{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T16:59:04Z","timestamp":1790873944061,"version":"4.1.0"},"reference-count":57,"publisher":"Cold Spring Harbor Laboratory","issue":"10","funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62261018"],"award-info":[{"award-number":["62261018"]}],"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":["62262015"],"award-info":[{"award-number":["62262015"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genome Res."],"accepted":{"date-parts":[[2026,8,25]]},"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:p>Spatial transcriptomics (STs) have become a valuable approach for understanding the growth and development of organisms. Despite the recent emergence of numerous ST models, accurately identifying spatial domains remains challenging owing to the trade-off between preserving local details and reducing noise. Here, we introduce STAMGC, which is a dual-contrastive learning framework built upon graph convolutional networks. This model leverages regional and topological contrastive learning to jointly optimize the model, effectively reducing the noise in spatial domain identification and enhancing the extraction of detailed features. In this study, Gaussian smoothing, originally developed in the image processing field, is introduced to process ST data, providing a foundation for region-level contrastive learning by mitigating spatial discontinuities of gene expression signals. Experimental results indicate that STAMGC outperforms existing methods across multiple data sets according to comprehensive evaluations. Furthermore, STAMGC not only identifies finer structures in the mouse brain but also brings new discoveries for human breast cancer research.<\/jats:p>","DOI":"10.1101\/gr.281999.126","type":"journal-article","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T19:40:19Z","timestamp":1789587619000},"page":"2091-2103","source":"Crossref","is-referenced-by-count":0,"title":["Dual-contrastive learning for spatial domain identification in spatial transcriptomics with STAMGC"],"prefix":"10.1101","volume":"36","author":[{"given":"Zhuoyue","family":"Zhang","sequence":"first","affiliation":[{"name":"School of Computer Science and Technology, Hainan University, Haikou 570228, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qianmao","family":"Wen","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Hainan University, Haikou 570228, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junlin","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan 430081, Hubei, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yajie","family":"Meng","sequence":"additional","affiliation":[{"name":"School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan 430200 Hubei, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feifei","family":"Cui","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Hainan University, Haikou 570228, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zilong","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Hainan University, Haikou 570228, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"246","published-online":{"date-parts":[[2026,9,16]]},"reference":[{"key":"2026100109051458000_36.10.2091.1","doi-asserted-by":"publisher","DOI":"10.1080\/0954898X.2023.2237587"},{"key":"2026100109051458000_36.10.2091.2","doi-asserted-by":"publisher","DOI":"10.1038\/sj.bjc.6603494"},{"key":"2026100109051458000_36.10.2091.3","doi-asserted-by":"publisher","DOI":"10.1126\/science.abk2066"},{"key":"2026100109051458000_36.10.2091.4","doi-asserted-by":"publisher","DOI":"10.1145\/3341981.3344221"},{"key":"2026100109051458000_36.10.2091.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.06.038"},{"key":"2026100109051458000_36.10.2091.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2022.04.003"},{"key":"2026100109051458000_36.10.2091.7","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4419-5913-3_21"},{"key":"2026100109051458000_36.10.2091.8","doi-asserted-by":"publisher","DOI":"10.1002\/1099-128X(200007\/08)14:4&lt;351::AID-CEM598&gt;3.0.CO;2-Q"},{"key":"2026100109051458000_36.10.2091.9","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-29439-6"},{"key":"2026100109051458000_36.10.2091.10","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1012409"},{"key":"2026100109051458000_36.10.2091.11","doi-asserted-by":"publisher","DOI":"10.1109\/TNN.2008.2005601"},{"key":"2026100109051458000_36.10.2091.12","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-01911-1"},{"key":"2026100109051458000_36.10.2091.13","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac757"},{"key":"2026100109051458000_36.10.2091.14","doi-asserted-by":"publisher","DOI":"10.1016\/j.biotechadv.2026.108807"},{"key":"2026100109051458000_36.10.2091.15","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2021.04.048"},{"key":"2026100109051458000_36.10.2091.16","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-021-01255-8"},{"key":"2026100109051458000_36.10.2091.17","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-26614-z"},{"key":"2026100109051