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- dc50_best_arch_ensemble/best_config-model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-task=dc50-group=scaffold.yaml +22 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=0_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=0_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=10_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=10_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=11_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=11_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=12_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=12_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=13_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=13_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=14_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=14_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=15_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=15_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=16_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=16_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=17_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=17_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=18_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=18_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=19_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=19_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=1_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=1_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=20_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=20_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=21_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=21_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=22_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=22_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=23_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=23_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=24_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=24_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=2_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=2_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=3_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=3_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=4_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=4_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=5_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=5_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=6_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=6_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=7_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=7_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=8_hparams.yaml +60 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=8_state.pt +3 -0
- dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=9_hparams.yaml +60 -0
dc50_best_arch_ensemble/best_config-model=mlp_dc50_protac-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-task=dc50-group=scaffold.yaml
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model_config:
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learning_rate: 0.0007485278176691929
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hidden_dim:
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- 256
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head_depth: 1
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dropout: 0.0
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head_dropout: 0.1
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task_type: point
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lr_scheduler_type: reduce_on_plateau
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warmup_ratio: 0.0
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norm_type: layer
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activation: relu
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input_dim: 509
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training_config:
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max_epochs: 200
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gradient_clip_val: 1.0
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enable_checkpointing: true
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enable_progress_bar: false
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enable_model_summary: true
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accelerator: auto
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devices: 1
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precision: 16-mixed
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dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=0_hparams.yaml
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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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| 11 |
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treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
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labels:
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- DC50
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| 14 |
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normalize_labels: true
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| 15 |
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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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| 18 |
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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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| 23 |
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use_poi_sequence_embedding: false
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| 24 |
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use_poi_name_embedding: true
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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: false
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| 43 |
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use_cell_name_embedding: true
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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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| 56 |
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num_workers: 0
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| 57 |
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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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dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=0_state.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:2cbee6d87a1698c39cb2896ccd26d43633122a1977deb14e45caa6093cd7d78c
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| 3 |
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size 164527
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dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=10_hparams.yaml
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smiles_col: SMILES
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| 2 |
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ligase_col: Ligase_Name
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| 3 |
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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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| 5 |
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poi_sequence_col: POI_Sequence
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| 6 |
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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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| 12 |
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labels:
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| 13 |
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- DC50
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| 14 |
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normalize_labels: true
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| 15 |
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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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| 18 |
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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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| 23 |
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use_poi_sequence_embedding: false
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| 24 |
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use_poi_name_embedding: true
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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
|
| 33 |
+
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
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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
|
| 40 |
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use_ligase_pca: false
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| 41 |
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ligase_pca_n_components: null
|
| 42 |
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use_cell_description_embedding: false
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| 43 |
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use_cell_name_embedding: true
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| 44 |
+
use_tokenizer: false
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| 45 |
+
tokenizer_name: google-bert/bert-base-cased
|
| 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
|
| 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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| 58 |
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verbose: 0
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| 59 |
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sort_features: true
|
| 60 |
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categorical_encoding: onehot
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=10_state.pt
ADDED
|
@@ -0,0 +1,3 @@
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|
|
|
|
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|
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|
|
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|
| 1 |
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version https://git-lfs.github.com/spec/v1
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oid sha256:27f73287b64adf1bd821daccc230c4b69c0ab2f462b4ff639d219e5283f85cea
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| 3 |
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size 164533
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=11_hparams.yaml
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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|
|
|
|
|
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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 |
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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
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| 5 |
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poi_sequence_col: POI_Sequence
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| 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
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| 9 |
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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)
|
| 12 |
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labels:
|
| 13 |
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- DC50
|
| 14 |
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| 18 |
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radius: 16
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| 19 |
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| 22 |
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| 23 |
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|
| 24 |
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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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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: false
|
| 43 |
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use_cell_name_embedding: true
|
| 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
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| 47 |
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| 48 |
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label_task_col: Value_Type
|
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|
| 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 |
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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
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=11_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
