{"id":"https://openalex.org/W7222018709","doi":"https://doi.org/10.64898/2026.10.07.757371","title":"SVC: A Vision Transformer-based Spatially and Virtually Embedded Cell Model for Deciphering Subcellular Spatial Transcriptomic Heterogeneity","display_name":"SVC: A Vision Transformer-based Spatially and Virtually Embedded Cell Model for Deciphering Subcellular Spatial Transcriptomic Heterogeneity","publication_year":2026,"publication_date":"2026-10-14","ids":{"openalex":"https://openalex.org/W7222018709","doi":"https://doi.org/10.64898/2026.10.07.757371","pmid":"https://pubmed.ncbi.nlm.nih.gov/42999060","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13742411"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.07.757371","doi":"https://doi.org/10.64898/2026.10.07.757371","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.07.757371","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/14/2026.10.07.757371.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/14/2026.10.07.757371.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015679423","display_name":"Hui Song Wan","orcid":"https://orcid.org/0000-0003-4217-6250","observed_orcids":["https://orcid.org/0000-0003-4217-6250"]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hui Wan","raw_affiliation_strings":["Department of Statistics and Data Science, Yale University, New Haven, CT, 06511, USA"],"raw_orcid":"https://orcid.org/0000-0003-4217-6250","affiliations":[{"raw_affiliation_string":"Department of Statistics and Data Science, Yale University, New Haven, CT, 06511, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122125731","display_name":"Penghui Yang","orcid":"https://orcid.org/0000-0002-3131-1982","observed_orcids":["https://orcid.org/0000-0002-3131-1982"]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Penghui Yang","raw_affiliation_strings":["Department of Statistics and Data Science, Yale University, New Haven, CT, 06511, USA"],"raw_orcid":"https://orcid.org/0000-0002-3131-1982","affiliations":[{"raw_affiliation_string":"Department of Statistics and Data Science, Yale University, New Haven, CT, 06511, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033870400","display_name":"Siyu Hou","orcid":"https://orcid.org/0000-0002-5300-6495","observed_orcids":["https://orcid.org/0000-0002-5300-6495"]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Siyu Hou","raw_affiliation_strings":["Department of Statistics and Data Science, Yale University, New Haven, CT, 06511, USA"],"raw_orcid":"https://orcid.org/0000-0002-5300-6495","affiliations":[{"raw_affiliation_string":"Department of Statistics and Data Science, Yale University, New Haven, CT, 06511, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059547097","display_name":"Jade Xiaoqing Wang","orcid":"https://orcid.org/0000-0001-5377-0509","observed_orcids":["https://orcid.org/0000-0001-5377-0509"]},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jade Wang","raw_affiliation_strings":["Department of Statistics, Texas A&M University, College Station, TX, USA"],"raw_orcid":"https://orcid.org/0000-0001-5377-0509","affiliations":[{"raw_affiliation_string":"Department of Statistics, Texas A&M University, College Station, TX, USA","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051489598","display_name":"Xiang Zhou","orcid":"https://orcid.org/0000-0002-4331-7599","observed_orcids":["https://orcid.org/0000-0002-4331-7599"]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xiang Zhou","raw_affiliation_strings":["Department of Statistics and Data Science, Yale University, New Haven, CT, 06511, USA"],"raw_orcid":"https://orcid.org/0000-0002-4331-7599","affiliations":[{"raw_affiliation_string":"Department of Statistics and Data Science, Yale University, New Haven, CT, 06511, USA","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5051489598"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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":0.9994999766349792,"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":0.9994999766349792,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.0,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.0,"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/vision-transformer","display_name":"vision transformer","score":0.6859999895095825},{"id":"https://openalex.org/keywords/genetic-perturbation","display_name":"gene perturbation","score":0.7919999957084656},{"id":"https://openalex.org/keywords/tissue-microenvironment","display_name":"tissue