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- dmax_best_arch_ensemble/config-model=xgboost_dmax_protac-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-task=dmax-group=scaffold.yaml +18 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=0_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=0_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=10_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=10_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=11_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=11_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=12_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=12_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=13_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=13_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=14_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=14_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=15_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=15_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=16_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=16_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=17_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=17_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=18_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=18_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=19_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=19_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=1_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=1_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=20_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=20_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=21_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=21_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=22_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=22_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=23_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=23_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=24_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=24_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=2_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=2_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=3_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=3_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=4_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=4_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=5_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=5_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=6_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=6_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=7_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=7_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=8_hparams.yaml +60 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=8_state.pt +3 -0
- dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=9_hparams.yaml +60 -0
dmax_best_arch_ensemble/config-model=xgboost_dmax_protac-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-task=dmax-group=scaffold.yaml
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model_config:
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objective: reg:squarederror
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base_score: 0.0
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tree_method: hist
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n_estimators: 2000
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n_jobs: 8
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seed: 65
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learning_rate: 0.015930522616241012
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max_depth: 7
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min_child_weight: 1
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subsample: 0.9819459112971965
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colsample_bytree: 0.9162213204002109
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reg_alpha: 0.0070689749506246055
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reg_lambda: 0.005337032762603957
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gamma: 0.00541524411940254
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training_config:
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num_boost_round: 2000
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early_stopping_rounds: 30
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dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=0_hparams.yaml
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smiles_col: SMILES
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ligase_col: Ligase_Name
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ligase_sequence_col: Ligase_Sequence
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poi_col: POI_Name
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poi_sequence_col: POI_Sequence
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cell_line_col: Cell_Line_ID
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assay_type_col: Assay
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treatment_time_col: Assay_Time
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treatment_time_dmax_col: Assay_Time
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treatment_time_dc50_col: Assay_Time
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treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
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labels:
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- Dmax
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normalize_labels: true
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standardize_labels: false
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| 16 |
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impute_labels: true
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| 17 |
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fp_size: 512
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radius: 16
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| 19 |
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use_fingerprints: false
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| 20 |
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use_descriptors: true
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| 21 |
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use_relevant_descriptors: false
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| 22 |
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selected_descriptors: null
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use_poi_sequence_embedding: true
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use_poi_name_embedding: false
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| 25 |
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use_ligase_name_embedding: true
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| 26 |
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use_poi_precomputed_embedding: false
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| 27 |
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use_ligase_precomputed_embedding: false
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| 28 |
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poi_embeddings_file: null
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poi_embeddings_format: npz
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| 30 |
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poi_embeddings_per_residue: true
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| 31 |
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poi_residue_pooling: sum
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poi_embeddings_id_type: sequence
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| 33 |
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ligase_embeddings_file: null
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ligase_embeddings_format: npz
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| 35 |
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ligase_embeddings_per_residue: true
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ligase_residue_pooling: sum
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ligase_embeddings_id_type: sequence
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use_poi_pca: false
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poi_pca_n_components: null
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use_ligase_pca: false
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ligase_pca_n_components: null
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| 42 |
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use_cell_description_embedding: true
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use_cell_name_embedding: false
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use_tokenizer: false
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tokenizer_name: google-bert/bert-base-cased
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| 46 |
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max_length: 512
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| 47 |
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prompt_template: null
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| 48 |
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label_task_col: Value_Type
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| 49 |
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degrader_type_col: null
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| 50 |
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default_degrader_type: PROTAC
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| 51 |
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include_prompt: false
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| 52 |
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is_bert_multitask: false
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| 53 |
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use_assay_type_encoding: true
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| 54 |
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use_treatment_time: true
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batch_size: 32
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num_workers: 0
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num_proc: 1
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| 58 |
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verbose: 0
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| 59 |
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sort_features: true
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| 60 |
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categorical_encoding: onehot
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dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=0_state.pt
