Microbe-bridged disease-metabolite associations identification by heterogeneous graph fusion

Abstract

Abstract Motivation Metabolomics has developed rapidly in recent years, and metabolism-related databases are also gradually constructed. Nowadays, more and more studies are being carried out on diverse microbes, metabolites and diseases. However, the logics of various associations among microbes, metabolites and diseases are limited understanding in the biomedicine of gut microbial system. The collection and analysis of relevant microbial bioinformation play an important role in the revelation of microbe–metabolite–disease associations. Therefore, the dataset that integrates multiple relationships and the method based on complex heterogeneous graphs need to be developed. Results In this study, we integrated some databases and extracted a variety of associations data among microbes, metabolites and diseases. After obtaining the three interconnected bilateral association data (microbe–metabolite, metabolite–disease and disease–microbe), we considered building a heterogeneous graph to describe the association data. In our model, microbes were used as a bridge between diseases and metabolites. In order to fuse the information of disease–microbe–metabolite graph, we used the bipartite graph attention network on the disease–microbe and metabolite–microbe bipartite graph. The experimental results show that our model has good performance in the prediction of various disease–metabolite associations. Through the case study of type 2 diabetes mellitus, Parkinson’s disease, inflammatory bowel disease and liver cirrhosis, it is noted that our proposed methodology are valuable for the mining of other associations and the prediction of biomarkers for different human diseases. Availability and implementation: https://github.com/Selenefreeze/DiMiMe.git