diff --git a/dc50_best_arch_ensemble/best_config-model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-task=dc50-group=scaffold.yaml b/dc50_best_arch_ensemble/best_config-model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-task=dc50-group=scaffold.yaml new file mode 100644 index 0000000000000000000000000000000000000000..46fe9f86178e9e7ac080dc399f2b57cc066e30f9 --- /dev/null +++ b/dc50_best_arch_ensemble/best_config-model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-task=dc50-group=scaffold.yaml @@ -0,0 +1,22 @@ +model_config: + learning_rate: 0.0007485278176691929 + hidden_dim: + - 256 + head_depth: 1 + dropout: 0.0 + head_dropout: 0.1 + task_type: point + lr_scheduler_type: reduce_on_plateau + warmup_ratio: 0.0 + norm_type: layer + activation: relu + input_dim: 509 +training_config: + max_epochs: 200 + gradient_clip_val: 1.0 + enable_checkpointing: true + enable_progress_bar: false + enable_model_summary: true + accelerator: auto + devices: 1 + precision: 16-mixed diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=0_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=0_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=0_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=0_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=0_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..0c3e0fafd72e4d117919d018c0805484b2cef914 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=0_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2cbee6d87a1698c39cb2896ccd26d43633122a1977deb14e45caa6093cd7d78c +size 164527 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=10_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=10_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=10_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=10_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=10_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..833d0bb6240b4fc51f53821d96c969a1384539f7 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=10_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:27f73287b64adf1bd821daccc230c4b69c0ab2f462b4ff639d219e5283f85cea +size 164533 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=11_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=11_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=11_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=11_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=11_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..dcb5af9ded2183925595efd5b6734a349056f02a --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=11_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6842739643150101b82136db268accc6c15961e9c8f059649babb12dc5d75aa0 +size 164725 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=12_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=12_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=12_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=12_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=12_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..f56e9e03d181779f4f76a8f0079cbc546ab57d31 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=12_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:38b31a192842eaacb08d24a50c5b00bd3eaa5e2b4a81655e02f78c1ba0b59aab +size 164277 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=13_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=13_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=13_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=13_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=13_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..e28045d3a55ca4aed31cc33c88206edfa6137ec2 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=13_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:889528f14f5c53f64a764a17120c9de3afc5c362d2b997b8c01f53361f875086 +size 164469 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=14_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=14_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=14_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=14_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=14_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..57038e18d1c2dfe75e6b259e25522a8c7ecbe8b6 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=14_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e034797f28804fb7d7819d8fd8d3c45d409fa026646c25788649b167c9286ca1 +size 164533 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=15_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=15_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=15_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=15_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=15_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..b3e211b8c1efaf5e1a555562b52b7944bbe3bc17 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=15_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8ab45bec692bdeac8ac9224930401271537d061fe65bf17b1d34e509f28a2c7f +size 164405 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=16_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=16_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=16_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=16_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=16_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..4497472227b8e86aff61d8d3468edd883a3e0645 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=16_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a1b1a7285037227eb64829125999f1535444935dcc2eda19cb1b55fc439917cd +size 164597 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=17_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=17_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=17_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=17_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=17_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..0879374a7b38503ff044b18516c7922a110c9c44 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=17_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e51d09d134f771113e612b23c0fa603a92faa4fbbbd55927b1b1d46e90b055e9 +size 164469 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=18_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=18_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=18_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=18_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=18_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..f5382e72a67bd189255a81f4c5c583e40e5bfec7 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=18_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ebadedee8a424dca40477dad09b0c5668cb21086b5e4018ba51497bbe1b6900a +size 164341 