An Attention based Bidirectional LSTM Method to Predict the Binding of TCR and Epitope.

The T-cell epitope prediction has always been a long-term challenge in immunoinformatics and bioinformatics. Studying the specic recognition between T-cell receptor (TCR) and peptide-major histocompatibility complex (p-MHC) complexes can help us better understand the immune mechanism, its also make a signication contribution in developing vaccines and targeted drugs. Meanwhile, more advanced methods are needed for distinguishing TCRs binding from different epitopes. In this paper, we introduce a hybrid model composed of bidirectional long short-term memory networks (BiLSTM), attention and convolutional neural networks (CNN) that can identied the binding of TCRs to epitopes. The BiLSTM can more completely extract amino acid forward and backward information in the sequence, and attention mechanism can focus on amino acids at certain positions from complex sequences to capture the most important feature, then CNN was used to further extract salient features to predict the binding of TCR-epitope. In McPAS dataset, the AUC value (the area under ROC curve) of naive TCR-epitope binding is 0.974 and specic TCR-epitope binding is 0.887. The model has achieved better prediction results than other existing models (TCRGP, ERGO, NetTCR), and some experiments are used to analyze the advantages of our model. The algorithm is available at https://github.com/bijingshu/BiAttCNN.git.