SeqNovo: De Novo Peptide Sequencing Prediction in IoMT via Seq2Seq.

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Abstract

In the Internet of Medical Things (IoMT), de novo peptide sequencing prediction is one of the most important techniques for the fields of disease prediction, diagnosis, and treatment. Recently, deep-learning-based peptide sequencing prediction has been a new trend. However, most popular deep learning models for peptide sequencing prediction suffer from poor interpretability and poor ability to capture long-range dependencies. To solve these issues, we propose a model named SeqNovo, which has the encoding-decoding structure of sequence to sequence (Seq2Seq), the highly nonlinear properties of multilayer perceptron (MLP), and the ability of the attention mechanism to capture long-range dependencies. SeqNovo use MLP to improve the feature extraction and utilize the attention mechanism to discover key information. A series of experiments have been conducted to show that the SeqNovo is superior to the Seq2Seq benchmark model, DeepNovo. SeqNovo improves both the accuracy and interpretability of the predictions, which will be expected to support more related research.