├── .gitignore ├── README.md ├── contrastive_learning ├── contra_data.zip ├── contra_dataset.py ├── joint_model.py ├── kgnn.py ├── main.py ├── mgnn.py ├── run.sh └── try.ipynb ├── gode_data.zip ├── k_level_pretrain ├── KData.py ├── KGNN.py ├── __init__.py ├── pretrain.py ├── pretrain.sh └── test.ipynb └── m_level_pretrain_and_fine_tune ├── --features_generator ├── --restart ├── --save_path ├── data_pre.csv ├── exampledata ├── finetune │ ├── bace.csv │ ├── bbbp.csv │ ├── clintox.csv │ ├── esol.csv │ ├── freesolv.csv │ ├── lipo.csv │ ├── qm7.csv │ ├── qm8.csv │ ├── sider.csv │ ├── tox21.csv │ └── toxcast.csv └── pretrain │ ├── tryout.csv │ └── valid_smiles.csv ├── finetune_fg_kge_cls.sh ├── finetune_fg_kge_rgr.sh ├── finetune_fg_kgnn_cls.sh ├── finetune_fg_kgnn_rgr.sh ├── finetune_grover_cls.sh ├── finetune_grover_rgr.sh ├── finetune_kge_cls.sh ├── finetune_kge_rgr.sh ├── finetune_kgnn_3hop_cls.sh ├── finetune_kgnn_3hop_rgr.sh ├── finetune_kgnn_cls.sh ├── finetune_kgnn_no_kge_cls.sh ├── finetune_kgnn_no_kge_rgr.sh ├── finetune_kgnn_rgr.sh ├── fingerprint.sh ├── grover ├── data │ ├── __init__.py │ ├── dist_sampler.py │ ├── groverdataset.py │ ├── moldataset.py │ ├── moldataset_kgnn.py │ ├── molfeaturegenerator.py │ ├── molgraph.py │ ├── scaler.py │ ├── task_labels.py │ └── torchvocab.py ├── model │ ├── layers.py │ └── models.py └── util │ ├── metrics.py │ ├── multi_gpu_wrapper.py │ ├── nn_utils.py │ ├── parsing.py │ ├── scheduler.py │ └── utils.py ├── main.py ├── prepare_kge_emb.ipynb ├── prepare_kgnn_emb.ipynb ├── scripts ├── __init__.py ├── build_vocab.py ├── save_features.py └── split_data.py ├── setup.py └── task ├── __init__.py ├── cross_validate.py ├── cross_validate_kge.py ├── cross_validate_kgnn.py ├── cross_validate_kgnn_static.py ├── fingerprint.py ├── grovertrainer.py ├── predict.py ├── predict_kgnn.py ├── pretrain.py ├── run_evaluation.py ├── train.py ├── train_kge.py ├── train_kgnn.py └── train_kgnn_static.py /.gitignore: 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