{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T05:45:57Z","timestamp":1782452757121,"version":"3.54.5"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T00:00:00Z","timestamp":1781481600000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Science Foundation for Distinguished Young Scholars of China","award":["62225109"],"award-info":[{"award-number":["62225109"]}]},{"DOI":"10.13039\/501100005046","name":"Natural Science Foundation of Heilongjiang Province, China","doi-asserted-by":"crossref","award":["LH2024F003"],"award-info":[{"award-number":["LH2024F003"]}],"id":[{"id":"10.13039\/501100005046","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The rapid growth of spatial transcriptomics data holds potential for deep understanding of spatial specificity and tissue heterogeneity. Recognizing spatial domains is a fundamental step for deciphering tissue functional architecture and dissecting tissue heterogeneity. However, existing models typically define adjacency relations using static weights, which cannot dynamically adjust neighbor importance based on expression context, thereby limiting the accuracy and robustness of spatial domain recognition.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose spAttClu, a clustering model integrating spatially weighted graph attention with contrastive learning. It adaptively learns neighbor contributions in varying contexts through a distance-weighted graph attention mechanism and enhances embedding discriminability via multi-level contrastive learning. spAttClu demonstrates superior clustering performance on the DLPFC dataset. Moreover, it shows cross-platform adaptability and enables vertical\/horizontal inte-gration of multiple tissue slices.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag384","type":"journal-article","created":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T11:25:33Z","timestamp":1781522733000},"source":"Crossref","is-referenced-by-count":0,"title":["spAttClu: a spatial domain clustering model leveraging spatially weighted graph attention and contrastive learning"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9807-8620","authenticated-orcid":false,"given":"Tianjiao","family":"Zhang","sequence":"first","affiliation":[{"name":"School of Computer Science and Artificial Intelligence, Northeast Forestry University , Harbin, 150040,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruolan","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Artificial Intelligence, Northeast Forestry University , Harbin, 150040,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongfei","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Artificial Intelligence, Northeast Forestry University , Harbin, 150040,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-6754-7109","authenticated-orcid":false,"given":"Zhongqian","family":"Zhao","sequence":"additional","affiliation":[{"name":"School of Computer Science and Artificial Intelligence, Northeast Forestry University , Harbin, 150040,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruihan","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Artificial Intelligence, Northeast Forestry University , Harbin, 150040,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shenghe","family":"Li","sequence":"additional","affiliation":[{"name":"School of Computer Science and Artificial Intelligence, Northeast Forestry University , Harbin, 150040,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yucai","family":"Jiang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Artificial Intelligence, Northeast Forestry University , Harbin, 150040,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Binyang","family":"Wei","sequence":"additional","affiliation":[{"name":"School of Computer Science and Artificial Intelligence, Northeast Forestry University , Harbin, 150040,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7381-2374","authenticated-orcid":false,"given":"Guohua","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Artificial Intelligence, Northeast Forestry University , Harbin, 150040,","place":["China"]},{"name":"Faculty of Computing, Harbin Institute of Technology , Harbin, 150001,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,6,13]]},"reference":[{"key":"2026062600515793500_btag384-B1","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1038\/s42003-025-08015-w","article-title":"Spatially informed graph transformers for spatially resolved transcriptomics","volume":"8","author":"Bao","year":"2025","journal-title":"Commun Biol"},{"key":"2026062600515793500_btag384-B2","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1038\/s41592-022-01728-4","article-title":"Screening cell-cell communication in spatial transcriptomics via collective optimal transport","volume":"20","author":"Cang","year":"2023","journal-title":"Nat Methods"},{"key":"2026062600515793500_btag384-B3","doi-asserted-by":"publisher","first-page":"1777","DOI":"10.1016\/j.cell.2022.04.003","article-title":"Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays","volume":"185","author":"Chen","year":"2022","journal-title":"Cell"},{"key":"2026062600515793500_btag384-B4","doi-asserted-by":"crossref","first-page":"771229","DOI":"10.3389\/fnana.2021.771229","article-title":"High-throughput