{"id":"https://openalex.org/W7128996090","doi":"https://doi.org/10.48550/arxiv.2602.12651","title":"Uncovering spatial tissue domains and cell types in spatial omics through cross-scale profiling of cellular and genomic interactions","display_name":"Uncovering spatial tissue domains and cell types in spatial omics through cross-scale profiling of cellular and genomic interactions","publication_year":2026,"publication_date":"2026-02-13","ids":{"openalex":"https://openalex.org/W7128996090","doi":"https://doi.org/10.48550/arxiv.2602.12651"},"language":null,"primary_location":{"id":"pmh:doi:10.48550/arxiv.2602.12651","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":null,"any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5126098937","display_name":"Rui Yan","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Yan, Rui","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080589649","display_name":"Xiaohan Xing","orcid":"https://orcid.org/0000-0002-9992-3387"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xing, Xiaohan","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126128493","display_name":"Xun Wang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Xun","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126075067","display_name":"Zixia Zhou","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhou, Zixia","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101820739","display_name":"Md Tauhidul Islam","orcid":"https://orcid.org/0009-0000-9390-4487"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Islam, Md Tauhidul","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5126102102","display_name":"Lei Xing","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xing, Lei","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5126098937"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10505","display_name":"Pluripotent Stem Cells Research","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.5467000007629395},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.503600001335144},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.48500001430511475},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.4713999927043915},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.46050000190734863},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.4553999900817871},{"id":"https://openalex.org/keywords/multicellular-organism","display_name":"Multicellular organism","score":0.4016999900341034},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.38690000772476196},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.3813000023365021}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.63919997215271},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.5467000007629395},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5049999952316284},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.503600001335144},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.48500001430511475},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4837000072002411},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.4713999927043915},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.46050000190734863},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.4553999900817871},{"id":"https://openalex.org/C74318829","wikidata":"https://www.wikidata.org/wiki/Q36458","display_name":"Multicellular organism","level":3,"score":0.4016999900341034},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.38690000772476196},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3813000023365021},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.38100001215934753},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.3799000084400177},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.35989999771118164},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.34310001134872437},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.3416999876499176},{"id":"https://openalex.org/C64754055","wikidata":"https://www.wikidata.org/wiki/Q7574053","display_name":"Spatial contextual awareness","level":2,"score":0.34139999747276306},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33500000834465027},{"id":"https://openalex.org/C175779824","wikidata":"https://www.wikidata.org/wiki/Q7574078","display_name":"Spatial organization","level":2,"score":0.3176000118255615},{"id":"https://openalex.org/C158709400","wikidata":"https://www.wikidata.org/wiki/Q3578586","display_name":"Spatial ecology","level":2,"score":0.31189998984336853},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.29120001196861267},{"id":"https://openalex.org/C161078062","wikidata":"https://www.wikidata.org/wiki/Q1068690","display_name":"Functional genomics","level":5,"score":0.27059999108314514},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.2628999948501587},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.2619999945163727},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.2524999976158142}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:doi:10.48550/arxiv.2602.12651","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"doi:10.48550/arxiv.2602.12651","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2602.12651","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:doi:10.48550/arxiv.2602.12651","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Cellular":[0],"identity":[1],"and":[2,12,39,43,61,81,112,123,152,165,171],"function":[3],"are":[4],"linked":[5],"to":[6,27,73,89,103],"both":[7],"their":[8],"intrinsic":[9,82],"genomic":[10,83,124],"makeup":[11],"extrinsic":[13],"spatial":[14,42,79,134,149,155],"context":[15],"within":[16,48],"the":[17,41,76],"tissue":[18,121],"microenvironment.":[19],"Spatial":[20],"transcriptomics":[21,160],"(ST)":[22],"offers":[23],"an":[24,163],"unprecedented":[25],"opportunity":[26],"study":[28],"this,":[29],"providing":[30],"in":[31,120],"situ":[32],"gene":[33,138],"expression":[34],"profiles":[35],"at":[36],"single-cell":[37],"resolution":[38],"illuminating":[40],"functional":[44],"organization":[45],"of":[46,173],"cells":[47],"tissues.":[49],"However,":[50],"a":[51,98],"significant":[52],"hurdle":[53],"remains:":[54],"ST":[55,109,174],"data":[56,110],"is":[57],"inherently":[58],"noisy,":[59],"large,":[60],"structurally":[62],"complex.":[63],"This":[64,141],"complexity":[65],"makes":[66],"it":[67],"intractable":[68],"for":[69,107,168],"existing":[70],"computational":[71],"methods":[72],"effectively":[74],"capture":[75],"interplay":[77],"between":[78],"interactions":[80,119],"relationships,":[84],"thus":[85],"limiting":[86],"our":[87],"ability":[88],"discern":[90],"critical":[91],"biological":[92],"patterns.":[93],"Here,":[94],"we":[95],"present":[96],"CellScape,":[97],"deep":[99,169],"learning":[100],"framework":[101,167],"designed":[102],"overcome":[104],"these":[105],"limitations":[106],"high-performance":[108],"analysis":[111,170],"pattern":[113],"discovery.":[114],"CellScape":[115],"jointly":[116],"models":[117],"cellular":[118,156],"space":[122],"relationships":[125],"among":[126],"cells,":[127],"producing":[128],"comprehensive":[129,154],"representations":[130],"that":[131,147],"seamlessly":[132],"integrate":[133],"signals":[135],"with":[136],"underlying":[137],"regulatory":[139],"mechanisms.":[140],"technique":[142],"uncovers":[143],"biologically":[144],"informative":[145],"patterns":[146],"improve":[148],"domain":[150],"segmentation":[151],"supports":[153],"analyses":[157],"across":[158],"diverse":[159],"datasets,":[161],"offering":[162],"accurate":[164],"versatile":[166],"interpretation":[172],"data.w":[175]},"counts_by_year":[],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2026-02-17T00:00:00"}
