├── .gitignore ├── LICENSE ├── a_raw_datasets └── Nmodified_peptides.csv ├── b_preprocessing └── pretrain_tokenizer.py ├── c_transsafp ├── models_pretrain │ └── amp_pretrain_learner.h5 │ │ ├── saved_model.pb │ │ └── variables │ │ ├── variables.data-00000-of-00001 │ │ └── variables.index └── models_transfer │ └── amp_transfer_learner.h5 │ ├── saved_model.pb │ └── variables │ ├── variables.data-00000-of-00001 │ └── variables.index ├── d_src ├── a_raw_datasets │ └── Nmodified_peptides.csv ├── b_preprocessing │ ├── pretrain_tokenizer.py │ ├── transfer │ │ ├── all_label.npy │ │ ├── all_nterm.npy │ │ ├── all_seq.npy │ │ ├── train_label.npy │ │ ├── train_nterm.npy │ │ ├── train_seq.npy │ │ ├── valid_label.npy │ │ ├── valid_nterm.npy │ │ └── valid_seq.npy │ └── transfer_tokenizer.py ├── c_transfer_learning │ ├── layers │ │ ├── pretrain_layers.py │ │ └── transfer_layers.py │ ├── models_pretrain │ │ ├── amp_pretrain_learner.h5 │ │ │ ├── saved_model.pb │ │ │ └── variables │ │ │ │ ├── variables.data-00000-of-00001 │ │ │ │ └── variables.index │ │ └── amp_pretrain_learner_weights.h5 │ └── models_transfer │ │ ├── amp_transfer_learner.h5 │ │ ├── saved_model.pb │ │ └── variables │ │ │ ├── variables.data-00000-of-00001 │ │ │ └── variables.index │ │ └── amp_transfer_learner_weights.h5 ├── map_seq8.py ├── plot_pretrain_model.ipynb ├── plot_transfer_model.ipynb ├── pretrain_model.py ├── transfer_model.py └── transfer_model_eval.py ├── prediction.log ├── readme.md ├── run_pretrain.py └── run_transsafp.py /.gitignore: -------------------------------------------------------------------------------- 1 | __pycache__/ -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LiuHuayang27/TransSAFP/HEAD/LICENSE -------------------------------------------------------------------------------- /a_raw_datasets/Nmodified_peptides.csv: 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