ADDED
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version https://git-lfs.github.com/spec/v1
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oid sha256:d856d52331bdf6b3e6678d3b6b9bf593ca6834b752acd05ca600b8cde81510cb
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| 3 |
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size 169169
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dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=10_hparams.yaml
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smiles_col: SMILES
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ligase_col: Ligase_Name
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ligase_sequence_col: Ligase_Sequence
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| 4 |
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poi_col: POI_Name
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poi_sequence_col: POI_Sequence
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cell_line_col: Cell_Line_ID
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| 7 |
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assay_type_col: Assay
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| 8 |
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treatment_time_col: Assay_Time
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| 9 |
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treatment_time_dmax_col: Assay_Time
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| 10 |
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treatment_time_dc50_col: Assay_Time
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| 11 |
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treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
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labels:
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- Dmax
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| 14 |
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normalize_labels: true
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standardize_labels: false
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impute_labels: true
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fp_size: 512
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radius: 16
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use_fingerprints: false
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use_descriptors: true
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use_relevant_descriptors: false
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| 22 |
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selected_descriptors: null
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use_poi_sequence_embedding: true
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| 24 |
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use_poi_name_embedding: false
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| 25 |
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use_ligase_name_embedding: true
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| 26 |
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use_poi_precomputed_embedding: false
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| 27 |
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use_ligase_precomputed_embedding: false
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| 28 |
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poi_embeddings_file: null
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| 29 |
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poi_embeddings_format: npz
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| 30 |
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poi_embeddings_per_residue: true
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| 31 |
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poi_residue_pooling: sum
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| 32 |
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poi_embeddings_id_type: sequence
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| 33 |
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ligase_embeddings_file: null
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| 34 |
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ligase_embeddings_format: npz
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| 35 |
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ligase_embeddings_per_residue: true
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| 36 |
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ligase_residue_pooling: sum
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| 37 |
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ligase_embeddings_id_type: sequence
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| 38 |
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use_poi_pca: false
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| 39 |
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poi_pca_n_components: null
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| 40 |
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use_ligase_pca: false
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| 41 |
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ligase_pca_n_components: null
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| 42 |
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use_cell_description_embedding: true
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| 43 |
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use_cell_name_embedding: false
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| 44 |
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use_tokenizer: false
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| 45 |
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tokenizer_name: google-bert/bert-base-cased
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| 46 |
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max_length: 512
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| 47 |
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prompt_template: null
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| 48 |
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label_task_col: Value_Type
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| 49 |
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degrader_type_col: null
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| 50 |
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default_degrader_type: PROTAC
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| 51 |
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include_prompt: false
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| 52 |
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is_bert_multitask: false
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| 53 |
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use_assay_type_encoding: true
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| 54 |
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use_treatment_time: true
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| 55 |
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batch_size: 32
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num_workers: 0
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num_proc: 1
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| 58 |
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verbose: 0
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| 59 |
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sort_features: true
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| 60 |
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categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=10_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:be6ba69794e1812b38e1b29a1916ad017f655d2701995ef2bbb3c04c52614954
|
| 3 |
+
size 169239
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=11_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
+
ligase_col: Ligase_Name
|
| 3 |
+
ligase_sequence_col: Ligase_Sequence
|
| 4 |
+
poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
+
standardize_labels: false
|
| 16 |
+
impute_labels: true
|
| 17 |
+
fp_size: 512
|
| 18 |
+
radius: 16
|
| 19 |
+
use_fingerprints: false
|
| 20 |
+
use_descriptors: true
|
| 21 |
+
use_relevant_descriptors: false
|
| 22 |
+
selected_descriptors: null
|
| 23 |
+
use_poi_sequence_embedding: true
|
| 24 |
+
use_poi_name_embedding: false
|
| 25 |
+
use_ligase_name_embedding: true
|
| 26 |
+
use_poi_precomputed_embedding: false
|
| 27 |
+
use_ligase_precomputed_embedding: false
|
| 28 |
+
poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
+
poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
+
ligase_embeddings_per_residue: true
|
| 36 |
+
ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
+
use_cell_description_embedding: true
|
| 43 |
+
use_cell_name_embedding: false
|
| 44 |
+
use_tokenizer: false
|
| 45 |
+
tokenizer_name: google-bert/bert-base-cased
|
| 46 |
+
max_length: 512
|
| 47 |
+
prompt_template: null
|
| 48 |
+
label_task_col: Value_Type
|
| 49 |
+
degrader_type_col: null
|
| 50 |
+
default_degrader_type: PROTAC
|
| 51 |
+
include_prompt: false
|
| 52 |
+
is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
+
use_treatment_time: true
|
| 55 |
+
batch_size: 32
|
| 56 |
+
num_workers: 0
|
| 57 |
+
num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=11_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:3c66e7ab098d34bb6100073f39c3fc025cf45b0a98352e807746ecc5f26468c8
|
| 3 |
+
size 169239
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=12_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
+
ligase_col: Ligase_Name
|
| 3 |
+
ligase_sequence_col: Ligase_Sequence
|
| 4 |
+
poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
+
standardize_labels: false
|
| 16 |
+
impute_labels: true
|
| 17 |
+
fp_size: 512
|
| 18 |
+
radius: 16
|
| 19 |
+
use_fingerprints: false
|
| 20 |
+
use_descriptors: true
|
| 21 |
+
use_relevant_descriptors: false
|
| 22 |
+
selected_descriptors: null
|
| 23 |
+
use_poi_sequence_embedding: true
|
| 24 |
+
use_poi_name_embedding: false
|
| 25 |
+
use_ligase_name_embedding: true
|
| 26 |
+
use_poi_precomputed_embedding: false
|
| 27 |
+
use_ligase_precomputed_embedding: false
|
| 28 |
+
poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
+
poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
+
ligase_embeddings_per_residue: true
|
| 36 |
+
ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
+
use_cell_description_embedding: true
|
| 43 |
+
use_cell_name_embedding: false
|
| 44 |
+
use_tokenizer: false
|
| 45 |
+
tokenizer_name: google-bert/bert-base-cased
|
| 46 |
+
max_length: 512
|
| 47 |
+
prompt_template: null
|
| 48 |
+
label_task_col: Value_Type
|
| 49 |
+
degrader_type_col: null
|
| 50 |
+
default_degrader_type: PROTAC
|
| 51 |
+
include_prompt: false
|
| 52 |
+
is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
