Integrating Sequence and Network Information to Enhance Protein-Protein Interaction Prediction Using Graph Convolutional Networks

Abstract

Identification of protein-protein interactions (PPIs) is an important problem in biology, since PPIs are related to many essential cellular processes. The development of large-scale high-throughput experiments has produced a large number of PPIs data, however, these data are often noisy and their coverage is still limited. To overcome the shortcomings of experimental methods, many computational methods have been proposed for the prediction of PPIs. Among these methods, most of them solely take the amino acid sequence of protein as input information to make predictions. As PPIs data form the PPIs networks graph, the position information of proteins in the graph can reflect the properties of proteins to some extent, which is an important complement to protein sequence information. But previous works did not consider the graph structure information to improve the prediction performance. In this work, we first time apply graph convolutional networks (GCNs) to capture the protein's position information in the graph and combine amino acid sequence information and position information to make representations in the prediction task. Our experimental results show that our work outperforms the state-of-the-art sequence-based methods on several benchmark datasets and our work computationally is more efficient compared with previous works.