├── .gitignore ├── LICENSE ├── README.md ├── config ├── data │ ├── embedding.json │ ├── fluorescence.json │ ├── homology.json │ ├── localization.json │ ├── pfam_p-elmo.json │ ├── pfam_plus-rnn.json │ ├── pfam_plus-tfm.json │ ├── secstr.json │ ├── solubility.json │ ├── stability.json │ └── transmembrane.json ├── model │ ├── p-elmo.json │ ├── p-elmo_fluorescence_pr.json │ ├── p-elmo_lm.json │ ├── p-elmo_localization_pr.json │ ├── p-elmo_secstr_pr.json │ ├── p-elmo_solubility_pr.json │ ├── p-elmo_stability_pr.json │ ├── p-elmo_transmembrane_pr.json │ ├── plus-rnn_base.json │ ├── plus-rnn_base_fluorescence_pr.json │ ├── plus-rnn_base_localization_pr.json │ ├── plus-rnn_base_secstr_pr.json │ ├── plus-rnn_base_solubility_pr.json │ ├── plus-rnn_base_stability_pr.json │ ├── plus-rnn_base_transmembrane_pr.json │ ├── plus-rnn_large.json │ ├── plus-rnn_large_fluorescence_pr.json │ ├── plus-rnn_large_localization_pr.json │ ├── plus-rnn_large_secstr_pr.json │ ├── plus-rnn_large_solubility_pr.json │ ├── plus-rnn_large_stability_pr.json │ ├── plus-rnn_large_transmembrane_pr.json │ ├── plus-tfm.json │ └── rnn_pr_cands │ │ ├── rnn_pr1.json │ │ ├── rnn_pr2.json │ │ ├── rnn_pr3.json │ │ └── rnn_pr4.json └── run │ ├── embedding.json │ ├── p-elmo_fluorescence.json │ ├── p-elmo_homology.json │ ├── p-elmo_localization.json │ ├── p-elmo_pfam.json │ ├── p-elmo_secstr.json │ ├── p-elmo_solubility.json │ ├── p-elmo_stability.json │ ├── p-elmo_transmembrane.json │ ├── plus-rnn_base_fluorescence.json │ ├── plus-rnn_base_homology.json │ ├── plus-rnn_base_localization.json │ ├── plus-rnn_base_pfam.json │ ├── plus-rnn_base_secstr.json │ ├── plus-rnn_base_solubility.json │ ├── plus-rnn_base_stability.json │ ├── plus-rnn_base_transmembrane.json │ ├── plus-rnn_large_fluorescence.json │ ├── plus-rnn_large_homology.json │ ├── plus-rnn_large_localization.json │ ├── plus-rnn_large_pfam.json │ ├── plus-rnn_large_secstr.json │ ├── plus-rnn_large_solubility.json │ ├── plus-rnn_large_stability.json │ ├── plus-rnn_large_transmembrane.json │ ├── plus-tfm_homology.json │ ├── plus-tfm_others.json │ ├── plus-tfm_pfam.json │ └── rnn_pr_cands │ ├── rnn_pr1.json │ ├── rnn_pr2.json │ ├── rnn_pr3.json │ └── rnn_pr4.json ├── eval_plus_fluorescence.py ├── eval_plus_homology.py ├── eval_plus_localization.py ├── eval_plus_pfam.py ├── eval_plus_secstr.py ├── eval_plus_solubility.py ├── eval_plus_stability.py ├── eval_plus_transmembrane.py ├── plus ├── __init__.py ├── config.py ├── data │ ├── __init__.py │ ├── alphabets.py │ ├── dataset.py │ ├── fasta.py │ ├── fluorescence.py │ ├── homology.py │ ├── localization.py │ ├── pfam.py │ ├── secstr.py │ ├── solubility.py │ ├── stability.py │ └── transmembrane.py ├── model │ ├── __init__.py │ ├── cnn.py │ ├── mlp.py │ ├── p_elmo.py │ ├── plus_rnn.py │ ├── plus_tfm.py │ └── transformer.py ├── optim.py ├── preprocess.py ├── train.py └── utils.py ├── plus_embedding.py ├── poetry.lock ├── pyproject.toml ├── requirements.txt ├── train_plus_fluorescence.py ├── 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