+
use_treatment_time: true
|
| 55 |
+
batch_size: 32
|
| 56 |
+
num_workers: 0
|
| 57 |
+
num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=12_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:9a8ffea24fcace78effc9e6a6811253203b395e3ed032bfd9f05009122da35b9
|
| 3 |
+
size 169239
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=13_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
+
ligase_col: Ligase_Name
|
| 3 |
+
ligase_sequence_col: Ligase_Sequence
|
| 4 |
+
poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
+
standardize_labels: false
|
| 16 |
+
impute_labels: true
|
| 17 |
+
fp_size: 512
|
| 18 |
+
radius: 16
|
| 19 |
+
use_fingerprints: false
|
| 20 |
+
use_descriptors: true
|
| 21 |
+
use_relevant_descriptors: false
|
| 22 |
+
selected_descriptors: null
|
| 23 |
+
use_poi_sequence_embedding: true
|
| 24 |
+
use_poi_name_embedding: false
|
| 25 |
+
use_ligase_name_embedding: true
|
| 26 |
+
use_poi_precomputed_embedding: false
|
| 27 |
+
use_ligase_precomputed_embedding: false
|
| 28 |
+
poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
+
poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
+
ligase_embeddings_per_residue: true
|
| 36 |
+
ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
+
use_cell_description_embedding: true
|
| 43 |
+
use_cell_name_embedding: false
|
| 44 |
+
use_tokenizer: false
|
| 45 |
+
tokenizer_name: google-bert/bert-base-cased
|
| 46 |
+
max_length: 512
|
| 47 |
+
prompt_template: null
|
| 48 |
+
label_task_col: Value_Type
|
| 49 |
+
degrader_type_col: null
|
| 50 |
+
default_degrader_type: PROTAC
|
| 51 |
+
include_prompt: false
|
| 52 |
+
is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
+
use_treatment_time: true
|
| 55 |
+
batch_size: 32
|
| 56 |
+
num_workers: 0
|
| 57 |
+
num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=13_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:5f965bb03e287d1d7bd1cce59e636dbd48e0a22642cb01981e223a03310e8a04
|
| 3 |
+
size 169239
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=14_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
+
ligase_col: Ligase_Name
|
| 3 |
+
ligase_sequence_col: Ligase_Sequence
|
| 4 |
+
poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
+
standardize_labels: false
|
| 16 |
+
impute_labels: true
|
| 17 |
+
fp_size: 512
|
| 18 |
+
radius: 16
|
| 19 |
+
use_fingerprints: false
|
| 20 |
+
use_descriptors: true
|
| 21 |
+
use_relevant_descriptors: false
|
| 22 |
+
selected_descriptors: null
|
| 23 |
+
use_poi_sequence_embedding: true
|
| 24 |
+
use_poi_name_embedding: false
|
| 25 |
+
use_ligase_name_embedding: true
|
| 26 |
+
use_poi_precomputed_embedding: false
|
| 27 |
+
use_ligase_precomputed_embedding: false
|
| 28 |
+
poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
+
poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
+
ligase_embeddings_per_residue: true
|
| 36 |
+
ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
+
use_cell_description_embedding: true
|
| 43 |
+
use_cell_name_embedding: false
|
| 44 |
+
use_tokenizer: false
|
| 45 |
+
tokenizer_name: google-bert/bert-base-cased
|
| 46 |
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max_length: 512
|
| 47 |
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prompt_template: null
|
| 48 |
+
label_task_col: Value_Type
|
| 49 |
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degrader_type_col: null
|
| 50 |
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|
| 51 |
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include_prompt: false
|
| 52 |
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is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
+
use_treatment_time: true
|
| 55 |
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batch_size: 32
|
| 56 |
+
num_workers: 0
|
| 57 |
+
num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=14_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:dbf8bac8d41725656bf3a5fa1044eadda6631a683070e8b8f5356ea8cec6b354
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| 3 |
+
size 169175
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=15_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
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|
|
|
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|
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|
|
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| 1 |
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smiles_col: SMILES
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| 2 |
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ligase_col: Ligase_Name
|
| 3 |
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ligase_sequence_col: Ligase_Sequence
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| 4 |
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poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
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cell_line_col: Cell_Line_ID
|
| 7 |
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assay_type_col: Assay
|
| 8 |
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treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
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normalize_labels: true
|
| 15 |
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standardize_labels: false
|
| 16 |
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impute_labels: true
|
| 17 |
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fp_size: 512
|
| 18 |
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radius: 16
|
| 19 |
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| 20 |
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use_descriptors: true
|
| 21 |
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|
| 22 |
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selected_descriptors: null
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| 23 |
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|
| 24 |
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use_poi_name_embedding: false
|
| 25 |
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use_ligase_name_embedding: true
|
| 26 |
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use_poi_precomputed_embedding: false
|
| 27 |
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use_ligase_precomputed_embedding: false
|
| 28 |
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poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
+
poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
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ligase_embeddings_per_residue: true
|
| 36 |
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ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
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use_cell_description_embedding: true
|
| 43 |
+
use_cell_name_embedding: false
|
| 44 |
+
use_tokenizer: false
|
| 45 |
+
tokenizer_name: google-bert/bert-base-cased
|
| 46 |
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max_length: 512
|
| 47 |
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prompt_template: null
|
| 48 |
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label_task_col: Value_Type
|
| 49 |
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degrader_type_col: null
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| 50 |
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default_degrader_type: PROTAC
|
| 51 |
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include_prompt: false
|
| 52 |
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is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
+
use_treatment_time: true
|
| 55 |
+
batch_size: 32
|
| 56 |
+
num_workers: 0
|
| 57 |
+
num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=15_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:0a17a84b212e23f13cd82f7dc7769f22671274df446f8345dce523de4ec2e548
|
| 3 |
+
size 169239
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=16_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
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|
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|
| 1 |
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smiles_col: SMILES
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| 2 |
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ligase_col: Ligase_Name
|
| 3 |
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ligase_sequence_col: Ligase_Sequence
|
| 4 |
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poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
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treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
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standardize_labels: false
|
| 16 |
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impute_labels: true
|
| 17 |
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fp_size: 512
|
| 18 |
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radius: 16
|
| 19 |
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use_fingerprints: false
|
| 20 |
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use_descriptors: true
|
| 21 |
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|
| 22 |
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selected_descriptors: null
|
| 23 |
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use_poi_sequence_embedding: true
|
| 24 |
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|
| 25 |
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|
| 26 |
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use_poi_precomputed_embedding: false
|
| 27 |
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use_ligase_precomputed_embedding: false
|
| 28 |
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poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
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poi_embeddings_id_type: sequence
|
| 33 |
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ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
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ligase_embeddings_per_residue: true
|
| 36 |
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ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
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use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
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use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
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use_cell_description_embedding: true
|
| 43 |
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use_cell_name_embedding: false
|
| 44 |
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use_tokenizer: false
|
| 45 |
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tokenizer_name: google-bert/bert-base-cased
|
| 46 |
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max_length: 512
|
| 47 |
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prompt_template: null
|
| 48 |
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label_task_col: Value_Type
