Abstract
Accumulating studies have shown that microbes are closely related to human diseases. In this paper, a novel method called MSBMFHMDA was designed to predict potential microbe–disease associations by adopting multi-similarities bilinear matrix factorization. In MSBMFHMDA, a microbe multiple similarities matrix was constructed first based on the Gaussian interaction profile kernel similarity and cosine similarity for microbes. Then, we use the Gaussian interaction profile kernel similarity, cosine similarity, and symptom similarity for diseases to compose the disease multiple similarities matrix. Finally, we integrate these two similarity matrices and the microbe-disease association matrix into our model to predict potential associations. The results indicate that our method can achieve reliable AUCs of 0.9186 and 0.9043 ± 0.0048 in the framework of leave-one-out cross validation (LOOCV) and fivefold cross validation, respectively. What is more, experimental results indicated that there are 10, 10, and 8 out of the top 10 related microbes for asthma, inflammatory bowel disease, and type 2 diabetes mellitus, respectively, which were confirmed by experiments and literatures. Therefore, our model has favorable performance in predicting potential microbe–disease associations.
Highlights
Microorganisms are the general names of all tiny organisms that individuals cannot observe with the naked eye, but are closely related to humans
The problem of microbe–disease associations prediction can be seen as a classification or regression problem, usually using cross-validation to evaluate the generalization capabilities of the new sample
In leave-one-out cross validation (LOOCV), each confirmed microbe–disease association was chosen as a test sample in turn, and the rest of the associations were used to train
Summary
Microorganisms are the general names of all tiny organisms that individuals cannot observe with the naked eye, but are closely related to humans. Microorganisms include bacteria, viruses, fungi, and a large group of small protozoa, microalgae (The Human Microbiome Project Consortium, 2012). We all know that microbes can cause diseases and make food, cloth, and leather moldy and decay, but it has a beneficial side. One of the most important effects of microbes on human beings is to lead to the spread of infectious diseases. Viruses are the cause of 50% of human diseases, microbes can greatly influence human health. Identifying disease-related microbes is one of the important tasks in the study of complex disease pathology. One of the useful values of biological research is its application in the field of medicine for the benefit of human health.
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