GCN-MF: Disease-gene association identification by graph convolutional networks and matrix factorization

Abstract

Discovering disease-gene association is a fundamental and critical biomedical task, which assists biologists and physicians to discover pathogenic mechanism of syndromes. With various clinical biomarkers measuring the similarities among genes and disease phenotypes, network-based semi-supervised learning (NSSL) has been commonly utilized by these studies to address this class-imbalanced large-scale data issue. However, most existing NSSL approaches are based on linear models and suffer from two major limitations: 1) They implicitly consider a local-structure representation for each candidate; 2) They are unable to capture nonlinear associations between diseases and genes. In this paper, we propose a new framework for disease-gene association task by combining Graph Convolutional Network (GCN) and matrix factorization, named GCN-MF. With the help of GCN, we could capture nonlinear interactions and exploit measured similarities. Moreover, we define a margin control loss function to reduce the effect of sparsity. Empirical results demonstrate that the proposed deep learning algorithm outperforms all other state-of-the-art methods on most of metrics.