├── .github └── workflows │ └── comment_bot.yml ├── .gitignore ├── LICENSE.md ├── README.md ├── docs └── CONTRIBUTING.md ├── protein_lm.yml ├── protein_lm ├── __init__.py ├── configs │ └── train │ │ ├── toy_hf.yaml │ │ └── toy_localcsv.yaml ├── dataset │ ├── __init__.py │ ├── cluster_dataset.py │ └── uniref │ │ └── uniref50_trimmed.csv ├── evaluation │ ├── __init__.py │ ├── scripts.py │ │ ├── download_proteingym_data.py │ │ ├── fitness_supervised.py │ │ ├── fitness_zero_shot_AR.py │ │ └── fitness_zero_shot_ESM.py │ └── scripts │ │ ├── Protein-gym.py │ │ ├── contact_prediction.py │ │ └── utils.py ├── modeling │ ├── __init__.py │ ├── getters │ │ ├── __init__.py │ │ ├── data_collator.py │ │ ├── dataset.py │ │ ├── model.py │ │ ├── tokenizer.py │ │ ├── training_args.py │ │ └── wandb_log.py │ ├── models │ │ ├── __init__.py │ │ └── apt │ │ │ ├── __init__.py │ │ │ ├── config.py │ │ │ └── model_pytorch.py │ ├── scripts │ │ └── train.py │ └── utils │ │ ├── __init__.py │ │ ├── alibi_embedding.py │ │ ├── modules.py │ │ ├── rerope_embedding.py │ │ ├── rotary_embedding.py │ │ └── scaled_rope_embedding.py ├── tests │ ├── tensors │ │ ├── 1a3a.pkl │ │ ├── 1xcr.pkl │ │ ├── 5ahw.pkl │ │ ├── 5ahw_1_A_jacobian.pkl │ │ ├── dynamic_rope.pkl │ │ ├── linear_rope.pkl │ │ ├── rerope.pkl │ │ └── rope.pkl │ ├── test_attention.py │ ├── test_cl.py │ ├── test_cl_continuous.py │ ├── test_contact_prediction.py │ ├── test_data │ │ ├── 1a3a_1_A.a3m │ │ ├── 1xcr_1_A.a3m │ │ └── 5ahw_1_A.a3m │ ├── test_encoding.py │ └── test_tokenizer.py └── tokenizer │ ├── __init__.py │ ├── rust_trie │ ├── .github │ │ └── workflows │ │ │ └── CI.yml │ ├── .gitignore │ ├── Cargo.toml │ ├── pyproject.toml │ └── src │ │ └── lib.rs │ └── tokenizer.py ├── protein_lm_cuda.yml └── setup.py /.github/workflows/comment_bot.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OpenBioML/protein-lm-scaling/HEAD/.github/workflows/comment_bot.yml 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