|
| 49 |
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degrader_type_col: null
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| 50 |
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default_degrader_type: PROTAC
|
| 51 |
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include_prompt: false
|
| 52 |
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is_bert_multitask: false
|
| 53 |
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use_assay_type_encoding: true
|
| 54 |
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use_treatment_time: true
|
| 55 |
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batch_size: 32
|
| 56 |
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num_workers: 0
|
| 57 |
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num_proc: 1
|
| 58 |
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verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=16_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:f4f0d31bc875d15f676069c5f4e1f0ef8435e62e20bee0cdefe2d09a1bf19d21
|
| 3 |
+
size 169175
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=17_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
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|
|
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|
|
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|
|
|
|
|
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|
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|
|
|
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|
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|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
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|
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|
|
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|
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|
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|
|
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|
|
|
|
|
|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
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ligase_col: Ligase_Name
|
| 3 |
+
ligase_sequence_col: Ligase_Sequence
|
| 4 |
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poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
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treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
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normalize_labels: true
|
| 15 |
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standardize_labels: false
|
| 16 |
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impute_labels: true
|
| 17 |
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fp_size: 512
|
| 18 |
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radius: 16
|
| 19 |
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|
| 20 |
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use_descriptors: true
|
| 21 |
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use_relevant_descriptors: false
|
| 22 |
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selected_descriptors: null
|
| 23 |
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use_poi_sequence_embedding: true
|
| 24 |
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use_poi_name_embedding: false
|
| 25 |
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use_ligase_name_embedding: true
|
| 26 |
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use_poi_precomputed_embedding: false
|
| 27 |
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use_ligase_precomputed_embedding: false
|
| 28 |
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poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
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poi_residue_pooling: sum
|
| 32 |
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poi_embeddings_id_type: sequence
|
| 33 |
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ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
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ligase_embeddings_per_residue: true
|
| 36 |
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ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
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use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
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use_cell_description_embedding: true
|
| 43 |
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use_cell_name_embedding: false
|
| 44 |
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use_tokenizer: false
|
| 45 |
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tokenizer_name: google-bert/bert-base-cased
|
| 46 |
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max_length: 512
|
| 47 |
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prompt_template: null
|
| 48 |
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label_task_col: Value_Type
|
| 49 |
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degrader_type_col: null
|
| 50 |
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default_degrader_type: PROTAC
|
| 51 |
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include_prompt: false
|
| 52 |
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is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
+
use_treatment_time: true
|
| 55 |
+
batch_size: 32
|
| 56 |
+
num_workers: 0
|
| 57 |
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num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=17_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:4f77429d44432534b39a8dfdc2fbd8db93e2a3d6189cb94eca8bf1284defa23b
|
| 3 |
+
size 169303
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=18_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
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|
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|
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|
|
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|
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|
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|
|
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|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
+
ligase_col: Ligase_Name
|
| 3 |
+
ligase_sequence_col: Ligase_Sequence
|
| 4 |
+
poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
+
standardize_labels: false
|
| 16 |
+
impute_labels: true
|
| 17 |
+
fp_size: 512
|
| 18 |
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radius: 16
|
| 19 |
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|
| 20 |
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|
| 21 |
+
use_relevant_descriptors: false
|
| 22 |
+
selected_descriptors: null
|
| 23 |
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|
| 24 |
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|
| 25 |
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use_ligase_name_embedding: true
|
| 26 |
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use_poi_precomputed_embedding: false
|
| 27 |
+
use_ligase_precomputed_embedding: false
|
| 28 |
+
poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
+
poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
+
ligase_embeddings_per_residue: true
|
| 36 |
+
ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
+
use_cell_description_embedding: true
|
| 43 |
+
use_cell_name_embedding: false
|
| 44 |
+
use_tokenizer: false
|
| 45 |
+
tokenizer_name: google-bert/bert-base-cased
|
| 46 |
+
max_length: 512
|
| 47 |
+
prompt_template: null
|
| 48 |
+
label_task_col: Value_Type
|
| 49 |
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degrader_type_col: null
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| 50 |
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default_degrader_type: PROTAC
|
| 51 |
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| 52 |
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is_bert_multitask: false
|
| 53 |
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use_assay_type_encoding: true
|
| 54 |
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use_treatment_time: true
|
| 55 |
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batch_size: 32
|
| 56 |
+
num_workers: 0
|
| 57 |
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num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=18_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:b9ffbdf09557d6833237c87e7055e736e614ef9f9ae16317721dd8ef8a419237
|
| 3 |
+
size 169303
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=19_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
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|
|
|
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|
|
| 1 |
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smiles_col: SMILES
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| 2 |
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ligase_col: Ligase_Name
|
| 3 |
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ligase_sequence_col: Ligase_Sequence
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| 4 |
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poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
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cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
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standardize_labels: false
|
| 16 |
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impute_labels: true
|
| 17 |
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fp_size: 512
|
| 18 |
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radius: 16
|
| 19 |
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use_fingerprints: false
|
| 20 |
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use_descriptors: true
|
| 21 |
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use_relevant_descriptors: false
|
| 22 |
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selected_descriptors: null
|
| 23 |
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use_poi_sequence_embedding: true
|
| 24 |
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use_poi_name_embedding: false
|
| 25 |
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use_ligase_name_embedding: true
|
| 26 |
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use_poi_precomputed_embedding: false
|
| 27 |
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use_ligase_precomputed_embedding: false
|
| 28 |
+
poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
+
poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
+
ligase_embeddings_per_residue: true
|
| 36 |
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ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
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use_poi_pca: false
|
| 39 |
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poi_pca_n_components: null
|
| 40 |
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use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
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use_cell_description_embedding: true
|
