DeepPPI: Boosting Prediction of Protein–Protein Interactions with Deep Neural Networks

• Published in: Journal of chemical information and modeling 2017-06, Vol.57 (6), p.1499-1510
• Main Authors: Du, Xiuquan, Sun, Shiwei, Hu, Changlin, Yao, Yu, Yan, Yuanting, Zhang, Yanping
• Format: Article
• Language: English
• Subjects: Artificial neural networks; Correlation coefficients; Eukaryotes; Experiments; Gene expression; Machine learning; Neural networks; Neural Networks (Computer); Predictions; Protein Interaction Mapping - methods; Proteins; Representations; Saccharomyces cerevisiae - metabolism
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.7b00028

The complex language of eukaryotic gene expression remains incompletely understood. Despite the importance suggested by many proteins variants statistically associated with human disease, nearly all such variants have unknown mechanisms, for example, protein–protein interactions (PPIs). In this study, we address this challenge using a recent machine learning advance-deep neural networks (DNNs). We aim at improving the performance of PPIs prediction and propose a method called DeepPPI (Deep neural networks for Protein–Protein Interactions prediction), which employs deep neural networks to learn effectively the representations of proteins from common protein descriptors. The experimental results indicate that DeepPPI achieves superior performance on the test data set with an Accuracy of 92.50%, Precision of 94.38%, Recall of 90.56%, Specificity of 94.49%, Matthews Correlation Coefficient of 85.08% and Area Under the Curve of 97.43%, respectively. Extensive experiments show that DeepPPI can learn useful features of proteins pairs by a layer-wise abstraction, and thus achieves better prediction performance than existing methods. The source code of our approach can be available via http://ailab.ahu.edu.cn:8087/DeepPPI/index.html.