{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T00:25:58Z","timestamp":1774830358337,"version":"3.50.1"},"reference-count":53,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,1,8]],"date-time":"2024-01-08T00:00:00Z","timestamp":1704672000000},"content-version":"vor","delay-in-days":47,"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":["62225209"],"award-info":[{"award-number":["62225209"]}],"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":["62320106009"],"award-info":[{"award-number":["62320106009"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Hunan Provincial Science and Technology Program","award":["2021RC4008"],"award-info":[{"award-number":["2021RC4008"]}]},{"DOI":"10.13039\/501100012476","name":"Fundamental Research Funds for the Central Universities of Central South University","doi-asserted-by":"publisher","award":["CX20220276"],"award-info":[{"award-number":["CX20220276"]}],"id":[{"id":"10.13039\/501100012476","id-type":"DOI","asserted-by":"publisher"}]},{"name":"High Performance Computing Center of Central South University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>With the development of spatially resolved transcriptomics technologies, it is now possible to explore the gene expression profiles of single cells while preserving their spatial context. Spatial clustering plays a key role in spatial transcriptome data analysis. In the past 2 years, several graph neural network-based methods have emerged, which significantly improved the accuracy of spatial clustering. However, accurately identifying the boundaries of spatial domains remains a challenging task. In this article, we propose stAA, an adversarial variational graph autoencoder, to identify spatial domain. stAA generates cell embedding by leveraging gene expression and spatial information using graph neural networks and enforces the distribution of cell embeddings to a prior distribution through Wasserstein distance. The adversarial training process can make cell embeddings better capture spatial domain information and more robust. Moreover, stAA incorporates global graph information into cell embeddings using labels generated by pre-clustering. Our experimental results show that stAA outperforms the state-of-the-art methods and achieves better clustering results across different profiling platforms and various resolutions. We also conducted numerous biological analyses and found that stAA can identify fine-grained structures in tissues, recognize different functional subtypes within tumors and accurately identify developmental trajectories.<\/jats:p>","DOI":"10.1093\/bib\/bbad500","type":"journal-article","created":{"date-parts":[[2024,1,8]],"date-time":"2024-01-08T11:56:34Z","timestamp":1704714994000},"source":"Crossref","is-referenced-by-count":12,"title":["stAA: adversarial graph autoencoder for spatial clustering task of spatially resolved transcriptomics"],"prefix":"10.1093","volume":"25","author":[{"given":"Zhaoyu","family":"Fang","sequence":"first","affiliation":[{"name":"School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5862-0518","authenticated-orcid":false,"given":"Teng","family":"Liu","sequence":"additional","affiliation":[{"name":"Clinical Research Center (CRC) , Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC), , Chongqing 404031 , China"},{"name":"Chongqing University Three Gorges Hospital, Chongqing University , Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC), , Chongqing 404031 , China"},{"name":"Translational Medicine Research Center (TMRC) , School of Medicine, , Chongqing 401331 , China"},{"name":"Chongqing University , School of Medicine, , Chongqing 401331 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6372-6798","authenticated-orcid":false,"given":"Ruiqing","family":"Zheng","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083 , China"}]},{"given":"Jin","family":"A","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083 , 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