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|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:6842739643150101b82136db268accc6c15961e9c8f059649babb12dc5d75aa0
|
| 3 |
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size 164725
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=12_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
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| 1 |
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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
|
| 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 |
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treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
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labels:
|
| 13 |
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- DC50
|
| 14 |
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| 15 |
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| 16 |
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| 17 |
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| 18 |
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| 19 |
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| 22 |
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|
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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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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: false
|
| 43 |
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use_cell_name_embedding: true
|
| 44 |
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|
| 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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degrader_type_col: null
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|
| 51 |
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include_prompt: false
|
| 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 |
+
verbose: 0
|
| 59 |
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sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=12_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:38b31a192842eaacb08d24a50c5b00bd3eaa5e2b4a81655e02f78c1ba0b59aab
|
| 3 |
+
size 164277
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=13_hparams.yaml
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
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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 |
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treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
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labels:
|
| 13 |
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- DC50
|
| 14 |
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|
| 15 |
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|
| 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 |
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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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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: false
|
| 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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max_length: 512
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| 47 |
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|
| 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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|
| 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
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=13_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:889528f14f5c53f64a764a17120c9de3afc5c362d2b997b8c01f53361f875086
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| 3 |
+
size 164469
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=14_hparams.yaml
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 |
+
- DC50
|
| 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 |
+
use_poi_sequence_embedding: false
|
| 24 |
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use_poi_name_embedding: true
|
| 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 |
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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 |
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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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| 41 |
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ligase_pca_n_components: null
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| 42 |
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|
| 43 |
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use_cell_name_embedding: true
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| 44 |
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use_tokenizer: false
|
| 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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| 48 |
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label_task_col: Value_Type
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| 53 |
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| 54 |
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| 55 |
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|
| 56 |
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num_workers: 0
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| 57 |
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num_proc: 1
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verbose: 0
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| 59 |
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sort_features: true
|
| 60 |
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categorical_encoding: onehot
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=14_state.pt
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
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version https://git-lfs.github.com/spec/v1
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oid sha256:e034797f28804fb7d7819d8fd8d3c45d409fa026646c25788649b167c9286ca1
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| 3 |
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size 164533
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dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=15_hparams.yaml
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
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ligase_sequence_col: Ligase_Sequence
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poi_col: POI_Name
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| 5 |
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| 6 |
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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)
|
| 12 |
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labels:
|
| 13 |
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- DC50
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| 14 |
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fp_size: 512
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| 18 |
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radius: 16
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| 19 |
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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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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
|
| 41 |
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ligase_pca_n_components: null
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| 42 |
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use_cell_description_embedding: false
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| 43 |
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use_cell_name_embedding: true
|
| 44 |
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use_tokenizer: false
|
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tokenizer_name: google-bert/bert-base-cased
|
| 46 |
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max_length: 512
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label_task_col: Value_Type
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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
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| 56 |
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num_workers: 0
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| 57 |
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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
|
| 60 |
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categorical_encoding: onehot
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=15_state.pt
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
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version https://git-lfs.github.com/spec/v1
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oid sha256:8ab45bec692bdeac8ac9224930401271537d061fe65bf17b1d34e509f28a2c7f
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| 3 |
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size 164405
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dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=16_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
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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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| 5 |
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poi_sequence_col: POI_Sequence
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| 6 |
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cell_line_col: Cell_Line_ID
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assay_type_col: Assay
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| 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 |
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treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
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labels:
|
| 13 |
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- DC50
|
| 14 |
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| 15 |
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| 16 |
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|
| 17 |
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|
| 18 |
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| 19 |
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| 20 |
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| 27 |
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use_ligase_precomputed_embedding: false
|
| 28 |
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poi_embeddings_file: null
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| 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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use_poi_pca: false
|
| 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
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| 42 |
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|
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| 44 |
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use_tokenizer: false
|
| 45 |
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tokenizer_name: google-bert/bert-base-cased
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label_task_col: Value_Type
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|
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use_assay_type_encoding: true
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batch_size: 32
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num_workers: 0
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| 57 |
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num_proc: 1
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verbose: 0
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| 59 |
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sort_features: true
|
| 60 |
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categorical_encoding: onehot
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=16_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
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|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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oid sha256:a1b1a7285037227eb64829125999f1535444935dcc2eda19cb1b55fc439917cd
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| 3 |
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size 164597
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=17_hparams.yaml
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
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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
|
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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 |
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treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
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labels:
|
| 13 |
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- DC50
|
| 14 |
