├── .gitignore ├── LICENSE ├── README.md ├── ckpt ├── pretrained_gcn │ └── checkpoints │ │ └── model.pth └── pretrained_gin │ └── checkpoints │ └── model.pth ├── config.yaml ├── config_finetune.yaml ├── dataset ├── dataset.py ├── dataset_mix.py ├── dataset_subgraph.py └── dataset_test.py ├── figs └── pipeline.gif ├── finetune.py ├── models ├── gcn_finetune.py ├── gcn_molclr.py ├── ginet_finetune.py └── ginet_molclr.py ├── molclr.py └── utils └── nt_xent.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/README.md -------------------------------------------------------------------------------- /ckpt/pretrained_gcn/checkpoints/model.pth: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/ckpt/pretrained_gcn/checkpoints/model.pth -------------------------------------------------------------------------------- /ckpt/pretrained_gin/checkpoints/model.pth: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/ckpt/pretrained_gin/checkpoints/model.pth -------------------------------------------------------------------------------- /config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/config.yaml -------------------------------------------------------------------------------- /config_finetune.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/config_finetune.yaml -------------------------------------------------------------------------------- /dataset/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/dataset/dataset.py -------------------------------------------------------------------------------- /dataset/dataset_mix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/dataset/dataset_mix.py -------------------------------------------------------------------------------- /dataset/dataset_subgraph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/dataset/dataset_subgraph.py -------------------------------------------------------------------------------- /dataset/dataset_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/dataset/dataset_test.py -------------------------------------------------------------------------------- /figs/pipeline.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/figs/pipeline.gif -------------------------------------------------------------------------------- /finetune.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/finetune.py -------------------------------------------------------------------------------- /models/gcn_finetune.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/models/gcn_finetune.py -------------------------------------------------------------------------------- /models/gcn_molclr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/models/gcn_molclr.py -------------------------------------------------------------------------------- /models/ginet_finetune.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/models/ginet_finetune.py -------------------------------------------------------------------------------- /models/ginet_molclr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/models/ginet_molclr.py -------------------------------------------------------------------------------- /molclr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/molclr.py -------------------------------------------------------------------------------- /utils/nt_xent.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yuyangw/MolCLR/HEAD/utils/nt_xent.py --------------------------------------------------------------------------------