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Running
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CPU Upgrade
| # configuration and utilities | |
| hydra-core | |
| pandas==2.0 | |
| # swifter | |
| pandarallel | |
| tensorboard | |
| biopython | |
| apscheduler | |
| tinydb | |
| email-validator | |
| # deep learning | |
| # Install with conda | |
| torch==2.1 | |
| torch_geometric | |
| lightning==2.1 | |
| torchdata==0.7.0 | |
| torchmetrics | |
| transformers | |
| scikit-learn | |
| dgl | |
| dgllife | |
| # model-specific requirements | |
| subword-nmt # MolTrans | |
| tape_proteins # TransformerCPI2 | |
| gensim | |
| fair-esm # CoaDTI-pro | |
| # apex # recommended by TAPE-BERT | |
| # feature extraction | |
| rdkit | |
| py3Dmol | |
| mordred | |
| networkx | |
| mhfp | |
| panel==1.3.6 | |
| bokeh | |
| plotly | |
| seaborn | |
| # tmap |