├── LICENSE ├── README.md ├── datasets ├── README.md └── dti_datasets │ ├── davis │ ├── preprocess.out │ └── preprocess.py │ └── kiba │ ├── preprocess.out │ └── preprocess.py ├── fig ├── baselines.png └── pipeline.png ├── legacy └── src_classification │ ├── pretrain_3D_hybrid_02.py │ ├── pretrain_3D_hybrid_03.py │ ├── run_pretrain_3D_hybrid_02.sh │ └── run_pretrain_3D_hybrid_03.sh ├── scripts_classification ├── run_fine_tuning_model.sh ├── submit_fine_tuning.sh ├── submit_pre_training_GraphMVP.sh ├── submit_pre_training_GraphMVP_hybrid.sh └── submit_pre_training_baselines.sh ├── scripts_regression ├── run_fine_tuning_model.sh ├── run_fine_tuning_model_DTI.sh ├── submit_fine_tuning.sh ├── submit_pre_training_GraphMVP.sh ├── submit_pre_training_GraphMVP_hybrid.sh └── submit_pre_training_baselines.sh ├── src_classification ├── GEOM_dataset_preparation.py ├── batch.py ├── config.py ├── dataloader.py ├── datasets │ ├── __init__.py │ ├── datasets_GPT.py │ ├── molecule_3D_dataset.py │ ├── molecule_3D_masking_dataset.py │ ├── molecule_contextual_datasets.py │ ├── molecule_contextual_datasets_utils.py │ ├── molecule_datasets.py │ ├── molecule_graphcl_dataset.py │ ├── molecule_graphcl_masking_dataset.py │ └── molecule_motif_datasets.py ├── models │ ├── __init__.py │ ├── auto_encoder.py │ ├── dti_model.py │ ├── molecule_gnn_model.py │ └── schnet.py ├── molecule_finetune.py ├── pretrain_AM.py ├── pretrain_CP.py ├── pretrain_Contextual.py ├── pretrain_EP.py ├── pretrain_GPT_GNN.py ├── pretrain_GraphCL.py ├── pretrain_GraphLoG.py ├── pretrain_GraphMVP.py ├── pretrain_GraphMVP_hybrid.py ├── pretrain_IG.py ├── pretrain_JOAO.py ├── pretrain_JOAOv2.py ├── pretrain_Motif.py ├── run_molecule_finetune.sh ├── run_pretrain_AM.sh ├── run_pretrain_CP.sh ├── run_pretrain_Contextual.sh ├── run_pretrain_EP.sh ├── run_pretrain_GPT_GNN.sh ├── run_pretrain_GraphCL.sh ├── run_pretrain_GraphLoG.sh ├── run_pretrain_GraphMVP.sh ├── run_pretrain_GraphMVP_hybrid.sh ├── run_pretrain_IG.sh ├── run_pretrain_JOAO.sh ├── run_pretrain_JOAOv2.sh ├── run_pretrain_Motif.sh ├── splitters.py └── util.py └── src_regression ├── GEOM_dataset_preparation.py ├── datasets_complete_feature ├── __init__.py ├── dti_datasets.py ├── molecule_datasets.py └── molecule_graphcl_dataset.py ├── dti_finetune.py ├── models_complete_feature ├── __init__.py └── molecule_gnn_model.py ├── molecule_finetune_regression.py ├── pretrain_AM.py ├── pretrain_CP.py ├── pretrain_GraphCL.py ├── pretrain_GraphMVP.py ├── pretrain_GraphMVP_hybrid.py ├── pretrain_JOAO.py ├── pretrain_JOAOv2.py ├── run_dti_finetune.sh ├── run_molecule_finetune_regression.sh ├── run_pretrain_AM.sh ├── run_pretrain_CP.sh ├── run_pretrain_GraphCL.sh ├── run_pretrain_GraphMVP.sh ├── run_pretrain_GraphMVP_hybrid.sh ├── run_pretrain_JOAO.sh ├── run_pretrain_JOAOv2.sh └── util_complete_feature.py /LICENSE: -------------------------------------------------------------------------------- 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