Deep Residual Convolutional Neural Network for Protein-Protein Interaction Extraction

Abstract

Knowledge extracted from the protein-protein interaction (PPI) network can help researchers reveal the molecular mechanisms of biological processes. With the rapid growth in the volume of the biomedical literature, manually detecting and annotating PPIs from raw literature has become increasingly difficult. Hence, automatically extracting PPIs by machine learning methods from raw literature has gained significance in the biomedical research. In this paper, we propose a novel PPI extraction method based on the residual convolutional neural network (CNN). This is the first time that the residual CNN is applied to the PPI extraction task. In addition, the previous state-of-the-art PPI extraction models heavily rely on parsing results from natural language processing tools, such as dependence parsers. Our model does not rely on any parsing tools. We evaluated our model based on five benchmark PPI extraction corpora, AIMed, BioInfer, HPRD50, IEPA, and LLL. The experimental results showed that our model achieved the best results compared with the previous kernel-based and CNN-based PPI extraction models. Compared with the previous recurrent neural network-based PPI extraction models, our model achieved better or comparable performance.

Keywords

• Deep learning
• natural language processing
• protein–protein interaction extraction
• residual convolutional neural network