├── .dockerignore ├── .gitignore ├── LICENSE ├── README.md ├── conda.yml ├── figures ├── aa_embedding_by_property.pdf ├── aa_embedding_by_property_dendrogram.pdf └── architecture_small.png ├── paccmann_proteomics ├── __init__.py ├── data │ ├── datasets │ │ ├── __init__.py │ │ ├── language_modeling.py │ │ ├── seq_clf.py │ │ └── token_clf.py │ └── processors │ │ ├── __init__.py │ │ ├── lm_utils.py │ │ ├── seq_clf.py │ │ └── seq_clf_utils.py ├── embedding_toolkit.py ├── masked_language_modeling.py ├── run_language_modeling.py ├── run_sequence_classification.py ├── run_token_classification.py └── utils │ └── metrics_clf.py ├── paper └── filipavicius_2020_neurips_mlsb.pdf ├── requirements.txt ├── scripts ├── README.md ├── initialize_longformer_from_roberta.py ├── predict_masked_lm.py ├── run_language_modeling_script.sh ├── run_seq_clf_script.sh ├── run_token_clf_script.sh ├── train_byte_level_bpe.py ├── train_char_level_bpe.py ├── train_sentencepiece.py └── train_wordpiece.py ├── setup.py 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