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=19_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=19_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=19_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=19_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=19_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..4a7750bfe8cbfef849d5f3cd8244fd7e29abe0a4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=19_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f6c4d24355023ef142adecbd50b5cee3599da96801eea1e50ff376fd333cda15 +size 164469 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=1_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=1_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=1_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=1_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=1_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..9a13b2ca88a741ad268dbdaf756f3ee408bce0c9 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=1_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2d092dde180e964b979b0d6854cd724ba7d2ac89dc01990be3567c27833aafd3 +size 164591 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=20_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=20_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=20_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=20_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=20_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..57976ab91807c3fd59f4cf368cf11037819190c1 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=20_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d8a701c5d7110e3daf1f0a2d75491e2a7c8f0badace9510758a8f5946d12a763 +size 164661 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=21_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=21_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=21_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=21_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=21_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..a501b07e5c9811bc1984d733ff69efa46b6cb734 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=21_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:55593c6ba1509655fec879f4e21511aa54f32cf0875b3ce616ad593d6da666d2 +size 164469 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=22_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=22_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=22_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=22_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=22_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..359101aa6a849f2e63dec7e80fa56c6095a06670 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=22_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ce312732dbb919a9a289cb6d7bac7048a515fa1d5947380c1b7d94cfeb361c79 +size 164469 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=23_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=23_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=23_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=23_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=23_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..108f353747c8ceb07b2ce552bdbfdbdf04fb4b61 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=23_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:73581bd6112b82411356bf6bd8c4276347d50699c0e7d82f33a65bf15041b706 +size 164213 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=24_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=24_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=24_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=24_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=24_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..508dc91dc210a8162083151fe458df7e2d85c096 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=24_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fdce4d615a7aba08ba30453aac46238c3f372945a86b1f53f053622a00ef5d47 +size 164597 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=2_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=2_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=2_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=2_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=2_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..7fc73bd7cfadad208a7a4f250b97ea4a8bcf9c7d --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=2_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:646473aa2c5aa682b5e2f3e813daed111e6178f18f6fe00d8a620eda877d0ee7 +size 164463 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=3_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=3_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=3_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=3_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=3_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..e8afb3fd73fd32a73d5320a424040a740643c26b --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=3_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7ee0a67b811502da1e0f43c308a182cb6ab40e00ada2397cf9d37578844ed60d +size 164399 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=4_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=4_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=4_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=4_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=4_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..85fcc0a36741f3e6013dd4d0c16748a4f19e2c7e --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=4_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3ec0db035fdfa5597e043f22785ceca028050a30fcf89847979d08cdff55954e +size 164335 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=5_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=5_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=5_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=5_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=5_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..e6d39bad41f847b8b4e13dcfa83294250b5e681c --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=5_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d9bcc01ad91f4c46feba71f065767eeed083fc823d6c99a1f965751649076271 +size 164527 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=6_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=6_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=6_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=6_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=6_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..e1e994ad0be86d6a58cf32921cc7cbeec017b582 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=6_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5fff3de2c6222914ff5960fb616ad94b48f5b8b26d5688333bc3a0a4e9d50170 +size 164399 