 +1,6 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..17b92c9493a45d51b3463dc069a73295fc22eb4f
--- /dev/null
+++ b/configs/model/predictor/decoder/concat_mlp.yaml
@@ -0,0 +1,6 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..b6ee28076224a373a6879ece9296491dccfd280c
--- /dev/null
+++ b/configs/model/predictor/decoder/mlp_deepdta.yaml
@@ -0,0 +1,6 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..832863817e37fed6e5ef54eba4de99341310c4dc
--- /dev/null
+++ b/configs/model/predictor/decoder/mlp_lazy.yaml
@@ -0,0 +1,5 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..7f6cfc42a5e850554e0825d803f79575abdcdb1b
--- /dev/null
+++ b/configs/model/predictor/deep_dta.yaml
@@ -0,0 +1,15 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..453ef99dec6c2a5db821181e72eef24c9faab966
--- /dev/null
+++ b/configs/model/predictor/drug_encoder/cnn.yaml
@@ -0,0 +1,9 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..97bf3a4870e224b2bc7a5eab946d38b57c279d26
--- /dev/null
+++ b/configs/model/predictor/drug_encoder/cnn_deepdta.yaml
@@ -0,0 +1,7 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..3b8dddd5ab5fac2b3cefff8191c01d3ab393c8a5
--- /dev/null
+++ b/configs/model/predictor/drug_encoder/gat.yaml
@@ -0,0 +1,5 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..5e2da337b324610297bd76b6783340d03bd681a8
--- /dev/null
+++ b/configs/model/predictor/drug_encoder/gcn.yaml
@@ -0,0 +1,5 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..caf5820c158ff7956b2440d25f7b5f901936f683
--- /dev/null
+++ b/configs/model/predictor/drug_encoder/gin.yaml
@@ -0,0 +1,5 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/model/predictor/drug_encoder/transformer.yaml b/configs/model/predictor/drug_encoder/transformer.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..5eee1571675bcb2d2d539dbaa69ea0268c7b3908
--- /dev/null
+++ b/configs/model/predictor/drug_encoder/transformer.yaml
@@ -0,0 +1,11 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..8ee31b6b3e5a62bec7998d3bdb4c4619ecd27e7f
--- /dev/null
+++ b/configs/model/predictor/drug_vqa.yaml
@@ -0,0 +1,15 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..35bfdf8adc5ab69b780e81c828a195e48e8ec1a0
--- /dev/null
+++ b/configs/model/predictor/graph_dta.yaml
@@ -0,0 +1,16 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..87dde659688073d247953fce5ceef65a38786789
--- /dev/null
+++ b/configs/model/predictor/hyper_attention_dti.yaml
@@ -0,0 +1,8 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/model/predictor/protein_encoder/cnn.yaml b/configs/model/predictor/protein_encoder/cnn.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..9363e5e6130a5292d173b90eba8430c12edef3d1
--- /dev/null
+++ b/configs/model/predictor/protein_encoder/cnn.yaml
@@ -0,0 +1,7 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..8ac5f6d9064695cdfe2739946c1e55d55aa588d5
--- /dev/null
+++ b/configs/model/predictor/protein_encoder/cnn_deepdta.yaml
@@ -0,0 +1,7 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/model/predictor/protein_encoder/tape_bert.yaml b/configs/model/predictor/protein_encoder/tape_bert.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..6a64b46c70850a5d796a19615ba553e69cb26a39
--- /dev/null
+++ b/configs/model/predictor/protein_encoder/tape_bert.yaml
@@ -0,0 +1,3 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..4fb7c9761bc098da84773f56bc949ce7c7d34c5f
--- /dev/null
+++ b/configs/model/predictor/protein_encoder/transformer.yaml
@@ -0,0 +1,12 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..c7d137ba108186e77e67878c4ad6ba40dbad52d3
--- /dev/null
+++ b/configs/model/predictor/transformer_cpi.yaml
@@ -0,0 +1,10 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..2f9439a99c02720650635f2024acb36ef45b18fa
--- /dev/null
+++ b/configs/model/predictor/transformer_cpi_2.yaml
@@ -0,0 +1,14 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..a319ea4099d233cec67de9477bbce25744368a91
--- /dev/null
+++ b/configs/model/scheduler/default.yaml
@@ -0,0 +1,11 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/model/scheduler/reduce_lr_on_plateau.yaml b/configs/model/scheduler/reduce_lr_on_plateau.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..221efd82d131473c6a51da966d153bb2ec85b69c
--- /dev/null
