{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,19]],"date-time":"2025-12-19T00:00:39Z","timestamp":1766102439641,"version":"3.48.0"},"reference-count":61,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Nature Science Foundation of China","doi-asserted-by":"publisher","award":["NSFC, 62272270"],"award-info":[{"award-number":["NSFC, 62272270"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Human-associated microbes play a critical role in physiological processes and disease development, including cancer. Predicting microbe\u2013drug associations (MDAs) can aid drug discovery and personalized medicine. However, existing methods cannot predict MDAs involving microbes or drugs absent from labeled data, and they fail to model the underlying biological mechanisms between microbes and drugs. To address these limitations, we propose a novel computational framework, named MetaMDA, for predicting MDAs by performing random walks on a microbe\u2013metabolite\u2013drug heterogeneous network. MetaMDA first constructs a heterogeneous graph that integrates microbes, metabolites, and drugs, enabling the modeling of complex biological interactions. A random walk algorithm with tailored transition probabilities is subsequently applied to the graph, effectively capturing features from multiple node types on a unified scale.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Experimental results across multiple datasets demonstrate that MetaMDA consistently outperforms state-of-the-art methods, achieving an average improvement of 26%. Notably, we show MetaMDA\u2019s unique ability to predict MDAs involving microbes or drugs absent from labeled data, as illustrated by associations related to acarbose. Furthermore, mechanistic analysis of MetaMDA provides biological explanations for the associations between Escherichia coli and escitalopram, highlighting its potential to reveal a deeper mechanistic understanding of microbe\u2013drug associations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The code and datasets are available on Zenodo https:\/\/doi.org\/10.5281\/zenodo.17348446 and GitHub https:\/\/github.com\/wqlyt17\/MetaMDA.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf649","type":"journal-article","created":{"date-parts":[[2025,11,28]],"date-time":"2025-11-28T13:13:15Z","timestamp":1764335595000},"source":"Crossref","is-referenced-by-count":0,"title":["MetaMDA: explainable prediction of microbe\u2013drug association utilizing random walks on a microbe\u2013metabolite\u2013drug heterogeneous 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250100,","place":["China"]},{"name":"Shandong National Center for Applied Mathematics , Jinan, Shandong 250100,","place":["China"]},{"name":"State Key Laboratory of Cryptography and Digital Economy Security, Shandong University , Jinan, Shandong 250100,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,12,1]]},"reference":[{"key":"2025121818562279100_btaf649-B1","doi-asserted-by":"crossref","first-page":"110296","DOI":"10.1016\/j.intimp.2023.110296","article-title":"Aspirin ameliorates atherosclerotic immuno-inflammation through regulating the treg\/Th17 axis and CD39-CD73 adenosine signaling via remodeling the gut microbiota in ApoE-\/-mice","volume":"120","author":"Bai","year":"2023","journal-title":"Int Immunopharmacol"},{"key":"2025121818562279100_btaf649-B2","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1038\/s41586-021-04091-0","article-title":"The human microbiome encodes resistance to the antidiabetic drug 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