{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T04:51:32Z","timestamp":1791953492961,"version":"4.3.4"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T00:00:00Z","timestamp":1790640000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007129","name":"Shandong Provincial Natural Science Foundation","doi-asserted-by":"publisher","award":["ZR2024QF081"],"award-info":[{"award-number":["ZR2024QF081"]}],"id":[{"id":"10.13039\/501100007129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004761","name":"Hainan Provincial Natural Science Foundation","doi-asserted-by":"publisher","award":["626MS0266"],"award-info":[{"award-number":["626MS0266"]}],"id":[{"id":"10.13039\/501100004761","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004761","name":"Hainan Provincial Natural Science Foundation","doi-asserted-by":"publisher","award":["526QN0672"],"award-info":[{"award-number":["526QN0672"]}],"id":[{"id":"10.13039\/501100004761","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Single-cell multi-omics clustering requires integrating complementary omics layers while accounting for their unequal reliability across individual cells. However, cell-wise reliability can vary substantially within each omics layer, causing different omics to provide reliable signals for some cells but ambiguous or noisy signals for others. This challenge is further complicated by omics-level heterogeneity, where differences in sparsity, signal distribution, and biological resolution may introduce cross-omics conflicts and bias the fused representation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present scURL, an uncertainty-sharpened representation learning framework for single-cell multi-omics clustering. scURL introduces representation uncertainty (RU) and establishes its connection to clustering generalization risk (GR), enabling the derivation of cell-wise omics weights for uncertainty-aware fusion (UAF). To support stable uncertainty estimation, scURL further introduces a multi-granular calibration module (MCM) that calibrates omics-specific representations from both cluster-level semantic and local-level structural perspectives before fusion. Experiments on ten datasets demonstrate that scURL outperforms existing clustering methods, remains robust under dropout noise, and identifies biologically meaningful cell populations, as supported by marker gene analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>Source code is available at https:\/\/github.com\/Yaolab-fantastic\/scURL.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag723","type":"journal-article","created":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T11:21:19Z","timestamp":1790594479000},"source":"Crossref","is-referenced-by-count":0,"title":["scURL: uncertainty-sharpened representation learning for single-cell multi-omics clustering"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-1089-9398","authenticated-orcid":false,"given":"Hongwei","family":"Liu","sequence":"first","affiliation":[{"name":"College of Intelligent Systems Science and Engineering, Harbin Engineering University , Harbin, 150001,","place":["China"]},{"name":"Qingdao Innovation and Development Center of Harbin Engineering University , Qingdao, 266000,","place":["China"]},{"name":"Sanya Nanhai Innovation and Development Base of Harbin Engineering University , Sanya, 572024,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donghui","family":"Yu","sequence":"additional","affiliation":[{"name":"College of Intelligent Systems Science and Engineering, Harbin Engineering University , Harbin, 150001,","place":["China"]},{"name":"Qingdao Innovation and Development Center of Harbin Engineering University , Qingdao, 266000,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Li","sequence":"additional","affiliation":[{"name":"College of Intelligent Systems Science and Engineering, Harbin Engineering University , Harbin, 150001,","place":["China"]},{"name":"Qingdao Innovation and Development Center of Harbin Engineering University , Qingdao, 266000,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR , Singapore, 138672,","place":["Singapore"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ching-Yu","family":"Cheng","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore, 119228,","place":["Singapore"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9702-5524","authenticated-orcid":false,"given":"Huazhu","family":"Fu","sequence":"additional","affiliation":[{"name":"Institute of Advanced Intelligence and Computing (IAIC), A*STAR , Singapore, 138632,","place":["Singapore"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Liang","sequence":"additional","affiliation":[{"name":"College of Intelligent Systems Science and Engineering, Harbin Engineering University , Harbin, 150001,","place":["China"]},{"name":"Sanya Nanhai Innovation and Development Base of Harbin Engineering University , Sanya, 572024,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5981-7678","authenticated-orcid":false,"given":"Shan","family":"Cong","sequence":"additional","affiliation":[{"name":"College of Intelligent Systems Science and 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