├── LICENSE ├── Net ├── CNN.py ├── CRF.py ├── LSTM.py ├── LSTM_Attention.py ├── New_ComModel.py ├── ONLSTM.py ├── SelfAttention.py ├── SelfAttentionTorch.py ├── log.py └── transformer.py ├── README.md ├── data_processing.py ├── docs ├── USPNet_arch.png └── novel_SP.png ├── environment.yml ├── predict.py ├── predict_fast.py ├── test.py ├── test_fast.py └── utils_tools ├── Msa_Create_Embedding.py └── utils.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/LICENSE -------------------------------------------------------------------------------- /Net/CNN.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/Net/CNN.py -------------------------------------------------------------------------------- /Net/CRF.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/Net/CRF.py -------------------------------------------------------------------------------- /Net/LSTM.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/Net/LSTM.py -------------------------------------------------------------------------------- /Net/LSTM_Attention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/Net/LSTM_Attention.py -------------------------------------------------------------------------------- /Net/New_ComModel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/Net/New_ComModel.py -------------------------------------------------------------------------------- /Net/ONLSTM.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/Net/ONLSTM.py -------------------------------------------------------------------------------- /Net/SelfAttention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/Net/SelfAttention.py -------------------------------------------------------------------------------- /Net/SelfAttentionTorch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/Net/SelfAttentionTorch.py -------------------------------------------------------------------------------- /Net/log.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/Net/log.py -------------------------------------------------------------------------------- /Net/transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/Net/transformer.py -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/README.md -------------------------------------------------------------------------------- /data_processing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/data_processing.py -------------------------------------------------------------------------------- /docs/USPNet_arch.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/docs/USPNet_arch.png -------------------------------------------------------------------------------- /docs/novel_SP.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/docs/novel_SP.png -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/environment.yml -------------------------------------------------------------------------------- /predict.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/predict.py -------------------------------------------------------------------------------- /predict_fast.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/predict_fast.py -------------------------------------------------------------------------------- /test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/test.py -------------------------------------------------------------------------------- /test_fast.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/test_fast.py -------------------------------------------------------------------------------- /utils_tools/Msa_Create_Embedding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/utils_tools/Msa_Create_Embedding.py -------------------------------------------------------------------------------- /utils_tools/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ml4bio/USPNet/HEAD/utils_tools/utils.py --------------------------------------------------------------------------------