{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T07:06:50Z","timestamp":1776323210475,"version":"3.50.1"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,7,10]],"date-time":"2025-07-10T00:00:00Z","timestamp":1752105600000},"content-version":"vor","delay-in-days":9,"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":["32470691 and T2495273"],"award-info":[{"award-number":["32470691 and T2495273"]}],"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":["32470689"],"award-info":[{"award-number":["32470689"]}],"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":["32400643"],"award-info":[{"award-number":["32400643"]}],"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":["62402144"],"award-info":[{"award-number":["62402144"]}],"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":["U24A20370 and 32270789"],"award-info":[{"award-number":["U24A20370 and 32270789"]}],"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":["T2325009 and 62032007"],"award-info":[{"award-number":["T2325009 and 62032007"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Science and Technology Major Project of China","award":["2022ZD0117702"],"award-info":[{"award-number":["2022ZD0117702"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Spatial transcriptomics (ST) encompasses rich multi-modal information related to cell state and organization. Precisely identifying spatial domains with consistent gene expression patterns and histological features is a critical task in ST analysis, which requires comprehensive integration of multi-modal information. Here, we propose TriCLFF, a contrastive learning-based multi-modal feature fusion framework, to effectively integrate spatial associations, gene expression levels, and histological features in a unified manner. Leveraging an advanced feature fusion mechanism, our proposed TriCLFF framework outperforms existing state-of-the-art methods in terms of accuracy and robustness across four datasets (mouse brain anterior, mouse olfactory bulb, human dorsolateral prefrontal cortex, and human breast cancer) from different platforms (10x Visium and Stereo-seq) for spatial domain identification. TriCLFF also facilitates the identification of finer-grained structures in breast cancer tissues and detects previously unknown gene expression patterns in the human dorsolateral prefrontal cortex, providing novel insights for understanding tissue functions. Overall, TriCLFF establishes an effective paradigm for integrating spatial multi-modal data, demonstrating its potential for advancing ST research. The source code of TriCLFF is available online at https:\/\/github.com\/HBZZ168\/TriCLFF.<\/jats:p>","DOI":"10.1093\/bib\/bbaf316","type":"journal-article","created":{"date-parts":[[2025,7,10]],"date-time":"2025-07-10T22:04:33Z","timestamp":1752185073000},"source":"Crossref","is-referenced-by-count":3,"title":["TriCLFF: a multi-modal feature fusion framework using contrastive learning for spatial domain identification"],"prefix":"10.1093","volume":"26","author":[{"given":"Fenglan","family":"Pang","sequence":"first","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin 150001, Heilongjiang Province ,","place":["China"]}]},{"given":"Guangfu","family":"Xue","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin 150001, Heilongjiang Province ,","place":["China"]}]},{"given":"Wenyi","family":"Yang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin 150001, Heilongjiang Province ,","place":["China"]}]},{"given":"Yideng","family":"Cai","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin 150001, Heilongjiang Province ,","place":["China"]}]},{"given":"Jinhao","family":"Que","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin 150001, Heilongjiang Province ,","place":["China"]}]},{"given":"Haoxiu","family":"Sun","sequence":"additional","affiliation":[{"name":"School of Interdisciplinary Medicine and Engineering, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin 150081, Heilongjiang Province ,","place":["China"]}]},{"given":"Pingping","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Interdisciplinary Medicine and Engineering, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin 150081, Heilongjiang Province ,","place":["China"]}]},{"given":"Shuaiyu","family":"Su","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin 150001, Heilongjiang Province ,","place":["China"]}]},{"given":"Xiyun","family":"Jin","sequence":"additional","affiliation":[{"name":"School of Interdisciplinary Medicine and Engineering, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin 150081, Heilongjiang Province ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6008-2085","authenticated-orcid":false,"given":"Qian","family":"Ding","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin 150001, Heilongjiang Province ,","place":["China"]}]},{"given":"Zuxiang","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Interdisciplinary Medicine and Engineering, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin 150081, Heilongjiang Province ,","place":["China"]}]},{"given":"Meng","family":"Luo","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin 150001, Heilongjiang Province ,","place":["China"]}]},{"given":"Yuexin","family":"Yang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin 150001, Heilongjiang Province ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2110-5368","authenticated-orcid":false,"given":"Yi","family":"Lin","sequence":"additional","affiliation":[{"name":"School of Interdisciplinary Medicine and Engineering, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin 150081, Heilongjiang Province ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6087-4584","authenticated-orcid":false,"given":"Renjie","family":"Tan","sequence":"additional","affiliation":[{"name":"School of Interdisciplinary Medicine and Engineering, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin 150081, Heilongjiang Province ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4950-6304","authenticated-orcid":false,"given":"Yusong","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Interdisciplinary Medicine and Engineering, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin 150081, Heilongjiang Province ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1799-5529","authenticated-orcid":false,"given":"Zhaochun","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Interdisciplinary Medicine and Engineering, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin 150081, Heilongjiang Province ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1827-0389","authenticated-orcid":false,"given":"Qinghua","family":"Jiang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang 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