| 43 |
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use_cell_name_embedding: false
|
| 44 |
+
use_tokenizer: false
|
| 45 |
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tokenizer_name: google-bert/bert-base-cased
|
| 46 |
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max_length: 512
|
| 47 |
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prompt_template: null
|
| 48 |
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label_task_col: Value_Type
|
| 49 |
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degrader_type_col: null
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|
| 51 |
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include_prompt: false
|
| 52 |
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is_bert_multitask: false
|
| 53 |
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use_assay_type_encoding: true
|
| 54 |
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use_treatment_time: true
|
| 55 |
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batch_size: 32
|
| 56 |
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num_workers: 0
|
| 57 |
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num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=19_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:48e2cacb9462112811c5cde0dd13fdee56682a97dbc253ee33d2ef09de981fe3
|
| 3 |
+
size 169303
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=1_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
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|
|
|
|
|
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|
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|
| 1 |
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smiles_col: SMILES
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| 2 |
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ligase_col: Ligase_Name
|
| 3 |
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ligase_sequence_col: Ligase_Sequence
|
| 4 |
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poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
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treatment_time_col: Assay_Time
|
| 9 |
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treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
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standardize_labels: false
|
| 16 |
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impute_labels: true
|
| 17 |
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fp_size: 512
|
| 18 |
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radius: 16
|
| 19 |
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|
| 20 |
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use_descriptors: true
|
| 21 |
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use_relevant_descriptors: false
|
| 22 |
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selected_descriptors: null
|
| 23 |
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use_poi_sequence_embedding: true
|
| 24 |
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use_poi_name_embedding: false
|
| 25 |
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use_ligase_name_embedding: true
|
| 26 |
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use_poi_precomputed_embedding: false
|
| 27 |
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use_ligase_precomputed_embedding: false
|
| 28 |
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poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
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poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
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ligase_embeddings_per_residue: true
|
| 36 |
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ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
+
use_cell_description_embedding: true
|
| 43 |
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use_cell_name_embedding: false
|
| 44 |
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use_tokenizer: false
|
| 45 |
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tokenizer_name: google-bert/bert-base-cased
|
| 46 |
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max_length: 512
|
| 47 |
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prompt_template: null
|
| 48 |
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label_task_col: Value_Type
|
| 49 |
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degrader_type_col: null
|
| 50 |
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default_degrader_type: PROTAC
|
| 51 |
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include_prompt: false
|
| 52 |
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is_bert_multitask: false
|
| 53 |
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use_assay_type_encoding: true
|
| 54 |
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use_treatment_time: true
|
| 55 |
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batch_size: 32
|
| 56 |
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num_workers: 0
|
| 57 |
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num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=1_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:ce2db97ff55fa1c54ca0891752ceeed521407a0159f6ea45a678fa083ff6796f
|
| 3 |
+
size 169297
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=20_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
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|
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|
|
|
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|
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|
|
|
|
|
|
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|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
+
ligase_col: Ligase_Name
|
| 3 |
+
ligase_sequence_col: Ligase_Sequence
|
| 4 |
+
poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
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standardize_labels: false
|
| 16 |
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impute_labels: true
|
| 17 |
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fp_size: 512
|
| 18 |
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radius: 16
|
| 19 |
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|
| 20 |
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use_descriptors: true
|
| 21 |
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use_relevant_descriptors: false
|
| 22 |
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selected_descriptors: null
|
| 23 |
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use_poi_sequence_embedding: true
|
| 24 |
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use_poi_name_embedding: false
|
| 25 |
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use_ligase_name_embedding: true
|
| 26 |
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use_poi_precomputed_embedding: false
|
| 27 |
+
use_ligase_precomputed_embedding: false
|
| 28 |
+
poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
+
poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
+
ligase_embeddings_per_residue: true
|
| 36 |
+
ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
+
use_cell_description_embedding: true
|
| 43 |
+
use_cell_name_embedding: false
|
| 44 |
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use_tokenizer: false
|
| 45 |
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tokenizer_name: google-bert/bert-base-cased
|
| 46 |
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max_length: 512
|
| 47 |
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prompt_template: null
|
| 48 |
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label_task_col: Value_Type
|
| 49 |
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degrader_type_col: null
|
| 50 |
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default_degrader_type: PROTAC
|
| 51 |
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include_prompt: false
|
| 52 |
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is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
+
use_treatment_time: true
|
| 55 |
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batch_size: 32
|
| 56 |
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num_workers: 0
|
| 57 |
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num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=20_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:af93f411109d99375dca334bb4ca64ebb2991be4fde08f79fa436316478d9ff2
|
| 3 |
+
size 169303
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=21_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
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|
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|
|
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|
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| 1 |
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| 3 |
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| 4 |
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| 5 |
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|
| 7 |
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|
| 8 |
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| 9 |
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|
| 10 |
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|
| 11 |
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treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
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|
| 15 |
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| 16 |
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| 17 |
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| 22 |
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| 26 |
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|
| 27 |
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| 28 |
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poi_embeddings_file: null
|
| 29 |
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poi_embeddings_format: npz
|
| 30 |
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poi_embeddings_per_residue: true
|
| 31 |
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poi_residue_pooling: sum
|
| 32 |
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poi_embeddings_id_type: sequence
|
| 33 |
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ligase_embeddings_file: null
|
| 34 |
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ligase_embeddings_format: npz
|
| 35 |
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ligase_embeddings_per_residue: true
|
| 36 |
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ligase_residue_pooling: sum
|
| 37 |
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ligase_embeddings_id_type: sequence
|
| 38 |
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|
| 39 |
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poi_pca_n_components: null
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| 40 |