+++ b/configs/model/scheduler/reduce_lr_on_plateau.yaml
@@ -0,0 +1,6 @@
+_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
new file mode 100644
index 0000000000000000000000000000000000000000..862261ca7797da591715936cfd88a047c1722da3
--- /dev/null
+++ b/configs/paths/default.yaml
@@ -0,0 +1,19 @@
+# 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/preset/bacpi.yaml.bak b/configs/preset/bacpi.yaml.bak
new file mode 100644
index 0000000000000000000000000000000000000000..9dbea130fd0f6b6fe07f009c340f33f6f8f6c558
--- /dev/null
+++ b/configs/preset/bacpi.yaml.bak
@@ -0,0 +1,37 @@
+# @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.bak b/configs/preset/coa_dti_pro.yaml.bak
new file mode 100644
index 0000000000000000000000000000000000000000..9ad501a6176a630b8edb97653607ef223946367d
--- /dev/null
+++ b/configs/preset/coa_dti_pro.yaml.bak
@@ -0,0 +1,28 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..025b151cf1539205f245feb41f9fd60f133c4497
--- /dev/null
+++ b/configs/preset/deep_conv_dti.yaml
@@ -0,0 +1,23 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..f72d5c942226d88e798cb6a2fd6fef080df69053
--- /dev/null
+++ b/configs/preset/deep_dta.yaml
@@ -0,0 +1,8 @@
+# @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/drug_ban.yaml b/configs/preset/drug_ban.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..537c9d79276383542e956ff4ef27178c4c358fc4
--- /dev/null
+++ b/configs/preset/drug_ban.yaml
@@ -0,0 +1,28 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..26361c45c25c936a1d9c9b28942343ba7a96a127
--- /dev/null
+++ b/configs/preset/drug_vqa.yaml
@@ -0,0 +1,21 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..159cb4e619f252663dccda18294600602674e01d
--- /dev/null
+++ b/configs/preset/graph_dta.yaml
@@ -0,0 +1,8 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..ae63593517d0ce34310ba3f0dbf1201f66e7e3a5
--- /dev/null
+++ b/configs/preset/hyper_attention_dti.yaml
@@ -0,0 +1,8 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..8609b499b94168c7c5da2b5779b310be5c769020
--- /dev/null
+++ b/configs/preset/m_graph_dta.yaml
@@ -0,0 +1,22 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..ed7fcf5ce9d43b0e047b9720cb544faf707fb64f
--- /dev/null
+++ b/configs/preset/mol_trans.yaml
@@ -0,0 +1,39 @@
+# @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/transformer_cpi.yaml b/configs/preset/transformer_cpi.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..c218ea5a4c51454e9fa4eeb45f97150ac2b99aae
--- /dev/null
+++ b/configs/preset/transformer_cpi.yaml
@@ -0,0 +1,21 @@
+# @package _global_
+defaults:
+  - override /data/drug_featurizer: mol_features
+  - override /data/protein_featurizer: word2vec
+
+model:
+  predictor:
+    _target_: deepscreen.models.predictors.transformer_cpi.TransformerCPI
+    protein_dim: 100
+    hidden_dim: 64
+    n_layers: 3
+    kernel_size: 5
+    dropout: 0.1
+    n_heads: 8
+    pf_dim: 256
+    atom_dim: 34
+
+data:
+  batch_size: 16
+  collator:
+    automatic_padding: True
diff --git a/configs/preset/transformer_cpi_2.yaml b/configs/preset/transformer_cpi_2.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..e1c224f88a6de1266ee4d836c15ff5e88b06f119
--- /dev/null
+++ b/configs/preset/transformer_cpi_2.yaml
@@ -0,0 +1,35 @@
+# @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/ddp_multirun.yaml b/configs/sweep/ddp_multirun.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..fbf6641a20019ae41cf8d231d01433b2562a9c77
--- /dev/null
+++ b/configs/sweep/ddp_multirun.yaml
@@ -0,0 +1,6 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..b404a86d52131cbde1d7b877be92a80d8000d5b8
--- /dev/null
+++ b/configs/sweep/dti_benchmark.yaml
@@ -0,0 +1,8 @@
+# @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_test.yaml b/configs/sweep/example_multirun_test.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..a609000341c88314547dfe300ec59e059c0d9825
--- /dev/null
+++ b/configs/sweep/example_multirun_test.yaml
@@ -0,0 +1,7 @@
+# @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_multirun_train.yaml b/configs/sweep/example_multirun_train.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..b2d7edad480a88165ca51475c7fd076110d2fef0
--- /dev/null
+++ b/configs/sweep/example_multirun_train.yaml
@@ -0,0 +1,6 @@
