{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T06:04:30Z","timestamp":1789625070673,"version":"build-2803163510"},"reference-count":66,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001459","name":"Ministry of Education - Singapore","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001459","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["advanced.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Advanced Science"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Multi\u2010omics technologies generate high\u2010dimensional molecular signatures that provide unprecedented opportunities to uncover biological mechanisms. However, translating complex molecular alterations into coherent and interpretable functional insights remains a major challenge. Existing module discovery methods can identify groups of related features, but often lack direct biological interpretability, whereas pathway\u2010based approaches frequently yield redundant results that complicate interpretation. Here, we present MAPA (Modular Analysis and Phenotype\u2010informed Annotation using large language models [LLMs]), a semantic\u2010biological network framework for functional module discovery and interpretation in multi\u2010omics data. MAPA integrates molecular interactions and pathway\u2010level functional context into a unified semantic\u2010biological network, and applies random walk with restart to quantify global functional relatedness among molecules and pathways for coherent module discovery across omics layers. MAPA further incorporates LLM\u2010assisted interpretation with retrieval\u2010augmented generation (RAG) to produce structured, literature\u2010informed module interpretation. Benchmarking against existing approaches shows that MAPA achieves superior module reconstruction and expert\u2010aligned functional interpretation. Applied to aging\u2010related multi\u2010omics datasets, MAPA reveals biologically coherent modules and biological insights that are difficult to obtain from conventional pathway analyses alone. MAPA provides a generalizable framework for organizing fragmented and heterogeneous molecular features into functional modules and comprehensive interpretations.<\/jats:p>","DOI":"10.1002\/advs.77774","type":"journal-article","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T05:46:15Z","timestamp":1789623975000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["MAPA: A Semantic Network Framework for Functional Module Discovery and Interpretation in Multi\u2010Omics Data"],"prefix":"10.1002","author":[{"given":"Yifei","family":"Ge","sequence":"first","affiliation":[{"name":"Lee Kong Chian School of Medicine Nanyang Technological University  Singapore Singapore"},{"name":"School of Chemistry Chemical Engineering and Biotechnology Nanyang Technological University  Singapore Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feifan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Lee Kong Chian School of Medicine Nanyang Technological University  Singapore Singapore"},{"name":"School of Chemistry Chemical Engineering and Biotechnology Nanyang Technological University  Singapore Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yijiang","family":"Liu","sequence":"additional","affiliation":[{"name":"Lee Kong Chian School of Medicine Nanyang Technological University  Singapore Singapore"},{"name":"School of Chemistry Chemical Engineering and Biotechnology Nanyang Technological University  Singapore Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0260-7271","authenticated-orcid":false,"given":"Chao","family":"Jiang","sequence":"additional","affiliation":[{"name":"Life Sciences Institute Zhejiang University  Hangzhou Zhejiang China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4311-584X","authenticated-orcid":false,"given":"Peng","family":"Gao","sequence":"additional","affiliation":[{"name":"Department of Environmental Health and Department of Molecular Metabolism Harvard T.H. 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