strategy for profiling sequential section with multiplex staining of mouse brain","volume":"15","author":"Chen","year":"2021","journal-title":"Front Neuroanat"},{"key":"2026062600515793500_btag384-B5","doi-asserted-by":"publisher","first-page":"1739","DOI":"10.1038\/s41467-022-29439-6","article-title":"Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder","volume":"13","author":"Dong","year":"2022","journal-title":"Nat Commun"},{"key":"2026062600515793500_btag384-B6","doi-asserted-by":"publisher","first-page":"e50","DOI":"10.1093\/nar\/gkab043","article-title":"Spotlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes","volume":"49","author":"Elosua-Bayes","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026062600515793500_btag384-B7","doi-asserted-by":"publisher","first-page":"3977","DOI":"10.1038\/s41467-025-59139-w","article-title":"Unveiling fine-scale spatial structures and amplifying gene expression signals in ultra-large ST slices with HERGAST","volume":"16","author":"Gong","year":"2025","journal-title":"Nat Commun"},{"key":"2026062600515793500_btag384-B8","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1214\/24-BA1431","article-title":"Default priors for the smoothness parameter in gaussian mat\u00e9rn random fields","volume":"20","author":"Han","year":"2025","journal-title":"Bayesian Anal"},{"key":"2026062600515793500_btag384-B9","doi-asserted-by":"publisher","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"2026062600515793500_btag384-B10","doi-asserted-by":"publisher","first-page":"1342","DOI":"10.1038\/s41592-021-01255-8","article-title":"Spagcn: integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network","volume":"18","author":"Hu","year":"2021","journal-title":"Nat Methods"},{"key":"2026062600515793500_btag384-B11","doi-asserted-by":"publisher","first-page":"1004","DOI":"10.3390\/life14081004","article-title":"The Mclust analysis of tumor budding unveils the role of the collagen family in cervical cancer progression","volume":"14","author":"Lee","year":"2024","journal-title":"Life"},{"key":"2026062600515793500_btag384-B12","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1186\/s13059-022-02734-7","article-title":"Bass: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies","volume":"23","author":"Li","year":"2022","journal-title":"Genome Biol"},{"key":"2026062600515793500_btag384-B13","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbae578","article-title":"Spagic: graph-informed clustering in spatial transcriptomics via self-supervised contrastive learning","volume":"25","author":"Liu","year":"2024","journal-title":"Brief Bioinform"},{"key":"2026062600515793500_btag384-B14","doi-asserted-by":"publisher","first-page":"1155","DOI":"10.1038\/s41467-023-36796-3","article-title":"Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST","volume":"14","author":"Long","year":"2023","journal-title":"Nat Commun"},{"key":"2026062600515793500_btag384-B15","doi-asserted-by":"publisher","first-page":"3591","DOI":"10.1038\/s41467-025-58439-5","article-title":"Identifying potential risk genes for clear cell renal cell carcinoma with deep reinforcement learning","volume":"16","author":"Lu","year":"2025","journal-title":"Nat Commun"},{"key":"2026062600515793500_btag384-B16","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbaf574","article-title":"Slgca: spatial cross-level graph contrastive autoencoder for multislice spatial domain identification and microenvironment exploration","volume":"26","author":"Lu","year":"2025","journal-title":"Brief Bioinform"},{"key":"2026062600515793500_btag384-B17","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1038\/s41593-021-00817-5","article-title":"Publisher correction: transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex","volume":"24","author":"Maynard","year":"2021","journal-title":"Nat Neurosci"},{"key":"2026062600515793500_btag384-B18","doi-asserted-by":"publisher","first-page":"e1012881","DOI":"10.1371\/journal.pcbi.1012881","article-title":"Spamask: dual masking graph autoencoder with contrastive learning for spatial transcriptomics","volume":"21","author":"Min","year":"2025","journal-title":"PLoS Comput Biol"},{"key":"2026062600515793500_btag384-B19","doi-asserted-by":"publisher","DOI":"10.1126\/science.aau5324","article-title":"Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region","volume":"362.","author":"Moffitt","year":"2018","journal-title":"Science"},{"key":"2026062600515793500_btag384-B20","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1038\/s41576-022-00515-3","article-title":"The emerging landscape of spatial profiling technologies","volume":"23","author":"Moffitt","year":"2022","journal-title":"Nat Rev Genet"},{"key":"2026062600515793500_btag384-B21","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1038\/s41592-022-01409-2","article-title":"Museum of spatial transcriptomics","volume":"19","author":"Moses","year":"2022","journal-title":"Nat Methods"},{"key":"2026062600515793500_btag384-B22","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-025-03489-7","article-title":"Spatialleiden: spatially aware Leiden clustering","volume":"26.","author":"M\u00fcller-B\u00f6tticher","year":"2025","journal-title":"Genome