{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T16:47:09Z","timestamp":1785775629090,"version":"3.56.0"},"reference-count":102,"publisher":"Wiley","issue":"43","license":[{"start":{"date-parts":[[2026,5,10]],"date-time":"2026-05-10T00:00:00Z","timestamp":1778371200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,5,10]],"date-time":"2026-05-10T00:00:00Z","timestamp":1778371200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2020YFA0712400"],"award-info":[{"award-number":["2020YFA0712400"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62272270"],"award-info":[{"award-number":["62272270"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["advanced.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Advanced Science"],"published-print":{"date-parts":[[2026,8]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Spatial transcriptomics provides high\u2010throughput measurement of gene expression while retaining spatial context; however, inferring accurate cell\u2010type compositions within individual spots remains a major challenge. Here, we present STAID, a unified framework that effectively integrates pseudo\u2010spot generation with deep learning training through iterative pseudo\u2010spot refinement and leverages graph signal processing to capture higher\u2010order gene\u2010wise relationships. By creating a self\u2010reinforcing cycle, STAID enables accurate spot\u2010level deconvolution of cell\u2010type compositions for spatial transcriptomics data. Comprehensive benchmarking demonstrates that STAID outperforms existing methods, accurately reconstructs cell\u2010type spatial distributions, and effectively resolves the cellular colocalization. In clinical breast cancer sections, STAID precisely infers tumor epithelial distributions and reveals their spatial associations with immune cells. In human embryonic limb datasets, STAID captures the ordered spatial distributions of key progenitor populations, reflecting hierarchical tissue organization and demonstrating that incorporating cell\u2010type composition information can enhance tissue segmentation. STAID also resolves the spatial cellular organization in Crohn's disease and reveals the characteristics of TLS\u2010like immune niches. Collectively, by delivering high\u2010resolution cell\u2010type distributions, STAID provides deeper insights into tissue organization and cellular heterogeneity.<\/jats:p>","DOI":"10.1002\/advs.75607","type":"journal-article","created":{"date-parts":[[2026,5,10]],"date-time":"2026-05-10T17:29:46Z","timestamp":1778434186000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["STAID: A Self\u2010Refining Deep Learning Framework for Spatial Cell\u2010Type Deconvolution with Biologically Informed Modeling"],"prefix":"10.1002","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-8133-8956","authenticated-orcid":false,"given":"Jixin","family":"Liu","sequence":"first","affiliation":[{"name":"School of Mathematics Shandong University  Jinan Shandong China"},{"name":"Mathematical Research Center Shandong University  Jinan Shandong China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuli","family":"Sun","sequence":"additional","affiliation":[{"name":"Research Center for Mathematics and Interdisciplinary Sciences (Frontiers Science Center for Nonlinear Expectations) Shandong University  Qingdao China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhengliang","family":"Lv","sequence":"additional","affiliation":[{"name":"School of Mathematics Shandong University  Jinan Shandong China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5629-8550","authenticated-orcid":false,"given":"Xinyu","family":"Liu","sequence":"additional","affiliation":[{"name":"Breast Center The Second Hospital of Shandong University  Jinan Shandong China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yihua","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Mathematics Shandong University  Jinan Shandong China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5734-1135","authenticated-orcid":false,"given":"Bingqiang","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Mathematics Shandong University  Jinan Shandong China"},{"name":"State Key Laboratory of Cryptography and Digital Economy Security Shandong University  Jinan Shandong China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,5,10]]},"reference":[{"key":"e_1_2_12_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010022\u201001409\u20102"},{"key":"e_1_2_12_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2023.04.007"},{"key":"e_1_2_12_4_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaf2403"},{"key":"e_1_2_12_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.omtn.2021.12.009"},{"key":"e_1_2_12_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587\u2010021\u201000935\u20102"},{"key":"e_1_2_12_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010021\u201003634\u20109"},{"key":"e_1_2_12_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41580\u2010024\u201000768\u20102"},{"key":"e_1_2_12_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010022\u201001728\u20104"},{"key":"e_1_2_12_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41582\u2010023\u201000809\u2010y"},{"key":"e_1_2_12_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41593\u2010022\u201001011\u2010x"},{"key":"e_1_2_12_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.06.038"},{"key":"e_1_2_12_13_