{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T10:12:58Z","timestamp":1784110378494,"version":"3.55.0"},"reference-count":57,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,3,7]],"date-time":"2025-03-07T00:00:00Z","timestamp":1741305600000},"content-version":"vor","delay-in-days":6,"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":["62402382"],"award-info":[{"award-number":["62402382"]}],"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":["62371423"],"award-info":[{"award-number":["62371423"]}],"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":["62102319"],"award-info":[{"award-number":["62102319"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Natural Science Project of Shanxi Provincial Department of Education","award":["23JK0562"],"award-info":[{"award-number":["23JK0562"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Spatial transcriptomics (ST) technology provides gene expression profiles with spatial context, offering critical insights into cellular interactions and tissue architecture. A core task in ST is spatial domain identification, which involves detecting coherent regions with similar spatial expression patterns. However, existing methods often fail to fully exploit spatial information, leading to limited representational capacity and suboptimal clustering accuracy. Here, we introduce MAEST, a novel graph neural network model designed to address these limitations in ST data. MAEST leverages graph masked autoencoders to denoise and refine representations while incorporating graph contrastive learning to prevent feature collapse and enhance model robustness. By integrating one-hop and multi-hop representations, MAEST effectively captures both local and global spatial relationships, improving clustering precision. Extensive experiments across diverse datasets, including the human brain, mouse hippocampus, olfactory bulb, brain, and embryo, demonstrate that MAEST outperforms seven state-of-the-art methods in spatial domain identification. Furthermore, MAEST showcases its ability to integrate multi-slice data, identifying joint domains across horizontal tissue sections with high accuracy. These results highlight MAEST\u2019s versatility and effectiveness in unraveling the spatial organization of complex tissues. The source code of MAEST can be obtained at https:\/\/github.com\/clearlove2333\/MAEST.<\/jats:p>","DOI":"10.1093\/bib\/bbaf086","type":"journal-article","created":{"date-parts":[[2025,3,7]],"date-time":"2025-03-07T10:40:36Z","timestamp":1741344036000},"source":"Crossref","is-referenced-by-count":16,"title":["MAEST: accurately spatial domain detection in spatial transcriptomics with graph masked autoencoder"],"prefix":"10.1093","volume":"26","author":[{"given":"Pengfei","family":"Zhu","sequence":"first","affiliation":[{"name":"School of Computer Science , Northwestern Polytechnical University, 1 Dongxiang Road, Xi\u2019an 710072,","place":["China"]},{"name":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Road, Xi\u2019an 710072,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han","family":"Shu","sequence":"additional","affiliation":[{"name":"School of Computer Science , Northwestern Polytechnical University, 1 Dongxiang Road, Xi\u2019an 710072,","place":["China"]},{"name":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Road, Xi\u2019an 710072,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongtian","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Computer Science , Northwestern Polytechnical University, 1 Dongxiang Road, Xi\u2019an 710072,","place":["China"]},{"name":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Road, Xi\u2019an 710072,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaofeng","family":"Wang","sequence":"additional","affiliation":[{"name":"General Surgery Department , The Affiliated Hospital of Northwest University: Xi\u2019an No 3 Hospital, Xi\u2019an 710018,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Zhao","sequence":"additional","affiliation":[{"name":"School of Computer Science , Northwestern Polytechnical University, 1 Dongxiang Road, Xi\u2019an 710072,","place":["China"]},{"name":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Road, Xi\u2019an 710072,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jialu","family":"Hu","sequence":"additional","affiliation":[{"name":"School of Computer Science , Northwestern Polytechnical University, 1 Dongxiang Road, Xi\u2019an 710072,","place":["China"]},{"name":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Road, Xi\u2019an 710072,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiajie","family":"Peng","sequence":"additional","affiliation":[{"name":"School of Computer Science , Northwestern Polytechnical University, 1 Dongxiang Road, Xi\u2019an 710072,","place":["China"]},{"name":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Road, Xi\u2019an 710072,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuequn","family":"Shang","sequence":"additional","affiliation":[{"name":"School of Computer Science , Northwestern Polytechnical University, 1 Dongxiang Road, Xi\u2019an 710072,","place":["China"]},{"name":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Road, Xi\u2019an 710072,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Tian","sequence":"additional","affiliation":[{"name":"School of Computer Science and Artificial Intelligence , Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering , Xi\u2019an University of Technology, No. 5 South Jinhua Road, Xi\u2019an 710048,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Computer Science , Northwestern Polytechnical University, 1 Dongxiang Road, Xi\u2019an 710072,","place":["China"]},{"name":"Key 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