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=7_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=7_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=7_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=7_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=7_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..767d93e44dc07c73de90cbb92b24fce8e079386e --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=7_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b3a39aba80bc245929c05947000682cd53f917bc801d709350b60388cee5d94f +size 164591 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=8_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=8_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=8_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=8_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=8_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..9b8a10e9dbd87553e554566562d48a2e89602b6b --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=8_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:49e39dc8c01636473201b26350131d187f9bf2e5c4fc890bc0fa0457440c8853 +size 164655 diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=9_hparams.yaml b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=9_hparams.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a21387ce25a24bd878aa7837f60fabcbc741fa4 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=9_hparams.yaml @@ -0,0 +1,60 @@ +smiles_col: SMILES +ligase_col: Ligase_Name +ligase_sequence_col: Ligase_Sequence +poi_col: POI_Name +poi_sequence_col: POI_Sequence +cell_line_col: Cell_Line_ID +assay_type_col: Assay +treatment_time_col: Assay_Time +treatment_time_dmax_col: Assay_Time +treatment_time_dc50_col: Assay_Time +treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50) +labels: +- DC50 +normalize_labels: true +standardize_labels: false +impute_labels: true +fp_size: 512 +radius: 16 +use_fingerprints: false +use_descriptors: true +use_relevant_descriptors: false +selected_descriptors: null +use_poi_sequence_embedding: false +use_poi_name_embedding: true +use_ligase_name_embedding: true +use_poi_precomputed_embedding: false +use_ligase_precomputed_embedding: false +poi_embeddings_file: null +poi_embeddings_format: npz +poi_embeddings_per_residue: true +poi_residue_pooling: sum +poi_embeddings_id_type: sequence +ligase_embeddings_file: null +ligase_embeddings_format: npz +ligase_embeddings_per_residue: true +ligase_residue_pooling: sum +ligase_embeddings_id_type: sequence +use_poi_pca: false +poi_pca_n_components: null +use_ligase_pca: false +ligase_pca_n_components: null +use_cell_description_embedding: false +use_cell_name_embedding: true +use_tokenizer: false +tokenizer_name: google-bert/bert-base-cased +max_length: 512 +prompt_template: null +label_task_col: Value_Type +degrader_type_col: null +default_degrader_type: PROTAC +include_prompt: false +is_bert_multitask: false +use_assay_type_encoding: true +use_treatment_time: true +batch_size: 32 +num_workers: 0 +num_proc: 1 +verbose: 0 +sort_features: true +categorical_encoding: onehot diff --git a/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=9_state.pt b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=9_state.pt new file mode 100644 index 0000000000000000000000000000000000000000..d002bfc51abef30110685c3d13c0b90148bb3d38 --- /dev/null +++ b/dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=9_state.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:57ab9604b25995448e70bff3b99f6fb494a8ba4bce9a2ba49b7957da36908455 +size 164399 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=0.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=0.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..97073fac2c801d84d5b198389becdfbf7da7c93c --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=0.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0367e0495d8431f0382c8be5bb841328ed68d7a50fac400bd58356cba2d98bc2 +size 1750689 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=1.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=1.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..58d67dc6c95b674f81e5f076ae86519a823ed442 --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=1.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f7da5e1bba9465a165c57f2be0b63d87f74eb3bc6cb2d1113d40f3ecc9555052 +size 1799969 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=10.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=10.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..26c2e1d81ed35f0d83a2fcdbfeec7d19bc7d048c --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=10.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ce4dc242274239f955b02810bd031866281fb11e4993e3fb904f6e841f56fdf4 +size 1744545 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=11.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=11.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..71c0bfd3b8c0ab1a03f43ee17dbeb17c489b9db1 --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=11.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:be30069f3f2d2a3f1602f44eef2d29075b1b8d2f33f6c8193b52e65d0cf581c7 +size 1778529 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=12.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=12.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..73db436157f694f3ab66d65b820c146ef9706ddf --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=12.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:21de97fa78bcfecee21ea94d1a4558176c6789e49673eb1cbfa6117fddd91689 +size 1719713 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=13.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=13.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..6a6f5ddcead6e265b819b91e59551ef1ea31a757 --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=13.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:94a9465a0931cf1af71fe02e793fd46a649f95f12b4ed22fc777fe0b189d929e +size 1765985 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=14.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=14.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..5a4496ea0c8aa091c4068bd0977f25cad8f4df7a --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=14.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bad50a43c3b77bcc8677d24bc32ad8f766685c9ce8441b598f1131ea16adfaaf +size 1769121 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=15.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=15.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..644c55a605b7398efbb32f78fb36a157305ff798 --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=15.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d99c64a8a4b202fec364ed28aa3354eacafe2ae55150b1488c1b0bf534794b0d +size 1756705 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=16.