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normalize_labels: true
|
| 15 |
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|
| 16 |
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|
| 17 |
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fp_size: 512
|
| 18 |
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|
| 19 |
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|
| 22 |
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|
| 24 |
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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 |
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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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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
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| 42 |
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|
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tokenizer_name: google-bert/bert-base-cased
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| 46 |
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| 48 |
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label_task_col: Value_Type
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|
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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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num_workers: 0
|
| 57 |
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num_proc: 1
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verbose: 0
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| 59 |
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sort_features: true
|
| 60 |
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categorical_encoding: onehot
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=17_state.pt
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:e51d09d134f771113e612b23c0fa603a92faa4fbbbd55927b1b1d46e90b055e9
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| 3 |
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size 164469
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dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=18_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
|
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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 |
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treatment_time_dc50_col: Assay_Time
|
| 11 |
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treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
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labels:
|
| 13 |
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- DC50
|
| 14 |
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|
| 15 |
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|
| 16 |
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| 17 |
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| 18 |
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| 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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|
| 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 |
+
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 |
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ligase_pca_n_components: null
|
| 42 |
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use_cell_description_embedding: false
|
| 43 |
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use_cell_name_embedding: true
|
| 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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|
| 48 |
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label_task_col: Value_Type
|
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|
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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 |
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sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=18_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
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|
|
|
|
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|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:ebadedee8a424dca40477dad09b0c5668cb21086b5e4018ba51497bbe1b6900a
|
| 3 |
+
size 164341
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=19_hparams.yaml
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 |
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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 |
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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 |
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treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- DC50
|
| 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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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: false
|
| 24 |
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use_poi_name_embedding: true
|
| 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 |
+
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 |
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use_ligase_pca: false
|
| 41 |
+
ligase_pca_n_components: null
|
| 42 |
+
use_cell_description_embedding: false
|
| 43 |
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use_cell_name_embedding: true
|
| 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
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=19_state.pt
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:f6c4d24355023ef142adecbd50b5cee3599da96801eea1e50ff376fd333cda15
|
| 3 |
+
size 164469
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=1_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
|
|
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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 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- DC50
|
| 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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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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|
| 24 |
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use_poi_name_embedding: true
|
| 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 |
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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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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: false
|
| 43 |
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use_cell_name_embedding: true
|
| 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 |
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verbose: 0
|
| 59 |
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sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=1_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:2d092dde180e964b979b0d6854cd724ba7d2ac89dc01990be3567c27833aafd3
|
| 3 |
+
size 164591
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=20_hparams.yaml
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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|
|
|
|
|
|
|
|
|
| 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 |
+
- DC50
|
| 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: false
|
| 24 |
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use_poi_name_embedding: true
|
| 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 |
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use_cell_description_embedding: false
|
| 43 |
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use_cell_name_embedding: true
|
| 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
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=20_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:d8a701c5d7110e3daf1f0a2d75491e2a7c8f0badace9510758a8f5946d12a763
|
| 3 |
+
size 164661
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=21_hparams.yaml
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 |
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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 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- DC50
|
| 14 |
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normalize_labels: true
|
| 15 |
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|
| 16 |
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|
| 17 |
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|
| 18 |
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| 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 |
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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 |
+
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: false
|
| 43 |
+
use_cell_name_embedding: true
|
| 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 |
+
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 |
+
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
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=21_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:55593c6ba1509655fec879f4e21511aa54f32cf0875b3ce616ad593d6da666d2
|
| 3 |
+
size 164469
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=22_hparams.yaml
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 |
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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 |
+
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 |
+
- DC50
|
| 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 |
+
use_poi_sequence_embedding: false
|
| 24 |
+
use_poi_name_embedding: true
|
| 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: false
|
| 43 |
+
use_cell_name_embedding: true
|
| 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
|
| 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
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=22_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:ce312732dbb919a9a289cb6d7bac7048a515fa1d5947380c1b7d94cfeb361c79
|
| 3 |
+
size 164469
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=23_hparams.yaml
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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|
|
|
|
|
|
|
|
|
|
|
|
|
| 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 |
+
- DC50
|
| 14 |
+
normalize_labels: true
|
| 15 |
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standardize_labels: false
|
| 16 |
+
impute_labels: true
|
| 17 |
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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: false
|
| 24 |
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use_poi_name_embedding: true
|
| 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: false
|
| 43 |
+
use_cell_name_embedding: true
|
| 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
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=23_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:73581bd6112b82411356bf6bd8c4276347d50699c0e7d82f33a65bf15041b706
|
| 3 |
+
size 164213
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=24_hparams.yaml
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 |
+
- DC50
|
| 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: false
|
| 24 |
+
use_poi_name_embedding: true
|
| 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: false
|
| 43 |
+
use_cell_name_embedding: true
|
| 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
|
| 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
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=24_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
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|
| 1 |
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version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:fdce4d615a7aba08ba30453aac46238c3f372945a86b1f53f053622a00ef5d47
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| 3 |
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size 164597
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dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=2_hparams.yaml
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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|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
+
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 |
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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 |
+
- DC50
|
| 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
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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
|
| 22 |
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selected_descriptors: null
|
| 23 |
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use_poi_sequence_embedding: false
|
| 24 |
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use_poi_name_embedding: true
|
| 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 |
+
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 |
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use_poi_pca: false
|
| 39 |
+
poi_pca_n_components: null
|
| 40 |
+
use_ligase_pca: false
|
| 41 |
