{"title":"Drug repositioning with metapath guidance and adaptive negative sampling enhancement.","authors":"Yaozheng Zhou, Xingyu Shi, Lingfeng Wang, Jin Xu, Demin Li, Congzhou Chen","doi":"10.1016/j.jbi.2025.104916","DOIUrl":null,"url":null,"abstract":"<p><strong>Objective: </strong>Drug repositioning plays a pivotal role in expediting the drug discovery pipeline. The rapid development of computational methods has opened new avenues for predicting drug-disease associations (DDAs). Despite advancements in existing methodologies, challenges such as insufficient exploration of diverse relationships in heterogeneous biological networks and inadequate quality of negative samples have persisted.</p><p><strong>Methods: </strong>In this study, we introduce DRMGNE, a novel drug repositioning framework that harnesses metapath-guided learning and adaptive negative enhancement for DDA prediction. DRMGNE initiates with an autoencoder to extract semantic features based on similarity matrices. Subsequently, a comprehensive set of metapaths is designed to generate subgraphs, and graph convolutional networks are utilized to extract enriched node representations reflecting topological structures. Furthermore, the adaptive negative enhancement strategy is employed to improve the quality of negative samples, ensuring balanced learning.</p><p><strong>Results: </strong>Experimental evaluations demonstrate that DRMGNE outperforms state-of-the-art algorithms across three benchmark datasets. Additionally, case studies and molecular docking validations further underscore its potential in facilitating drug discovery and accelerating drug repurposing efforts.</p><p><strong>Conclusion: </strong>DRMGNE is a novel framework for DDA prediction that leverages metapath-based guidance and adaptive negative enhancement. Experiments on benchmark datasets show superior performance over existing methods, underscoring its potential impact in drug discovery.</p>","PeriodicalId":15263,"journal":{"name":"Journal of Biomedical Informatics","volume":" ","pages":"104916"},"PeriodicalIF":4.5000,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Biomedical Informatics","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1016/j.jbi.2025.104916","RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS","Score":null,"Total":0}
引用次数: 0
Abstract
Objective: Drug repositioning plays a pivotal role in expediting the drug discovery pipeline. The rapid development of computational methods has opened new avenues for predicting drug-disease associations (DDAs). Despite advancements in existing methodologies, challenges such as insufficient exploration of diverse relationships in heterogeneous biological networks and inadequate quality of negative samples have persisted.
Methods: In this study, we introduce DRMGNE, a novel drug repositioning framework that harnesses metapath-guided learning and adaptive negative enhancement for DDA prediction. DRMGNE initiates with an autoencoder to extract semantic features based on similarity matrices. Subsequently, a comprehensive set of metapaths is designed to generate subgraphs, and graph convolutional networks are utilized to extract enriched node representations reflecting topological structures. Furthermore, the adaptive negative enhancement strategy is employed to improve the quality of negative samples, ensuring balanced learning.
Results: Experimental evaluations demonstrate that DRMGNE outperforms state-of-the-art algorithms across three benchmark datasets. Additionally, case studies and molecular docking validations further underscore its potential in facilitating drug discovery and accelerating drug repurposing efforts.
Conclusion: DRMGNE is a novel framework for DDA prediction that leverages metapath-based guidance and adaptive negative enhancement. Experiments on benchmark datasets show superior performance over existing methods, underscoring its potential impact in drug discovery.
期刊介绍:
The Journal of Biomedical Informatics reflects a commitment to high-quality original research papers, reviews, and commentaries in the area of biomedical informatics methodology. Although we publish articles motivated by applications in the biomedical sciences (for example, clinical medicine, health care, population health, and translational bioinformatics), the journal emphasizes reports of new methodologies and techniques that have general applicability and that form the basis for the evolving science of biomedical informatics. Articles on medical devices; evaluations of implemented systems (including clinical trials of information technologies); or papers that provide insight into a biological process, a specific disease, or treatment options would generally be more suitable for publication in other venues. Papers on applications of signal processing and image analysis are often more suitable for biomedical engineering journals or other informatics journals, although we do publish papers that emphasize the information management and knowledge representation/modeling issues that arise in the storage and use of biological signals and images. System descriptions are welcome if they illustrate and substantiate the underlying methodology that is the principal focus of the report and an effort is made to address the generalizability and/or range of application of that methodology. Note also that, given the international nature of JBI, papers that deal with specific languages other than English, or with country-specific health systems or approaches, are acceptable for JBI only if they offer generalizable lessons that are relevant to the broad JBI readership, regardless of their country, language, culture, or health system.