microenvironment","score":0.7509999871253967},{"id":"https://openalex.org/keywords/cell-clustering","display_name":"cell clustering","score":0.5},{"id":"https://openalex.org/keywords/spatial-domain-detection","display_name":"spatial domain detection","score":0.9459999799728394}],"concepts":[{"id":"https://openalex.org/C2776879804","wikidata":"https://www.wikidata.org/wiki/Q7630919","display_name":"Subcellular localization","level":3,"score":0.8845000267028809},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.6854000091552734},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.616599977016449},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5956000089645386},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5338000059127808},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4641000032424927},{"id":"https://openalex.org/C140051345","wikidata":"https://www.wikidata.org/wiki/Q7251501","display_name":"Protein subcellular localization prediction","level":3,"score":0.45489999651908875},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4212000072002411},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.415800005197525},{"id":"https://openalex.org/C64754055","wikidata":"https://www.wikidata.org/wiki/Q7574053","display_name":"Spatial contextual awareness","level":2,"score":0.367900013923645},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.3447999954223633},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3294000029563904},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.32339999079704285},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.31690001487731934},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.314300000667572},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.30239999294281006},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.299699991941452},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.2944999933242798},{"id":"https://openalex.org/C175779824","wikidata":"https://www.wikidata.org/wiki/Q7574078","display_name":"Spatial organization","level":2,"score":0.2870999872684479},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.2842000126838684},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.26989999413490295},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25529998540878296}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.64898/2026.10.07.757371","doi":"https://doi.org/10.64898/2026.10.07.757371","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.07.757371","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/14/2026.10.07.757371.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:42999060","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42999060","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.64898/2026.10.07.757371","doi":"https://doi.org/10.64898/2026.10.07.757371","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.07.757371","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/14/2026.10.07.757371.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G9000892906","display_name":"New Computational Tools for Advanced Analytics in Genome-wide Association Studies","funder_award_id":"R01HG009124","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7222018709.pdf","grobid_xml":"https://content.openalex.org/works/W7222018709.grobid-xml"},"referenced_works_count":66,"referenced_works":["https://openalex.org/W1969786859","https://openalex.org/W1984829958","https://openalex.org/W1991750502","https://openalex.org/W1998728023","https://openalex.org/W2007499520","https://openalex.org/W2014643949","https://openalex.org/W2018404810","https://openalex.org/W2030383070","https://openalex.org/W2061556393","https://openalex.org/W2066379001","https://openalex.org/W2072832230","https://openalex.org/W2104567497","https://openalex.org/W2111062891","https://openalex.org/W2153316018","https://openalex.org/W2220068888","https://openalex.org/W2335947287","https://openalex.org/W2345356016","https://openalex.org/W2415341492","https://openalex.org/W2471536144","https://openalex.org/W2511326256","https://openalex.org/W2520858613","https://openalex.org/W2525481091","https://openalex.org/W2611496024","https://openalex.org/W2617226928","https://openalex.org/W2760103357","https://openalex.org/W2782073709","https://openalex.org/W2800801906","https://openalex.org/W2803144214","https://openalex.org/W2907514116","https://openalex.org/W2915848182","https://openalex.org/W2928665623","https://openalex.org/W2944323400","https://openalex.org/W2949693884","https://openalex.org/W2952631022","https