Graph Convolution Networks Using Message Passing and Multi-Source Similarity Features for Predicting circRNA-Disease Association

Abstract

Graphs can be used to effectively represent complex data structures. Learning these irregular data in graphs is challenging and still suffers from shallow learning. Applying deep learning on graphs has recently showed good performance in many applications in social analysis, bioinformatics etc. A message passing graph convolution network is such a powerful method which has expressive power to learn graph structures. Meanwhile, circRNA is a type of non-coding RNA which plays a critical role in human diseases. Identifying the associations between circRNAs and diseases is important to diagnosis and treatment of complex diseases. However, there are limited number of known associations between them and conducting biological experiments to identify new associations is time consuming and expensive. As a result, there is a need of building efficient and feasible computation methods to predict potential circRNA-disease associations. In this paper, we propose a novel graph convolution network framework to learn features from a graph built with multi-source similarity information to predict circRNA-disease associations. First we use multi-source information of circRNA similarity, disease and circRNA Gaussian Interaction Profile (GIP) kernel similarity to extract the features using first graph convolution. Then we predict disease associations for each circRNA with second graph convolution. Proposed framework with five-fold cross validation on various experiments shows promising results in predicting circRNA-disease association and outperforms other existing methods.