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=16.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..46704863f6be89c3be4a36eb4491fba0da065433 --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=16.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5b706b0624183f4d4ef88f32faf81e89ae4a01c5a3eddc13487a2c971f55d43c +size 1790689 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=17.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=17.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..dbd9bc6b223666a7711d8782dcec13abd32adb64 --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=17.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c7fbc27770e0c7bf82643e594dc3f40da0627f671c3877e1e2692e89435471f7 +size 1775265 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=18.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=18.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..05eee9c590830be41dcdba6b604a0625a0853071 --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=18.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b0f44e2e6cd1c326d0491d11e2a1d887919502a28ee4a4aa252cafbe7f379fa0 +size 1728993 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=19.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=19.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..f0a65a09d24d43ad628190da3365e5eeb70a424e --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=19.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f4a4bc4abeb7832a167f002522f973595a4464a89b671e924c8c96f0c4d7530a +size 1726049 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=2.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=2.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..c627c33b96e4137e1076d721e93a0d9868d5e328 --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=2.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3af95e7328aa40f15f3033aa1cd9484335f0002ffed97c095163e68448ee09c8 +size 1759841 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=20.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=20.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..f22b40d32db9e853aa2d4995ca15cb8b53669260 --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=20.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:39416149bd335f4af2fb0eebe774bfbdf478b45c567ac18c6fbdcfbd2a9cfc06 +size 1784609 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=21.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=21.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..76ef4b9549bb667960daf3aeafe5f7e0677f932d --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=21.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c8f63c57e055831ceb2f38decc2cf07d61eb5374d5dfb0f124119534c7e8c0a7 +size 1759841 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=22.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=22.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..5969203d1ee0c6bd6ba83bc3b37b92b2a9256ebb --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=22.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e249f719522942018ef448d0e18d32d7d2744907b07ead1f9b7d37b19c481f73 +size 1753761 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=23.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=23.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..147eff305f18b0526492b22294a6dd0cb0089b2d --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=23.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7d91b729501c5568c5c80c5e58b92d4a481c2d2dd29a9dbdf76de93c97d0c38c +size 1710433 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=24.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=24.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..6520507b51076e967c7ab49e9dc07e10eee599be --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=24.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f63298dfe2ff7b65dc382606324bc0c34e92a91f37af3ae12c599b82c268c261 +size 1772321 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=3.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=3.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..c782d0950ad190eba3fb1db668e8d9a9a19cf951 --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=3.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:cd640689eaf08c5c2b3cf551fb2f93b7ab34e2194b042c3fb15e31e5b377c0ed +size 1747489 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=4.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=4.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..025cb00ecdcc61af240b258217a80144d18f220b --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=4.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ed636dd7e10d4a8f68592d5a4ba6d609363ce66eba41ed177d8e9f63c01b64bb +size 1738209 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=5.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=5.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..988a506571ee6a09998d67f450159095c4de2df4 --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=5.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3f1b339867800da5c9a96d849d04e3996f12aa77cadb7de6cc8260fe02e49440 +size 1753825 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=6.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=6.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..b8a0443f4c744eeea86a9a180ccd97dd1db4f8ae --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=6.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f8d672a0c3b1f665fcb67daa0d8bb7452f2b89db3a64a57d4e1203e5a870d01e +size 1753633 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=7.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=7.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..0b4e6eae717478e3bf22cae23777e0fcd229add2 --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=7.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:eb05d754341969a2d28b525807bafc8659eea9e2f2d9f32d01f923bdbebad6a9 +size 1732385 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=8.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=8.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..db2d5ee5662608ba0bc5e4eb17ffadcb0f4303bd --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=8.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:323ffef0317951233a8af5d49577ca5bab69d0e1e159f6181d0fb44bf32856c5 +size 1796897 diff --git a/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=9.ckpt b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=9.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..4fe91c989bcb681cbaf6cd3c1d7600273a5ae694 --- /dev/null +++ b/dc50_best_arch_ensemble/model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=9.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ae73e5148bd17a411ce289da22a9302d2a73a3859e4161b2a8d645b0c6b9c1e8 +size 1744417