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use_ligase_pca: false
|
| 41 |
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ligase_pca_n_components: null
|
| 42 |
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use_cell_description_embedding: true
|
| 43 |
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|
| 44 |
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|
| 45 |
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tokenizer_name: google-bert/bert-base-cased
|
| 46 |
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|
| 47 |
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| 48 |
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|
| 53 |
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use_assay_type_encoding: true
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| 54 |
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|
| 55 |
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batch_size: 32
|
| 56 |
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|
| 57 |
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num_proc: 1
|
| 58 |
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verbose: 0
|
| 59 |
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sort_features: true
|
| 60 |
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categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=21_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:c03364af7e9c87fa4548a878d249e06178e25b34ff1b77475ca6f7d44c57be5e
|
| 3 |
+
size 169303
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=22_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
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|
|
|
|
|
|
|
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|
|
|
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|
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| 1 |
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smiles_col: SMILES
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| 2 |
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ligase_col: Ligase_Name
|
| 3 |
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ligase_sequence_col: Ligase_Sequence
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| 4 |
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poi_col: POI_Name
|
| 5 |
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poi_sequence_col: POI_Sequence
|
| 6 |
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cell_line_col: Cell_Line_ID
|
| 7 |
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assay_type_col: Assay
|
| 8 |
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treatment_time_col: Assay_Time
|
| 9 |
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treatment_time_dmax_col: Assay_Time
|
| 10 |
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treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
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standardize_labels: false
|
| 16 |
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impute_labels: true
|
| 17 |
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fp_size: 512
|
| 18 |
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radius: 16
|
| 19 |
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| 20 |
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| 21 |
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| 22 |
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| 23 |
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|
| 24 |
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|
| 25 |
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|
| 26 |
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use_poi_precomputed_embedding: false
|
| 27 |
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use_ligase_precomputed_embedding: false
|
| 28 |
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poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
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poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
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ligase_embeddings_per_residue: true
|
| 36 |
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ligase_residue_pooling: sum
|
| 37 |
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ligase_embeddings_id_type: sequence
|
| 38 |
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use_poi_pca: false
|
| 39 |
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poi_pca_n_components: null
|
| 40 |
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use_ligase_pca: false
|
| 41 |
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ligase_pca_n_components: null
|
| 42 |
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use_cell_description_embedding: true
|
| 43 |
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use_cell_name_embedding: false
|
| 44 |
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use_tokenizer: false
|
| 45 |
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tokenizer_name: google-bert/bert-base-cased
|
| 46 |
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max_length: 512
|
| 47 |
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prompt_template: null
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| 48 |
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label_task_col: Value_Type
|
| 49 |
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| 50 |
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|
| 51 |
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|
| 52 |
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|
| 53 |
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use_assay_type_encoding: true
|
| 54 |
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use_treatment_time: true
|
| 55 |
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batch_size: 32
|
| 56 |
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num_workers: 0
|
| 57 |
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num_proc: 1
|
| 58 |
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verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=22_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:de5ef50a73a80d03deac6701914ef1b0792917bff1fd68b05ea3514891420a3c
|
| 3 |
+
size 169303
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=23_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
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|
|
|
|
|
|
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|
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|
| 1 |
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smiles_col: SMILES
|
| 2 |
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ligase_col: Ligase_Name
|
| 3 |
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ligase_sequence_col: Ligase_Sequence
|
| 4 |
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poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
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cell_line_col: Cell_Line_ID
|
| 7 |
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assay_type_col: Assay
|
| 8 |
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treatment_time_col: Assay_Time
|
| 9 |
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treatment_time_dmax_col: Assay_Time
|
| 10 |
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treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
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normalize_labels: true
|
| 15 |
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standardize_labels: false
|
| 16 |
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impute_labels: true
|
| 17 |
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fp_size: 512
|
| 18 |
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radius: 16
|
| 19 |
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|
| 20 |
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|
| 21 |
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|
| 22 |
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| 23 |
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|
| 24 |
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|
| 25 |
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|
| 26 |
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|
| 27 |
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use_ligase_precomputed_embedding: false
|
| 28 |
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poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
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poi_residue_pooling: sum
|
| 32 |
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poi_embeddings_id_type: sequence
|
| 33 |
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ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
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ligase_embeddings_per_residue: true
|
| 36 |
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ligase_residue_pooling: sum
|
| 37 |
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ligase_embeddings_id_type: sequence
|
| 38 |
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use_poi_pca: false
|
| 39 |
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poi_pca_n_components: null
|
| 40 |
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use_ligase_pca: false
|
| 41 |
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ligase_pca_n_components: null
|
| 42 |
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use_cell_description_embedding: true
|
| 43 |
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use_cell_name_embedding: false
|
| 44 |
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use_tokenizer: false
|
| 45 |
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tokenizer_name: google-bert/bert-base-cased
|
| 46 |
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max_length: 512
|
| 47 |
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prompt_template: null
|
| 48 |
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label_task_col: Value_Type
|
| 49 |
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degrader_type_col: null
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| 50 |
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default_degrader_type: PROTAC
|
| 51 |
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include_prompt: false
|
| 52 |
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is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
+
use_treatment_time: true
|
| 55 |
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batch_size: 32
|
| 56 |
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num_workers: 0
|
| 57 |
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num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=23_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:da014958a5eaa63d05db394caa0f5441e0cda8784ad504bec47eb1d76d945da8
|
| 3 |
+
size 169367
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=24_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
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|
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|
