{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,19]],"date-time":"2026-06-19T22:23:33Z","timestamp":1781907813186,"version":"3.54.5"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,4,12]],"date-time":"2025-04-12T00:00:00Z","timestamp":1744416000000},"content-version":"vor","delay-in-days":42,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62372494"],"award-info":[{"award-number":["62372494"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007847","name":"Natural Science Foundation of Jilin Province","doi-asserted-by":"publisher","award":["20240302086GX"],"award-info":[{"award-number":["20240302086GX"]}],"id":[{"id":"10.13039\/100007847","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007847","name":"Natural Science Foundation of Jilin Province","doi-asserted-by":"publisher","award":["20220101117JC"],"award-info":[{"award-number":["20220101117JC"]}],"id":[{"id":"10.13039\/100007847","id-type":"DOI","asserted-by":"publisher"}]}],"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>Identifying spatial domains for spatial transcriptomics is crucial for achieving comprehensive insights into the pathogenesis of gene expression. Increasingly, computational methods based on graph neural networks are being developed for spatial transcriptomics. However, previous methods have solely focused on the Euclidean manifold. To effectively exploit and explore the informative and deeper topological structures of inherent manifolds, we presented a Multi-Manifolds fusing hyperbolic graph network, balanced by Pareto optimization, for identifying spatial domains in Spatial Transcriptomics (MManiST). First, we developed multi-manifolds encoders for distinct manifolds using the hyperbolic neural network. Features from different manifolds were then combined using an attention mechanism, with multiple reconstruction losses balanced by Pareto optimization. Extensive experiments on commonly used benchmark datasets show that our method consistently outperforms seven state-of-the-art methods. Additionally, we investigated the validity of each component and the impact of fusion methods in ablation experiments.<\/jats:p>","DOI":"10.1093\/bib\/bbaf162","type":"journal-article","created":{"date-parts":[[2025,4,12]],"date-time":"2025-04-12T21:10:49Z","timestamp":1744492249000},"source":"Crossref","is-referenced-by-count":1,"title":["Multi-Manifolds fusing hyperbolic graph network balanced by pareto optimization for identifying spatial domains of spatial transcriptomics"],"prefix":"10.1093","volume":"26","author":[{"given":"Ying","family":"Li","sequence":"first","affiliation":[{"name":"Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education , College of Computer Science and Technology, Jilin University, Qianjin Street 2699, Changchun 130012, Jilin,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qifeng","family":"Hu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education , College of Computer Science and Technology, Jilin University, Qianjin Street 2699, Changchun 130012, Jilin,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siyu","family":"Han","sequence":"additional","affiliation":[{"name":"TUM School of Medicine , Technical University of Munich, Ismaninger Stra\u00dfe 22, D-81675 Munich, Bavaria,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui","family":"Wang-Sattler","sequence":"additional","affiliation":[{"name":"Institute of Translational Genomics , Helmholtz Zentrum Munchen, Ingolstadter Landstra\u00dfe 1, D-85764 Neuherberg, Bavaria,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9872-4821","authenticated-orcid":false,"given":"Wei","family":"Du","sequence":"additional","affiliation":[{"name":"Key Laboratory of Symbol Computation and Knowledge Engineering of 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