458000_36.10.2091.18","doi-asserted-by":"publisher","DOI":"10.1111\/j.1460-9568.2010.07202.x"},{"key":"2026100109051458000_36.10.2091.19","doi-asserted-by":"publisher","DOI":"10.1088\/1742-6596\/1235\/1\/012015"},{"key":"2026100109051458000_36.10.2091.20","doi-asserted-by":"publisher","DOI":"10.3390\/biom12121860"},{"key":"2026100109051458000_36.10.2091.21","doi-asserted-by":"publisher","DOI":"10.1016\/j.tibtech.2020.05.006"},{"key":"2026100109051458000_36.10.2091.22","doi-asserted-by":"publisher","DOI":"10.1016\/j.molimm.2025.02.016"},{"key":"2026100109051458000_36.10.2091.23","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.10.026"},{"key":"2026100109051458000_36.10.2091.24","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-36796-3"},{"key":"2026100109051458000_36.10.2091.25","doi-asserted-by":"publisher","DOI":"10.1007\/s11432-024-4485-0"},{"key":"2026100109051458000_36.10.2091.26","doi-asserted-by":"publisher","DOI":"10.1186\/s43042-023-00446-6"},{"key":"2026100109051458000_36.10.2091.27","doi-asserted-by":"publisher","DOI":"10.1038\/s41593-020-00787-0"},{"key":"2026100109051458000_36.10.2091.28","doi-asserted-by":"publisher","DOI":"10.1080\/0954898X.2024.2435491"},{"key":"2026100109051458000_36.10.2091.29","doi-asserted-by":"publisher","DOI":"10.1007\/s11704-024-40060-2"},{"key":"2026100109051458000_36.10.2091.30","doi-asserted-by":"publisher","DOI":"10.3389\/fnana.2025.1535745"},{"key":"2026100109051458000_36.10.2091.31","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-43120-6"},{"key":"2026100109051458000_36.10.2091.32","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03634-9"},{"key":"2026100109051458000_36.10.2091.33","doi-asserted-by":"publisher","DOI":"10.1016\/j.acthis.2014.04.012"},{"key":"2026100109051458000_36.10.2091.34","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaw1219"},{"key":"2026100109051458000_36.10.2091.35","doi-asserted-by":"publisher","DOI":"10.1002\/ajmg.b.31191"},{"key":"2026100109051458000_36.10.2091.36","doi-asserted-by":"publisher","DOI":"10.3109\/08039488.2013.780260"},{"key":"2026100109051458000_36.10.2091.37","doi-asserted-by":"publisher","DOI":"10.1037\/1082-989X.9.3.386"},{"key":"2026100109051458000_36.10.2091.38","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-0739-1"},{"key":"2026100109051458000_36.10.2091.39","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2018.11.034"},{"key":"2026100109051458000_36.10.2091.40","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-41695-z"},{"key":"2026100109051458000_36.10.2091.41","doi-asserted-by":"publisher","DOI":"10.1186\/bcr2922"},{"key":"2026100109051458000_36.10.2091.42","doi-asserted-by":"publisher","DOI":"10.1186\/s12885-022-09736-5"},{"key":"2026100109051458000_36.10.2091.43","doi-asserted-by":"publisher","DOI":"10.1016\/j.cellbi.2006.09.011"},{"key":"2026100109051458000_36.10.2091.44","doi-asserted-by":"publisher","DOI":"10.1007\/s11432-024-4171-9"},{"key":"2026100109051458000_36.10.2091.45","doi-asserted-by":"publisher","DOI":"10.1126\/science.abp9444"},{"key":"2026100109051458000_36.10.2091.46","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1382-0"},{"key":"2026100109051458000_36.10.2091.47","doi-asserted-by":"publisher","DOI":"10.1111\/acel.14109"},{"key":"2026100109051458000_36.10.2091.48","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac901"},{"key":"2026100109051458000_36.10.2091.49","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-024-01283-x"},{"key":"2026100109051458000_36.10.2091.50","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-56276-0"},{"key":"2026100109051458000_36.10.2091.51","doi-asserted-by":"publisher","DOI":"10.1002\/advs.202410081"},{"key":"2026100109051458000_36.10.2091.52","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-01773-7"},{"key":"2026100109051458000_36.10.2091.53","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaa1934"},{"key":"2026100109051458000_36.10.2091.54","doi-asserted-by":"publisher","DOI":"10.1186\/s12888-019-2088-5"},{"key":"2026100109051458000_36.10.2091.55","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab105"},{"key":"2026100109051458000_36.10.2091.56","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-00935-2"},{"key":"2026100109051458000_36.10.2091.57","doi-asserted-by":"publisher","DOI":"10.4028\/www.scientific.net\/AMR.951.227"}],"container-title":["Genome Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/gr.281999.126","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T16:05:27Z","timestamp":1790870727000},"score":1,"resource":{"primary":{"URL":"http:\/\/genome.cshlp.org\/lookup\/doi\/10.1101\/gr.281999.126"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,16]]},"references-count":57,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2026,10,1]]},"published-print":{"date-parts":[[2026,10]]}},"alternative-id":["10.1101\/gr.281999.126"],"URL":"https:\/\/doi.org\/10.1101\/gr.281999.126","relation":{},"ISSN":["1088-9051","1549-5469"],"issn-type":[{"value":"1088-9051","type":"print"},{"value":"1549-5469","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,16]]}}}