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|
|
|
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|
|
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|
|
|
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|
|
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|
|
|
|
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|
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|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
+
ligase_col: Ligase_Name
|
| 3 |
+
ligase_sequence_col: Ligase_Sequence
|
| 4 |
+
poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
+
standardize_labels: false
|
| 16 |
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impute_labels: true
|
| 17 |
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fp_size: 512
|
| 18 |
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radius: 16
|
| 19 |
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use_fingerprints: false
|
| 20 |
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use_descriptors: true
|
| 21 |
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use_relevant_descriptors: false
|
| 22 |
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selected_descriptors: null
|
| 23 |
+
use_poi_sequence_embedding: true
|
| 24 |
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use_poi_name_embedding: false
|
| 25 |
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use_ligase_name_embedding: true
|
| 26 |
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use_poi_precomputed_embedding: false
|
| 27 |
+
use_ligase_precomputed_embedding: false
|
| 28 |
+
poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
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poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
+
ligase_embeddings_per_residue: true
|
| 36 |
+
ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
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use_cell_description_embedding: true
|
| 43 |
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use_cell_name_embedding: false
|
| 44 |
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use_tokenizer: false
|
| 45 |
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tokenizer_name: google-bert/bert-base-cased
|
| 46 |
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max_length: 512
|
| 47 |
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prompt_template: null
|
| 48 |
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label_task_col: Value_Type
|
| 49 |
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degrader_type_col: null
|
| 50 |
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default_degrader_type: PROTAC
|
| 51 |
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include_prompt: false
|
| 52 |
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is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
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use_treatment_time: true
|
| 55 |
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batch_size: 32
|
| 56 |
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num_workers: 0
|
| 57 |
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num_proc: 1
|
| 58 |
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verbose: 0
|
| 59 |
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sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=24_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:9d899c0332b8c3bb7be65ccd7ba2a47277d8925e653d13e1294c3f5a2fe7e52e
|
| 3 |
+
size 169303
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=2_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
+
ligase_col: Ligase_Name
|
| 3 |
+
ligase_sequence_col: Ligase_Sequence
|
| 4 |
+
poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
+
standardize_labels: false
|
| 16 |
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impute_labels: true
|
| 17 |
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fp_size: 512
|
| 18 |
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radius: 16
|
| 19 |
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|
| 20 |
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|
| 21 |
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use_relevant_descriptors: false
|
| 22 |
+
selected_descriptors: null
|
| 23 |
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|
| 24 |
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use_poi_name_embedding: false
|
| 25 |
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use_ligase_name_embedding: true
|
| 26 |
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use_poi_precomputed_embedding: false
|
| 27 |
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use_ligase_precomputed_embedding: false
|
| 28 |
+
poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
+
poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
+
ligase_embeddings_per_residue: true
|
| 36 |
+
ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
+
use_cell_description_embedding: true
|
| 43 |
+
use_cell_name_embedding: false
|
| 44 |
+
use_tokenizer: false
|
| 45 |
+
tokenizer_name: google-bert/bert-base-cased
|
| 46 |
+
max_length: 512
|
| 47 |
+
prompt_template: null
|
| 48 |
+
label_task_col: Value_Type
|
| 49 |
+
degrader_type_col: null
|
| 50 |
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default_degrader_type: PROTAC
|
| 51 |
+
include_prompt: false
|
| 52 |
+
is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
+
use_treatment_time: true
|
| 55 |
+
batch_size: 32
|
| 56 |
+
num_workers: 0
|
| 57 |
+
num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=2_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:c9ab3caf0b9215753907f82b1530ec1668823a78aa0d8802043822e4bce75e99
|
| 3 |
+
size 169297
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=3_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
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|
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|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
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|
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|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
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|
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|
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|
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|
|
|
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|
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|
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|
|
|
|
|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
+
ligase_col: Ligase_Name
|
| 3 |
+
ligase_sequence_col: Ligase_Sequence
|
| 4 |
+
poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
+
standardize_labels: false
|
| 16 |
+
impute_labels: true
|
| 17 |
+
fp_size: 512
|
| 18 |
+
radius: 16
|
| 19 |
+
use_fingerprints: false
|
| 20 |
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use_descriptors: true
|
| 21 |
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use_relevant_descriptors: false
|
| 22 |
+
selected_descriptors: null
|
| 23 |
+
use_poi_sequence_embedding: true
|
| 24 |
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use_poi_name_embedding: false
|
| 25 |
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use_ligase_name_embedding: true
|
| 26 |
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use_poi_precomputed_embedding: false
|
| 27 |
+
use_ligase_precomputed_embedding: false
|
| 28 |
+
poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
+
poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
+
ligase_embeddings_per_residue: true
|
| 36 |
+
ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
+
use_cell_description_embedding: true
|
| 43 |
+
use_cell_name_embedding: false
|
| 44 |
+
use_tokenizer: false
|
| 45 |
+
tokenizer_name: google-bert/bert-base-cased
|
| 46 |
+
max_length: 512
|
| 47 |
+
prompt_template: null
|
| 48 |
+
label_task_col: Value_Type
|
| 49 |
+
degrader_type_col: null
|
| 50 |
+
default_degrader_type: PROTAC
|
| 51 |
+
include_prompt: false
|
| 52 |
+
is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
+
use_treatment_time: true
|
| 55 |
+
batch_size: 32
|
| 56 |
+
num_workers: 0
|
| 57 |
+
num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=3_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:290e6d91c99cd3c177c1fde2499d3c07bae368ac181de3a0694777c05c80828e
|
| 3 |
+
size 169297
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=4_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
+
ligase_col: Ligase_Name
|
| 3 |
+
ligase_sequence_col: Ligase_Sequence
|
| 4 |
+
poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
+
standardize_labels: false
|
| 16 |
+
impute_labels: true
|
| 17 |
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fp_size: 512
|
| 18 |
+
radius: 16
|
| 19 |
+
use_fingerprints: false
|
| 20 |
+
use_descriptors: true
|
| 21 |
+
use_relevant_descriptors: false
|
| 22 |
+
selected_descriptors: null
|
| 23 |
+
use_poi_sequence_embedding: true
|
| 24 |
+
use_poi_name_embedding: false
|
| 25 |
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use_ligase_name_embedding: true
|
| 26 |
+
use_poi_precomputed_embedding: false
|
| 27 |
+
use_ligase_precomputed_embedding: false
|
| 28 |
+
poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
+
poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
+
ligase_embeddings_per_residue: true
|
| 36 |
+
ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
+
use_cell_description_embedding: true
|
| 43 |
+
use_cell_name_embedding: false
|
| 44 |
+
use_tokenizer: false
|
| 45 |
+
tokenizer_name: google-bert/bert-base-cased
|
| 46 |
+
max_length: 512
|
| 47 |
+
prompt_template: null
|
| 48 |
+
label_task_col: Value_Type
|
| 49 |
+
degrader_type_col: null
|
| 50 |
+
default_degrader_type: PROTAC
|
| 51 |
+
include_prompt: false
|
| 52 |
+
is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
+
use_treatment_time: true
|
| 55 |
+
batch_size: 32
|
| 56 |
+
num_workers: 0
|
| 57 |
+
num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=4_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:c70b656aadece6f184d3f187ecaa8220692d6d531b0346eb5c316d4c0d817775
|
| 3 |
+
size 169169
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=5_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
+
ligase_col: Ligase_Name
|
| 3 |
+
ligase_sequence_col: Ligase_Sequence
|
| 4 |
+
poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
+
standardize_labels: false
|
| 16 |
+
impute_labels: true
|
| 17 |
+
fp_size: 512
|
| 18 |
+
radius: 16
|
| 19 |
+
use_fingerprints: false
|
| 20 |
+
use_descriptors: true
|
| 21 |
+
use_relevant_descriptors: false
|
| 22 |
+
selected_descriptors: null
|
| 23 |
+
use_poi_sequence_embedding: true
|
| 24 |
+
use_poi_name_embedding: false
|
| 25 |
+
use_ligase_name_embedding: true
|
| 26 |
+
use_poi_precomputed_embedding: false
|
| 27 |
+
use_ligase_precomputed_embedding: false
|
| 28 |
+
poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
+
poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
+