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abb9536"},{"key":"e_1_2_12_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41556\u2010024\u201001597\u20103"},{"key":"e_1_2_12_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010023\u201001435\u20106"},{"key":"e_1_2_12_16_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12943\u2010024\u201002040\u20109"},{"key":"e_1_2_12_17_1","doi-asserted-by":"publisher","DOI":"10.1002\/ctm2.1515"},{"key":"e_1_2_12_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010023\u201040271\u20104"},{"key":"e_1_2_12_19_1","doi-asserted-by":"publisher","DOI":"10.1158\/0008\u20105472.Can\u201023\u20101418"},{"key":"e_1_2_12_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010025\u201002225\u2010y"},{"key":"e_1_2_12_21_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010022\u201035319\u2010w"},{"key":"e_1_2_12_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhep.2020.06.004"},{"key":"e_1_2_12_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/s44161\u2010022\u201000160\u20103"},{"key":"e_1_2_12_24_1","doi-asserted-by":"publisher","DOI":"10.1126\/sciimmunol.abq7991"},{"key":"e_1_2_12_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010024\u201051186\u2010z"},{"key":"e_1_2_12_26_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.05.035"},{"key":"e_1_2_12_27_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aat5691"},{"key":"e_1_2_12_28_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abm1741"},{"key":"e_1_2_12_29_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010025\u201063185\u20109"},{"key":"e_1_2_12_30_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa740"},{"key":"e_1_2_12_31_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010022\u201001480\u20109"},{"key":"e_1_2_12_32_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbae388"},{"key":"e_1_2_12_33_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41413\u2010025\u201000429\u2010w"},{"key":"e_1_2_12_34_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12967\u2010023\u201004150\u20102"},{"key":"e_1_2_12_35_1","doi-asserted-by":"publisher","DOI":"10.3389\/abp.2025.13922"},{"key":"e_1_2_12_36_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41576\u2010025\u201000845\u2010y"},{"key":"e_1_2_12_37_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010023\u201037168\u20107"},{"key":"e_1_2_12_38_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010023\u201002166\u20106"},{"key":"e_1_2_12_39_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059\u2010021\u201002362\u20107"},{"key":"e_1_2_12_40_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587\u2010021\u201001139\u20104"},{"key":"e_1_2_12_41_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587\u2010021\u201000830\u2010w"},{"key":"e_1_2_12_42_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbaa414"},{"key":"e_1_2_12_43_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059\u2010024\u201003353\u20100"},{"key":"e_1_2_12_44_1","doi-asserted-by":"crossref","unstructured":"D. C.MarcuandC.Grava \u201cThe Importance of Data Quality in Training a Deep Convolutional Neural Network \u201d in2023 17th International Conference on Engineering of Modern Electric Systems (EMES) (IEEE 2023).","DOI":"10.1109\/EMES58375.2023.10171785"},{"key":"e_1_2_12_45_1","doi-asserted-by":"publisher","DOI":"10.2202\/1544\u20106115.1128"},{"key":"e_1_2_12_46_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000117"},{"key":"e_1_2_12_47_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac901"},{"key":"e_1_2_12_48_1","first-page":"1740","volume-title":"Proceedings of the IEEE\/CVF Conference on Computer Vision and Pattern Recognition","author":"Xu K.","year":"2020"},{"key":"e_1_2_12_49_1","doi-asserted-by":"crossref","unstructured":"J.Li S.You andA.Robles\u2010Kelly \u201cA Frequency Domain Neural Network for Fast Image Super\u2010Resolution \u201d in2018 International Joint Conference on Neural Networks (IJCNN) (IEEE 2018).","DOI":"10.1109\/IJCNN.2018.8489155"},{"key":"e_1_2_12_50_1","doi-asserted-by":"publisher","DOI":"10.1017\/dce.2025.10023"},{"key":"e_1_2_12_51_1","doi-asserted-by":"publisher","DOI":"10.1109\/TSP.2014.2321121"},{"key":"e_1_2_12_52_1","doi-asserted-by":"publisher","DOI":"10.1109\/MSP.2020.3014590"},{"key":"e_1_2_12_53_1","doi-asserted-by":"publisher","DOI":"10.1109\/MSP.2020.3014591"},{"key":"e_1_2_12_54_1","doi-asserted-by":"publisher","DOI":"10.1109\/JPROC.2018.2820126"},{"key":"e_1_2_12_55_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587\u2010023\u201001697\u20109"},{"key":"e_1_2_12_56_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587\u2010020\u20100739\u20101"},{"key":"e_1_2_12_57_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010023\u201040458\u20109"},{"key":"e_1_2_12_58_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003\u2010020\u201001247\u2010y"},{"key":"e_1_2_12_59_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587\u2010022\u201001272\u20108"},{"key":"e_1_2_12_60_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab043"},{"key":"e_1_2_12_61_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbaf052"},{"key":"e_1_2_12_62_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010021\u201001264\u20107"},{"key":"e_1_2_12_63_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2021.09.004"},{"key":"e_1_2_12_64_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.crmeth.2024.100841"},{"key":"e_1_2_12_65_1","doi-asserted-by":"publisher","DOI":"10.21203