://openalex.org/W2953177586","https://openalex.org/W2972445800","https://openalex.org/W2998848181","https://openalex.org/W2999374936","https://openalex.org/W3091156754","https://openalex.org/W3094502228","https://openalex.org/W3134079572","https://openalex.org/W3178979628","https://openalex.org/W3203251881","https://openalex.org/W3208940117","https://openalex.org/W4220765071","https://openalex.org/W4224231300","https://openalex.org/W4229033508","https://openalex.org/W4233120011","https://openalex.org/W4297243391","https://openalex.org/W4310530587","https://openalex.org/W4318777402","https://openalex.org/W4364351837","https://openalex.org/W4389481214","https://openalex.org/W4389938094","https://openalex.org/W4393397152","https://openalex.org/W4393433028","https://openalex.org/W4402312165","https://openalex.org/W4402754294","https://openalex.org/W4403097691","https://openalex.org/W4403174218","https://openalex.org/W4407157130","https://openalex.org/W4408363679","https://openalex.org/W4409190839","https://openalex.org/W4415929068","https://openalex.org/W4416129989","https://openalex.org/W7172519674"],"related_works":["https://openalex.org/W4411035774","https://openalex.org/W4383823218","https://openalex.org/W7117627098","https://openalex.org/W4415930184","https://openalex.org/W4399830347","https://openalex.org/W7160182460","https://openalex.org/W6966866772","https://openalex.org/W4406986984","https://openalex.org/W4390838853","https://openalex.org/W4224218779"],"abstract_inverted_index":{"Abstract":[0],"Subcellular":[1],"transcript":[2,44,130,160,177,231],"localization":[3,60,131],"shapes":[4],"gene":[5,167,181],"regulation":[6],"and":[7,26,36,65,107,116,132,137,140,147,162,185,207,216,228],"cellular":[8,114,183],"function,":[9,182],"yet":[10],"profiling":[11],"it":[12],"at":[13],"scale":[14],"remains":[15],"difficult,":[16],"limiting":[17],"our":[18],"ability":[19],"to":[20,113,166,205],"study":[21],"subcellular":[22,43,59,76,111,129,142,176,230,240],"heterogeneity":[23],"across":[24,105,135],"tissues":[25,136],"disease.":[27],"Here,":[28],"we":[29],"present":[30],"SVC,":[31],"a":[32,223],"Vision":[33],"Transformer-based":[34],"spatially":[35,102,163],"virtually":[37],"embedded":[38],"cell":[39,72,90,97,214],"model":[40],"that":[41,82,109,193],"learns":[42],"organization":[45,112,178,232],"within":[46,69],"native":[47],"tissue":[48,117,186],"context":[49],"directly":[50],"from":[51],"subcellular-resolution":[52,121],"spatial":[53,80,92,122,191,217,241],"transcriptomics.":[54],"SVC":[55,99,125,154,171,221],"represents":[56],"each":[57],"gene\u2019s":[58],"as":[61,73],"an":[62],"image":[63],"patch":[64],"uses":[66],"other":[67],"genes":[68,106,146],"the":[70],"same":[71],"context,":[74,93],"enabling":[75,236],"contextual":[77],"learning":[78],"of":[79,144,158,239],"dependencies":[81],"govern":[83],"intracellular":[84,159],"organization.":[85],"By":[86],"integrating":[87],"gene-function":[88],"priors,":[89],"morphology,":[91],"and,":[94],"when":[95],"available,":[96],"identity,":[98],"captures":[100],"unified,":[101],"grounded":[103],"representations":[104,202],"cells":[108],"connect":[110],"state":[115],"microenvironment.":[118],"Across":[119],"diverse":[120],"transcriptomics":[123],"datasets,":[124],"accurately":[126],"predicts":[127],"cell-specific":[128],"co-organization,":[133],"generalizes":[134],"technical":[138],"platforms,":[139],"supports":[141],"imputation":[143],"unmeasured":[145],"in":[148,175,233],"silico":[149],"perturbation.":[150],"Leveraging":[151],"these":[152],"capabilities,":[153],"highlights":[155],"disease-associated":[156],"patterns":[157],"reorganization":[161],"heterogeneous":[164],"responses":[165],"perturbations.":[168],"Beyond":[169],"prediction,":[170],"reveals":[172],"systematic":[173],"variation":[174],"associated":[179],"with":[180],"states,":[184],"microenvironments,":[187],"uncovering":[188],"de":[189],"novo":[190],"biology":[192],"is":[194],"not":[195],"accessible":[196],"by":[197],"cell-level":[198,211],"analysis.":[199],"SVC\u2019s":[200],"learned":[201],"further":[203],"transfer":[204],"cell-":[206],"tissue-level":[208],"tasks,":[209],"including":[210],"expression":[212],"imputation,":[213],"clustering,":[215],"domain":[218],"detection.":[219],"Together,":[220],"provides":[222],"general":[224],"framework":[225],"for":[226],"modeling":[227],"interrogating":[229],"situ":[234],",":[235],"scalable":[237],"discovery":[238],"biology.":[242]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-10-16T00:00:00"}
