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# deep learning | |
# Install with conda | |
# torch>=2.0 | |
# torch_geometric | |
lightning>=2.0 | |
torchmetrics | |
transformers | |
scikit-learn | |
dgl | |
dgllife | |
# configuration and utilities | |
hydra-core | |
hydra-colorlog | |
hydra-optuna-sweeper | |
hydra-submitit-launcher | |
pandas | |
pre-commit | |
rich | |
pytest | |
tensorboard | |
# model-specific requirements | |
subword-nmt # MolTrans | |
tape_proteins # TransformerCPI2 | |
fair-esm # CoaDTI-pro | |
# apex # recommended by TAPE-BERT | |
# feature extraction | |
rdkit | |
mordred | |
networkx>=3.0 | |
mhfp | |
# tmap |