EGRET: edge aggregated graph attention networks and transfer learning improve protein–protein interaction site prediction

Abstract

Abstract Motivation Protein–protein interactions (PPIs) are central to most biological processes. However, reliable identification of PPI sites using conventional experimental methods is slow and expensive. Therefore, great efforts are being put into computational methods to identify PPI sites. Results We present Edge Aggregated GRaph Attention NETwork (EGRET), a highly accurate deep learning-based method for PPI site prediction, where we have used an edge aggregated graph attention network to effectively leverage the structural information. We, for the first time, have used transfer learning in PPI site prediction. Our proposed edge aggregated network, together with transfer learning, has achieved notable improvement over the best alternate methods. Furthermore, we systematically investigated EGRET’s network behavior to provide insights about the causes of its decisions. Availability EGRET is freely available as an open source project at https://github.com/Sazan-Mahbub/EGRET. Contact shams_bayzid@cse.buet.ac.bd