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| # deep learning | |
| # Install with conda | |
| torch>=2.1.0 | |
| torch_geometric | |
| lightning>=2.1.0 | |
| torchmetrics | |
| transformers | |
| scikit-learn | |
| dgl | |
| dglgo | |
| dgllife | |
| # configuration and utilities | |
| hydra-core | |
| # hydra-colorlog | |
| # hydra-optuna-sweeper | |
| # hydra-submitit-launcher | |
| pandas | |
| swifter | |
| # pre-commit | |
| # rich | |
| # pytest | |
| # tensorboard | |
| # feature extraction | |
| biopython | |
| rdkit | |
| networkx>=3.2.0 | |
| mhfp | |
| # tmap | |
| # model-specific requirements | |
| # subword-nmt # MONN | |
| tape_proteins # TransformerCPI2 | |
| gensim # TransformerCPI | |
| fair-esm # CoaDTI-pro | |
| # apex # recommended by TAPE-BERT | |
| # data visualization utilities | |
| seaborn | |
| plotly |