Biol"},{"key":"2026062600515793500_btag384-B23","doi-asserted-by":"crossref","DOI":"10.1016\/j.knosys.2020.105861","article-title":"Deep multiplex graph infomax: attentive multiplex network embedding using global information","volume":"197.","author":"Park","year":"2020","journal-title":"Knowl-Based Syst"},{"key":"2026062600515793500_btag384-B24","doi-asserted-by":"publisher","first-page":"4076","DOI":"10.1038\/s41467-022-31739-w","article-title":"Identifying multicellular spatiotemporal organization of cells with SpaceFlow","volume":"13","author":"Ren","year":"2022","journal-title":"Nat Commun"},{"key":"2026062600515793500_btag384-B25","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1038\/nmeth.4636","article-title":"Spatialde: identification of spatially variable genes","volume":"15","author":"Svensson","year":"2018","journal-title":"Nat Methods"},{"key":"2026062600515793500_btag384-B26","doi-asserted-by":"publisher","first-page":"1351","DOI":"10.1038\/s42003-024-07037-0","article-title":"Graph attention automatic encoder based on contrastive learning for domain recognition of spatial transcriptomics","volume":"7","author":"Wang","year":"2024","journal-title":"Commun Biol"},{"key":"2026062600515793500_btag384-B27","doi-asserted-by":"publisher","DOI":"10.1126\/science.aat5691","article-title":"Three-dimensional intact-tissue sequencing of single-cell transcriptional states","volume":"361","author":"Wang","year":"2018","journal-title":"Science"},{"key":"2026062600515793500_btag384-B28","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1186\/s13059-025-03636-0","article-title":"Spclue: a contrastive learning approach to unified spatial transcriptomics analysis across single-slice and multi-slice data","volume":"26","author":"Wang","year":"2025","journal-title":"Genome Biol"},{"key":"2026062600515793500_btag384-B29","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1186\/s13073-025-01449-1","article-title":"Mucst: restoring and integrating heterogeneous morphology images and spatial transcriptomics data with contrastive learning","volume":"17","author":"Wang","year":"2025","journal-title":"Genome Med"},{"key":"2026062600515793500_btag384-B30","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1186\/s13059-025-03601-x","article-title":"Mnsf: multi-sample non-negative spatial factorization","volume":"26","author":"Wang","year":"2025","journal-title":"Genome Biol"},{"key":"2026062600515793500_btag384-B31","doi-asserted-by":"crossref","DOI":"10.1038\/s43588-026-00976-0","article-title":"Dualgpt-AB: a dual-stage generative optimization framework for therapeutic antibody design","author":"Xie","year":"2026","journal-title":"Nat Comput Sci"},{"key":"2026062600515793500_btag384-B32","doi-asserted-by":"publisher","first-page":"e131","DOI":"10.1093\/nar\/gkac901","article-title":"Deepst: identifying spatial domains in spatial transcriptomics by deep learning","volume":"50","author":"Xu","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026062600515793500_btag384-B33","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1186\/s13059-025-03503-y","article-title":"Stdyer enables spatial domain clustering with dynamic graph embedding","volume":"26","author":"Xu","year":"2025","journal-title":"Genome Biol"},{"key":"2026062600515793500_btag384-B34","doi-asserted-by":"publisher","first-page":"e1011935","DOI":"10.1371\/journal.pcbi.1011935","article-title":"Stgic: a graph and image convolution-based method for spatial transcriptomic clustering","volume":"20","author":"Zhang","year":"2024","journal-title":"PLoS Comput Biol"},{"key":"2026062600515793500_btag384-B35","article-title":"Sgcd: high-resolution spatial domain characterization via data interpolation and cell-type deconvolution","volume":"12","author":"Zhang","year":"2025","journal-title":"Adv Sci"},{"key":"2026062600515793500_btag384-B36","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-025-03637-z","article-title":"Spamgcn: a graph convolutional network with autoencoder for spatial domain identification using multi-scale adaptation","volume":"26","author":"Zhang","year":"2025","journal-title":"Genome Biol"},{"key":"2026062600515793500_btag384-B37","doi-asserted-by":"publisher","first-page":"1375","DOI":"10.1038\/s41587-021-00935-2","article-title":"Spatial transcriptomics at subspot resolution with BayesSpace","volume":"39","author":"Zhao","year":"2021","journal-title":"Nat Biotechnol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag384\/68524509\/btag384.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/6\/btag384\/68524509\/btag384.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/6\/btag384\/68524509\/btag384.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T04:52:10Z","timestamp":1782449530000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag384\/8707842"}},"subtitle":[],"editor":[{"given":"Macha","family":"Nikolski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,6,1]]},"references-count":37,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2026,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag384","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,6]]},"published":{"date-parts":[[2026,6,1]]},"article-number":"btag384"}}