ligase_embeddings_per_residue: true
|
| 36 |
+
ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
+
use_cell_description_embedding: true
|
| 43 |
+
use_cell_name_embedding: false
|
| 44 |
+
use_tokenizer: false
|
| 45 |
+
tokenizer_name: google-bert/bert-base-cased
|
| 46 |
+
max_length: 512
|
| 47 |
+
prompt_template: null
|
| 48 |
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label_task_col: Value_Type
|
| 49 |
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degrader_type_col: null
|
| 50 |
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default_degrader_type: PROTAC
|
| 51 |
+
include_prompt: false
|
| 52 |
+
is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
+
use_treatment_time: true
|
| 55 |
+
batch_size: 32
|
| 56 |
+
num_workers: 0
|
| 57 |
+
num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=5_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:6097d0342175683eac418852d6ffbbcbd26ca5ff488e441a297a6110a4c5c763
|
| 3 |
+
size 169233
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=6_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
+
ligase_col: Ligase_Name
|
| 3 |
+
ligase_sequence_col: Ligase_Sequence
|
| 4 |
+
poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
+
standardize_labels: false
|
| 16 |
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impute_labels: true
|
| 17 |
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fp_size: 512
|
| 18 |
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radius: 16
|
| 19 |
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use_fingerprints: false
|
| 20 |
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use_descriptors: true
|
| 21 |
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use_relevant_descriptors: false
|
| 22 |
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selected_descriptors: null
|
| 23 |
+
use_poi_sequence_embedding: true
|
| 24 |
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use_poi_name_embedding: false
|
| 25 |
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use_ligase_name_embedding: true
|
| 26 |
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use_poi_precomputed_embedding: false
|
| 27 |
+
use_ligase_precomputed_embedding: false
|
| 28 |
+
poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
+
poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
+
ligase_embeddings_per_residue: true
|
| 36 |
+
ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
+
use_cell_description_embedding: true
|
| 43 |
+
use_cell_name_embedding: false
|
| 44 |
+
use_tokenizer: false
|
| 45 |
+
tokenizer_name: google-bert/bert-base-cased
|
| 46 |
+
max_length: 512
|
| 47 |
+
prompt_template: null
|
| 48 |
+
label_task_col: Value_Type
|
| 49 |
+
degrader_type_col: null
|
| 50 |
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default_degrader_type: PROTAC
|
| 51 |
+
include_prompt: false
|
| 52 |
+
is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
+
use_treatment_time: true
|
| 55 |
+
batch_size: 32
|
| 56 |
+
num_workers: 0
|
| 57 |
+
num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=6_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:e169a517b2287d1556a88aac032bf0b79c3d9a7e03a0002d6d01e71113144683
|
| 3 |
+
size 169233
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=7_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
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|
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|
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|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
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|
|
|
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|
|
|
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|
|
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|
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|
|
|
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|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
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|
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|
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|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
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ligase_col: Ligase_Name
|
| 3 |
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ligase_sequence_col: Ligase_Sequence
|
| 4 |
+
poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
+
standardize_labels: false
|
| 16 |
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impute_labels: true
|
| 17 |
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fp_size: 512
|
| 18 |
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radius: 16
|
| 19 |
+
use_fingerprints: false
|
| 20 |
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use_descriptors: true
|
| 21 |
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use_relevant_descriptors: false
|
| 22 |
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selected_descriptors: null
|
| 23 |
+
use_poi_sequence_embedding: true
|
| 24 |
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use_poi_name_embedding: false
|
| 25 |
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use_ligase_name_embedding: true
|
| 26 |
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use_poi_precomputed_embedding: false
|
| 27 |
+
use_ligase_precomputed_embedding: false
|
| 28 |
+
poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
+
poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
+
ligase_embeddings_per_residue: true
|
| 36 |
+
ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
+
use_cell_description_embedding: true
|
| 43 |
+
use_cell_name_embedding: false
|
| 44 |
+
use_tokenizer: false
|
| 45 |
+
tokenizer_name: google-bert/bert-base-cased
|
| 46 |
+
max_length: 512
|
| 47 |
+
prompt_template: null
|
| 48 |
+
label_task_col: Value_Type
|
| 49 |
+
degrader_type_col: null
|
| 50 |
+
default_degrader_type: PROTAC
|
| 51 |
+
include_prompt: false
|
| 52 |
+
is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
+
use_treatment_time: true
|
| 55 |
+
batch_size: 32
|
| 56 |
+
num_workers: 0
|
| 57 |
+
num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=7_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:382fbf3752c6439f532d687aac02d4dcc589bac663c63bc70c45805e2f68ff28
|
| 3 |
+
size 169233
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=8_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
+
ligase_col: Ligase_Name
|
| 3 |
+
ligase_sequence_col: Ligase_Sequence
|
| 4 |
+
poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
+
standardize_labels: false
|
| 16 |
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impute_labels: true
|
| 17 |
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fp_size: 512
|
| 18 |
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radius: 16
|
| 19 |
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use_fingerprints: false
|
| 20 |
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use_descriptors: true
|
| 21 |
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use_relevant_descriptors: false
|
| 22 |
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selected_descriptors: null
|
| 23 |
+
use_poi_sequence_embedding: true
|
| 24 |
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use_poi_name_embedding: false
|
| 25 |
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use_ligase_name_embedding: true
|
| 26 |
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use_poi_precomputed_embedding: false
|
| 27 |
+
use_ligase_precomputed_embedding: false
|
| 28 |
+
poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
+
poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
+
ligase_embeddings_per_residue: true
|
| 36 |
+
ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
+
use_cell_description_embedding: true
|
| 43 |
+
use_cell_name_embedding: false
|
| 44 |
+
use_tokenizer: false
|
| 45 |
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tokenizer_name: google-bert/bert-base-cased
|
| 46 |
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max_length: 512
|
| 47 |
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prompt_template: null
|
| 48 |
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label_task_col: Value_Type
|
| 49 |
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degrader_type_col: null
|
| 50 |
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default_degrader_type: PROTAC
|
| 51 |
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include_prompt: false
|
| 52 |
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is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
+
use_treatment_time: true
|
| 55 |
+
batch_size: 32
|
| 56 |
+
num_workers: 0
|
| 57 |
+
num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=8_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:4d38b8cd8e34e7729b5ce645f1c6475ac08157b0a3e34d4200383659003e9e5c
|
| 3 |
+
size 169361
|
dmax_best_arch_ensemble/datamodule-data=all_desc_poi_vec_lig_onehot_cell_text_assay_time_norm_labels_Dmax-group=scaffold-fold=9_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
+
ligase_col: Ligase_Name
|
| 3 |
+
ligase_sequence_col: Ligase_Sequence
|
| 4 |
+
poi_col: POI_Name
|
| 5 |
+
poi_sequence_col: POI_Sequence
|
| 6 |
+
cell_line_col: Cell_Line_ID
|
| 7 |
+
assay_type_col: Assay
|
| 8 |
+
treatment_time_col: Assay_Time
|
| 9 |
+
treatment_time_dmax_col: Assay_Time
|
| 10 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- Dmax
|
| 14 |
+
normalize_labels: true
|
| 15 |
+
standardize_labels: false
|
| 16 |
+
impute_labels: true
|
| 17 |
+
fp_size: 512
|
| 18 |
+
radius: 16
|
| 19 |
+
use_fingerprints: false
|
| 20 |
+
use_descriptors: true
|
| 21 |
+
use_relevant_descriptors: false
|
| 22 |
+
selected_descriptors: null
|
| 23 |
+
use_poi_sequence_embedding: true
|
| 24 |
+
use_poi_name_embedding: false
|
| 25 |
+
use_ligase_name_embedding: true
|
| 26 |
+
use_poi_precomputed_embedding: false
|
| 27 |
+
use_ligase_precomputed_embedding: false
|
| 28 |
+
poi_embeddings_file: null
|
| 29 |
+
poi_embeddings_format: npz
|
| 30 |
+
poi_embeddings_per_residue: true
|
| 31 |
+
poi_residue_pooling: sum
|
| 32 |
+
poi_embeddings_id_type: sequence
|
| 33 |
+
ligase_embeddings_file: null
|
| 34 |
+
ligase_embeddings_format: npz
|
| 35 |
+
ligase_embeddings_per_residue: true
|
| 36 |
+
ligase_residue_pooling: sum
|
| 37 |
+
ligase_embeddings_id_type: sequence
|
| 38 |
+
use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
+
use_cell_description_embedding: true
|
| 43 |
+
use_cell_name_embedding: false
|
| 44 |
+
use_tokenizer: false
|
| 45 |
+
tokenizer_name: google-bert/bert-base-cased
|
| 46 |
+
max_length: 512
|
| 47 |
+
prompt_template: null
|
| 48 |
+
label_task_col: Value_Type
|
| 49 |
+
degrader_type_col: null
|
| 50 |
+
default_degrader_type: PROTAC
|
| 51 |
+
include_prompt: false
|
| 52 |
+
is_bert_multitask: false
|
| 53 |
+
use_assay_type_encoding: true
|
| 54 |
+
use_treatment_time: true
|
| 55 |
+
batch_size: 32
|
| 56 |
+
num_workers: 0
|
| 57 |
+
num_proc: 1
|
| 58 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|