\/rs.3.rs\u20102481749\/v1"},{"key":"e_1_2_12_66_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010021\u201000911\u20101"},{"key":"e_1_2_12_67_1","doi-asserted-by":"publisher","DOI":"10.1002\/1097\u20100142(19940815)74:4<1275::aid\u2010cncr2820740416>3.0.co;2\u2010q"},{"key":"e_1_2_12_68_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1600\u20100560.2010.01506.x"},{"key":"e_1_2_12_69_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jri.2005.06.002"},{"key":"e_1_2_12_70_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41523\u2010024\u201000712\u20109"},{"key":"e_1_2_12_71_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12885\u2010020\u20106668\u2010z"},{"key":"e_1_2_12_72_1","doi-asserted-by":"publisher","DOI":"10.1002\/cam4.5207"},{"key":"e_1_2_12_73_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.matbio.2019.12.004"},{"key":"e_1_2_12_74_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010023\u201006806\u2010x"},{"key":"e_1_2_12_75_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2023.02.013"},{"key":"e_1_2_12_76_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2025.06.031"},{"key":"e_1_2_12_77_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010024\u201002371\u2010x"},{"key":"e_1_2_12_78_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598\u2010019\u201041695\u2010z"},{"key":"e_1_2_12_79_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13062\u2010020\u201000280\u20105"},{"key":"e_1_2_12_80_1","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2021.661931"},{"key":"e_1_2_12_81_1","doi-asserted-by":"publisher","DOI":"10.1002\/cphy.c170003"},{"key":"e_1_2_12_82_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41590\u2010025\u201002146\u20102"},{"key":"e_1_2_12_83_1","doi-asserted-by":"publisher","DOI":"10.3390\/cells2030621"},{"key":"e_1_2_12_84_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jid.2024.06.1275"},{"key":"e_1_2_12_85_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41581\u2010023\u201000706\u2010z"},{"key":"e_1_2_12_86_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587\u2010023\u201002019\u20109"},{"key":"e_1_2_12_87_1","doi-asserted-by":"publisher","DOI":"10.1038\/s44276\u2010025\u201000146\u20101"},{"key":"e_1_2_12_88_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13046\u2010025\u201003318\u20106"},{"key":"e_1_2_12_89_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010024\u201051590\u20105"},{"key":"e_1_2_12_90_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010025\u201057072\u20106"},{"key":"e_1_2_12_91_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010023\u201040503\u20107"},{"key":"e_1_2_12_92_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059\u2010017\u20101382\u20100"},{"key":"e_1_2_12_93_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587\u2010019\u20100392\u20108"},{"key":"e_1_2_12_94_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587\u2010019\u20100113\u20103"},{"key":"e_1_2_12_95_1","doi-asserted-by":"publisher","DOI":"10.1093\/biostatistics\/kxj037"},{"key":"e_1_2_12_96_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010023\u201002035\u20102"},{"key":"e_1_2_12_97_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2416516122"},{"key":"e_1_2_12_98_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2025.11.059"},{"key":"e_1_2_12_99_1","doi-asserted-by":"crossref","unstructured":"B.Xu L.Zhang andA.Song \u201cWavelet Transform Time\u2010Frequency Image and Convolutional Network\u2010Based Motor Imagery EEG Classification \u201d inIEEE Access(IEEE 2018) 6084\u20136093.","DOI":"10.1109\/ACCESS.2018.2889093"},{"key":"e_1_2_12_100_1","first-page":"1457","article-title":"Non\u2010Negative Matrix Factorization With Sparseness Constraints","volume":"5","author":"Hoyer P. O.","year":"2004","journal-title":"Journal of Machine Learning Research"},{"key":"e_1_2_12_101_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac757"},{"key":"e_1_2_12_102_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aau5324"},{"key":"e_1_2_12_103_1","unstructured":"Spatial Transcriptomics Dataset of Mouse Brains by SeekSpace https:\/\/ngdc.cncb.ac.cn\/omix\/release\/OMIX016242 (2026)."}],"container-title":["Advanced Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/advanced.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/advs.75607","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/advanced.onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/advs.75607","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/advanced.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/advs.75607","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T16:02:32Z","timestamp":1785772952000},"score":1,"resource":{"primary":{"URL":"https:\/\/advanced.onlinelibrary.wiley.com\/doi\/10.1002\/advs.75607"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,10]]},"references-count":102,"journal-issue":{"issue":"43","published-print":{"date-parts":[[2026,8]]}},"alternative-id":["10.1002\/advs.75607"],"URL":"https:\/\/doi.org\/10.1002\/advs.75607","archive":["Portico"],"relation":{},"ISSN":["2198-3844","2198-3844"],"issn-type":[{"value":"2198-3844","type":"print"},{"value":"2198-3844","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,10]]},"assertion":[{"value":"2026-02-10","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-04-28","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-05-10","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e75607"}}