MHDMF: Prediction of miRNA–disease associations based on Deep Matrix Factorization with Multi-source Graph Convolutional Network

Abstract

A growing number of works have proved that microRNAs (miRNAs) are a crucial biomarker in diverse bioprocesses affecting various diseases. As a good complement to high-cost wet experiment-based methods, numerous computational prediction methods have sprung up. However, there are still challenges that exist in making effective use of high false-negative associations and multi-source information for finding the potential associations. In this work, we develop an end-to-end computational framework, called MHDMF, which integrates the multi-source information on a heterogeneous network to discover latent disease–miRNA associations. Since high false-negative exist in the miRNA–disease associations, MHDMF utilizes the multi-source Graph Convolutional Network (GCN) to correct the false-negative association by reformulating the miRNA–disease association score matrix. The score matrix reformulation is based on different similarity profiles and known associations between miRNAs, genes, and diseases. Then, MHDMF employs Deep Matrix Factorization (DMF) to predict the miRNA–disease associations based on reformulated miRNA–disease association score matrix. The experimental results show that the proposed framework outperforms highly related comparison methods by a large margin on tasks of miRNA–disease association prediction. Furthermore, case studies suggest that MHDMF could be a convenient and efficient tool and may supply a new way to think about miRNA–disease association prediction.