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ligase_pca_n_components: null
|
| 42 |
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use_cell_description_embedding: false
|
| 43 |
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use_cell_name_embedding: true
|
| 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
|
| 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 |
+
verbose: 0
|
| 59 |
+
sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=2_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:646473aa2c5aa682b5e2f3e813daed111e6178f18f6fe00d8a620eda877d0ee7
|
| 3 |
+
size 164463
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=3_hparams.yaml
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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|
| 1 |
+
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 |
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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 |
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treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- DC50
|
| 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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use_relevant_descriptors: false
|
| 22 |
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selected_descriptors: null
|
| 23 |
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use_poi_sequence_embedding: false
|
| 24 |
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use_poi_name_embedding: true
|
| 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 |
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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 |
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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 |
+
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 |
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ligase_pca_n_components: null
|
| 42 |
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use_cell_description_embedding: false
|
| 43 |
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use_cell_name_embedding: true
|
| 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 |
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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
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=3_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:7ee0a67b811502da1e0f43c308a182cb6ab40e00ada2397cf9d37578844ed60d
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| 3 |
+
size 164399
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=4_hparams.yaml
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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|
|
|
| 1 |
+
smiles_col: SMILES
|
| 2 |
+
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 |
+
treatment_time_dc50_col: Assay_Time
|
| 11 |
+
treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
+
labels:
|
| 13 |
+
- DC50
|
| 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: false
|
| 24 |
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use_poi_name_embedding: true
|
| 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 |
+
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 |
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ligase_pca_n_components: null
|
| 42 |
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use_cell_description_embedding: false
|
| 43 |
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use_cell_name_embedding: true
|
| 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
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=4_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:3ec0db035fdfa5597e043f22785ceca028050a30fcf89847979d08cdff55954e
|
| 3 |
+
size 164335
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=5_hparams.yaml
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 |
+
- DC50
|
| 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: false
|
| 24 |
+
use_poi_name_embedding: true
|
| 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: false
|
| 43 |
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use_cell_name_embedding: true
|
| 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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|
| 47 |
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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
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| 54 |
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| 55 |
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batch_size: 32
|
| 56 |
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num_workers: 0
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| 57 |
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| 58 |
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verbose: 0
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| 59 |
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sort_features: true
|
| 60 |
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categorical_encoding: onehot
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=5_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
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|
|
|
|
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|
| 1 |
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version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:d9bcc01ad91f4c46feba71f065767eeed083fc823d6c99a1f965751649076271
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| 3 |
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size 164527
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=6_hparams.yaml
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 |
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smiles_col: SMILES
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| 2 |
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ligase_col: Ligase_Name
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| 3 |
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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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| 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
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| 9 |
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treatment_time_dmax_col: Assay_Time
|
| 10 |
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treatment_time_dc50_col: Assay_Time
|
| 11 |
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treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
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labels:
|
| 13 |
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- DC50
|
| 14 |
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fp_size: 512
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| 18 |
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radius: 16
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| 19 |
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| 23 |
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|
| 24 |
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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 |
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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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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: false
|
| 43 |
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use_cell_name_embedding: true
|
| 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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| 48 |
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label_task_col: Value_Type
|
| 49 |
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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 |
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verbose: 0
|
| 59 |
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sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=6_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
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|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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oid sha256:5fff3de2c6222914ff5960fb616ad94b48f5b8b26d5688333bc3a0a4e9d50170
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| 3 |
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size 164399
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=7_hparams.yaml
ADDED
|
@@ -0,0 +1,60 @@
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| 1 |
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smiles_col: SMILES
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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 |
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treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
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labels:
|
| 13 |
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- DC50
|
| 14 |
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|
| 15 |
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| 16 |
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| 17 |
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|
| 18 |
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|
| 19 |
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| 20 |
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|
| 22 |
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| 23 |
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|
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|
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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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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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|
| 43 |
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|
| 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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| 48 |
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label_task_col: Value_Type
|
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|
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|
| 53 |
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use_assay_type_encoding: true
|
| 54 |
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|
| 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 |
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categorical_encoding: onehot
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=7_state.pt
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:b3a39aba80bc245929c05947000682cd53f917bc801d709350b60388cee5d94f
|
| 3 |
+
size 164591
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=8_hparams.yaml
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
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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 |
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treatment_time_ic50_col: Treatment Time (h) (Cellular activities, IC50)
|
| 12 |
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labels:
|
| 13 |
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- DC50
|
| 14 |
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|
| 15 |
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|
| 16 |
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impute_labels: true
|
| 17 |
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fp_size: 512
|
| 18 |
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|
| 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 |
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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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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: false
|
| 43 |
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use_cell_name_embedding: true
|
| 44 |
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|
| 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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|
| 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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|
| 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 |
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sort_features: true
|
| 60 |
+
categorical_encoding: onehot
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=8_state.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:49e39dc8c01636473201b26350131d187f9bf2e5c4fc890bc0fa0457440c8853
|
| 3 |
+
size 164655
|
dc50_best_arch_ensemble/datamodule-data=all_desc_poi_onehot_lig_onehot_cell_onehot_assay_time_norm_labels_DC50-group=scaffold-fold=9_hparams.yaml
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 |
+
- DC50
|
| 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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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: false
|
| 24 |
+
use_poi_name_embedding: true
|
| 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: false
|
| 43 |
+
use_cell_name_embedding: true
|
| 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
|