{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T12:22:36Z","timestamp":1773145356269,"version":"3.50.1"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T00:00:00Z","timestamp":1773014400000},"content-version":"vor","delay-in-days":8,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["T2422010"],"award-info":[{"award-number":["T2422010"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62172170"],"award-info":[{"award-number":["62172170"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fundamental Research Funds for Central Universities"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Drug repurposing provides a cost-effective and time-efficient strategy to accelerate therapeutic discovery, yet most computational approaches fail to capture the multi-scale biomedical mechanisms underlying drug\u2013disease associations, limiting interpretability. We introduce BioMNEDR (mechanism-guided network embedding for drug repurposing) that integrates heterogeneous biomedical networks through biologically curated meta-paths. BioMNEDR generates low-dimensional embeddings preserving protein\u2013protein interactions and functional hierarchies. It further integrates multi-path predictions through an XGBoost classifier. The framework achieves state-of-the-art performance, consistently surpassing strong baselines across AUROC, AUPR, recall, and F1-score, while maintaining a balanced trade-off in precision. Case studies further highlight its practical utility, demonstrating the ability to rediscover approved drugs and prioritize promising candidates, such as cromoglicic acid for Alzheimer\u2019s disease. By explicitly modeling multi-scale mechanisms, BioMNEDR enhances both predictive accuracy and biomedical interpretability, offering a robust computational framework for systematic drug repurposing.<\/jats:p>","DOI":"10.1093\/bib\/bbag101","type":"journal-article","created":{"date-parts":[[2026,2,18]],"date-time":"2026-02-18T12:37:31Z","timestamp":1771418251000},"source":"Crossref","is-referenced-by-count":0,"title":["BioMNEDR: mechanism-guided network embedding for drug repurposing"],"prefix":"10.1093","volume":"27","author":[{"given":"Yizhou","family":"Zeng","sequence":"first","affiliation":[{"name":"School of Future Technology , Huazhong University of Science and Technology, Luoyu Road, 430074 Wuhan,","place":["China"]}]},{"given":"Lei","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Artificial Intelligence and Automation , State Key Laboratory of Digital Manufacturing Equipments and Technology, Institute of Medical Equipment Science and Engineering, Luoyu Road, 430074 Wuhan,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0676-9745","authenticated-orcid":false,"given":"Xueming","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Artificial Intelligence and Automation , State Key Laboratory of Digital Manufacturing Equipments and Technology, Institute of Medical Equipment Science and Engineering, Luoyu Road, 430074 Wuhan,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2026,3,9]]},"reference":[{"key":"2026030917190205100_ref1","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/nrd.2018.168","article-title":"Drug repurposing: progress, challenges and recommendations","volume":"18","author":"Pushpakom","year":"2019","journal-title":"Nat Rev Drug Discov"},{"key":"2026030917190205100_ref2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41573-025-01164-x","article-title":"Computational drug repurposing: approaches, evaluation of in silico resources and 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