├── .gitignore ├── LICENSE ├── README.md ├── ckpt └── gin_concat_R1000_E8000_lambda0.0001 │ └── checkpoints │ └── config.yaml ├── config.yaml ├── config_finetune.yaml ├── config_ml.yaml ├── config_representation.yaml ├── data ├── benchmark_data └── pubchem_data │ └── pubchem_100k_random.txt ├── dataset ├── dataset_representation.py ├── dataset_subgraph.py └── dataset_test.py ├── environment.yaml ├── examine_representation.ipynb ├── finetune.py ├── finetune_object.py ├── gather_representation.py ├── loss_function └── btwins.py ├── models ├── gcn_concat.py ├── gcn_concat_finetune.py ├── gcn_noconcat.py ├── gcn_noconcat_finetune.py ├── gin_molclr.py ├── ginet_concat.py ├── ginet_concat_finetune.py ├── ginet_noconcat.py ├── ginet_noconcat_finetune.py └── ml_params.py ├── pretrain.py └── train_ml.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/README.md -------------------------------------------------------------------------------- /ckpt/gin_concat_R1000_E8000_lambda0.0001/checkpoints/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/ckpt/gin_concat_R1000_E8000_lambda0.0001/checkpoints/config.yaml -------------------------------------------------------------------------------- /config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/config.yaml -------------------------------------------------------------------------------- /config_finetune.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/config_finetune.yaml -------------------------------------------------------------------------------- /config_ml.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/config_ml.yaml -------------------------------------------------------------------------------- /config_representation.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/config_representation.yaml -------------------------------------------------------------------------------- /data/benchmark_data: -------------------------------------------------------------------------------- 1 | ../../MolCLR/data/ -------------------------------------------------------------------------------- /data/pubchem_data/pubchem_100k_random.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/data/pubchem_data/pubchem_100k_random.txt -------------------------------------------------------------------------------- /dataset/dataset_representation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/dataset/dataset_representation.py -------------------------------------------------------------------------------- /dataset/dataset_subgraph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/dataset/dataset_subgraph.py -------------------------------------------------------------------------------- /dataset/dataset_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/dataset/dataset_test.py -------------------------------------------------------------------------------- /environment.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/environment.yaml -------------------------------------------------------------------------------- /examine_representation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/examine_representation.ipynb -------------------------------------------------------------------------------- /finetune.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/finetune.py -------------------------------------------------------------------------------- /finetune_object.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/finetune_object.py -------------------------------------------------------------------------------- /gather_representation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/gather_representation.py -------------------------------------------------------------------------------- /loss_function/btwins.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/loss_function/btwins.py -------------------------------------------------------------------------------- /models/gcn_concat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/models/gcn_concat.py -------------------------------------------------------------------------------- /models/gcn_concat_finetune.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/models/gcn_concat_finetune.py -------------------------------------------------------------------------------- /models/gcn_noconcat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/models/gcn_noconcat.py -------------------------------------------------------------------------------- /models/gcn_noconcat_finetune.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/models/gcn_noconcat_finetune.py -------------------------------------------------------------------------------- /models/gin_molclr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/models/gin_molclr.py -------------------------------------------------------------------------------- /models/ginet_concat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/models/ginet_concat.py -------------------------------------------------------------------------------- /models/ginet_concat_finetune.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/models/ginet_concat_finetune.py -------------------------------------------------------------------------------- /models/ginet_noconcat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/models/ginet_noconcat.py -------------------------------------------------------------------------------- /models/ginet_noconcat_finetune.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/models/ginet_noconcat_finetune.py -------------------------------------------------------------------------------- /models/ml_params.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/models/ml_params.py -------------------------------------------------------------------------------- /pretrain.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/pretrain.py -------------------------------------------------------------------------------- /train_ml.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rolayoalarcon/MolE/HEAD/train_ml.py --------------------------------------------------------------------------------