+# @package _global_
+hydra:
+  sweeper:
+    params:
+      preset: graph_dta,deep_dta
+      experiment: chembl_random
diff --git a/configs/sweep/example_submitit.yaml b/configs/sweep/example_submitit.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..510522a9cb855b9afd2ac3ebd6a0f50baea93459
--- /dev/null
+++ b/configs/sweep/example_submitit.yaml
@@ -0,0 +1,17 @@
+# @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
new file mode 100644
index 0000000000000000000000000000000000000000..73e924007e4c3936dadc918f7cece50574336c3e
--- /dev/null
+++ b/configs/sweep/experiment_summary.csv
@@ -0,0 +1,21 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..b2a3ee1ab0192c82662c03cf59ed07bda14b1862
--- /dev/null
+++ b/configs/sweep/experiment_summary_bindingdb.csv
@@ -0,0 +1,7 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..1cc9af384ea7c91cdc510d734862bbe56edc3f43
--- /dev/null
+++ b/configs/sweep/experiment_summary_davis.csv
@@ -0,0 +1,8 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..fea61408c0c735bb75f05494db511650a4beff79
--- /dev/null
+++ b/configs/sweep/experiment_summary_kiba.csv
@@ -0,0 +1,8 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..a1ce0b60c2e5c9e1cd678cc7a7a8867a2472d15f
--- /dev/null
+++ b/configs/sweep/experiment_summary_test.csv
@@ -0,0 +1,4 @@
+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/task/DTA.yaml b/configs/task/DTA.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..0de6eeb0179fcf63608df8a62719a5f6792baf1d
--- /dev/null
+++ b/configs/task/DTA.yaml
@@ -0,0 +1,12 @@
+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/task/DTI.yaml b/configs/task/DTI.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..31eafe56289ebcb591ddd4254a943015c0d3e429
--- /dev/null
+++ b/configs/task/DTI.yaml
@@ -0,0 +1,12 @@
+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/binary.yaml b/configs/task/binary.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..31eafe56289ebcb591ddd4254a943015c0d3e429
--- /dev/null
+++ b/configs/task/binary.yaml
@@ -0,0 +1,12 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..686e9f9b96c98839ec4bdad32351d29aca026618
--- /dev/null
+++ b/configs/task/multiclass.yaml
@@ -0,0 +1,12 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..0de6eeb0179fcf63608df8a62719a5f6792baf1d
--- /dev/null
+++ b/configs/task/regression.yaml
@@ -0,0 +1,12 @@
+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/trainer/cpu.yaml b/configs/trainer/cpu.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..b7d6767e60c956567555980654f15e7bb673a41f
--- /dev/null
+++ b/configs/trainer/cpu.yaml
@@ -0,0 +1,5 @@
+defaults:
+  - default
+
+accelerator: cpu
+devices: 1
diff --git a/configs/trainer/default.yaml b/configs/trainer/default.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..fd75aa3e6c1b2c9f38c6c666925d58069feb3e73
--- /dev/null
+++ b/configs/trainer/default.yaml
@@ -0,0 +1,19 @@
+_target_: lightning.Trainer
+
+default_root_dir: ${paths.output_dir}
+
+min_epochs: 1
+max_epochs: 50
+
+accelerator: auto
+precision: bf16
+
+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
new file mode 100644
index 0000000000000000000000000000000000000000..f9dc7f73609b2b2fe595d84288a3b556d8d3356c
--- /dev/null
+++ b/configs/trainer/gpu.yaml
@@ -0,0 +1,6 @@
+defaults:
+  - default
+
+accelerator: gpu
+devices: 1
+precision: 16-mixed
\ No newline at end of file
diff --git a/configs/webserver_inference.yaml b/configs/webserver_inference.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..85ab0acd3dd0d1ecdcd48f31ff6c5e1b734aeb2c
--- /dev/null
+++ b/configs/webserver_inference.yaml
@@ -0,0 +1,31 @@
+# @package _global_
+defaults:
+  - model: dti_model # fixed for web server version
+  - task: null
+  - data: dti_data # fixed for web server version
+  - callbacks: tqdm_progress_bar
+  - trainer: default
+  - paths: default
+  - extras: null
+  - hydra: null
+  - _self_
+  - preset: null
+  - experiment: null
+  - sweep: null
+  - debug: null
+  - optional local: default
+  - override model/metrics: null
+
+job_name: "webserver_inference"
+
+tags: null
+
+# passing checkpoint path is necessary for prediction
+ckpt_path: ???
+
+paths:
+  output_dir: null
+  work_dir: null
+
+data:
+  num_workers: 8
\ No newline at end of file