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Identifying disease-related metabolites is of great significance for the diagnosis, prevention and treatment of disease. In this study, we propose a novel computational model of multiple-network logistic matrix factorization (MN-LMF) for predicting metabolite-disease interactions, which is especially relevant for new diseases and new metabolites. First, MN-LMF builds disease (or metabolite) similarity network by integrating heterogeneous omics data. Second, it combines these similarities with known metabolite-disease interaction networks