ExamPle: explainable deep learning framework for the prediction of plant small secreted peptides

• Published in: Bioinformatics (Oxford, England) Vol. 39; no. 3
• Main Authors: Li, Zhongshen, Jin, Junru, Wang, Yu, Long, Wentao, Ding, Yuanhao, Hu, Haiyan, Wei, Leyi
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-03-2023
• Subjects: Amino Acids; Benchmarking; Deep Learning; Machine Learning; Original Paper; Peptides
• ISSN: 1367-4811; 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btad108

Abstract
Motivation
Plant Small Secreted Peptides (SSPs) play an important role in plant growth, development, and plant–microbe interactions. Therefore, the identification of SSPs is essential for revealing the functional mechanisms. Over the last few decades, machine learning-based methods have been developed, accelerating the discovery of SSPs to some extent. However, existing methods highly depend on handcrafted feature engineering, which easily ignores the latent feature representations and impacts the predictive performance.
Results
Here, we propose ExamPle, a novel deep learning model using Siamese network and multi-view representation for the explainable prediction of the plant SSPs. Benchmarking comparison results show that our ExamPle performs significantly better than existing methods in the prediction of plant SSPs. Also, our model shows excellent feature extraction ability. Importantly, by utilizing in silicomutagenesis experiment, ExamPle can discover sequential characteristics and identify the contribution of each amino acid for the predictions. The key novel principle learned by our model is that the head region of the peptide and some specific sequential patterns are strongly associated with the SSPs’ functions. Thus, ExamPle is expected to be a useful tool for predicting plant SSPs and designing effective plant SSPs.
Availability and implementation
Our codes and datasets are available at https://github.com/Johnsunnn/ExamPle.