{"id":"https://openalex.org/W7151402358","doi":"https://doi.org/10.48550/arxiv.2604.03630","title":"A Multimodal Foundation Model of Spatial Transcriptomics and Histology for Biological Discovery and Clinical Prediction","display_name":"A Multimodal Foundation Model of Spatial Transcriptomics and Histology for Biological Discovery and Clinical Prediction","publication_year":2026,"publication_date":"2026-04-04","ids":{"openalex":"https://openalex.org/W7151402358","doi":"https://doi.org/10.48550/arxiv.2604.03630"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2604.03630","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.03630","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":null,"license_id":null,"version":null,"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":"https://doi.org/10.48550/arxiv.2604.03630","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055991162","display_name":"Jinxi Xiang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiang, Jinxi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033870400","display_name":"Siyu Hou","orcid":"https://orcid.org/0000-0002-5300-6495"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hou, Siyu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133082842","display_name":"Yuchen Li","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Yuchen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011175130","display_name":"Ryan J. Quinton","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Quinton, Ryan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133066441","display_name":"Xiaoming Zhang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhang, Xiaoming","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019610947","display_name":"Feyisope Eweje","orcid":"https://orcid.org/0000-0003-1417-7096"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Eweje, Feyisope","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133071765","display_name":"Xiangde Luo","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Luo, Xiangde","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133093763","display_name":"Yijiang Chen","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chen, Yijiang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133064831","display_name":"Zhe Quan LI","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Zhe","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051472104","display_name":"Colin P. Bergstrom","orcid":"https://orcid.org/0000-0003-3271-0915"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bergstrom, Colin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013007331","display_name":"Ted Kim","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kim, Ted","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133130147","display_name":"Sierra Willens","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Willens, Sierra","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067557639","display_name":"Francesca Olguin","orcid":"https://orcid.org/0000-0002-7290-6579"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Olguin, Francesca Maria","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133097804","display_name":"Matthew Abikenari","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Abikenari, Matthew","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133115092","display_name":"Andrew Heider","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Heider, Andrew","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074665961","display_name":"Sanjeeth Rajaram","orcid":"https://orcid.org/0000-0002-9336-422X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rajaram, Sanjeeth","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034377849","display_name":"Joel W. Neal","orcid":"https://orcid.org/0000-0003-3119-9334"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Neal, Joel","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133096799","display_name":"Maximilian Diehn","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Diehn, Maximilian","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133143213","display_name":"Xiang Zhou","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhou, Xiang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5133132456","display_name":"Ruijiang Li","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Ruijiang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":20,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"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":0.9900000095367432,"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":0.9900000095367432,"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":0.0020000000949949026,"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/T10885","display_name":"Gene expression and cancer classification","score":0.0012000000569969416,"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/context","display_name":"Context (archaeology)","score":0.6269999742507935},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5153999924659729},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.4731000065803528},{"id":"https://openalex.org/keywords/spatial-contextual-awareness","display_name":"Spatial contextual awareness","score":0.33250001072883606},{"id":"https://openalex.org/keywords/foundation","display_name":"Foundation (evidence)","score":0.30480000376701355},{"id":"https://openalex.org/keywords/spatial-ecology","display_name":"Spatial ecology","score":0.28679999709129333}],"concepts":[{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6269999742507935},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5153999924659729},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48019999265670776},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.4731000065803528},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46810001134872437},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4643000066280365},{"id":"https://openalex.org/C64754055","wikidata":"https://www.wikidata.org/wiki/Q7574053","display_name":"Spatial contextual awareness","level":2,"score":0.33250001072883606},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32850000262260437},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32260000705718994},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.322299987077713},{"id":"https://openalex.org/C2780966255","wikidata":"https://www.wikidata.org/wiki/Q5474306","display_name":"Foundation (evidence)","level":2,"score":0.30480000376701355},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.28790000081062317},{"id":"https://openalex.org/C158709400","wikidata":"https://www.wikidata.org/wiki/Q3578586","display_name":"Spatial ecology","level":2,"score":0.28679999709129333},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2822999954223633},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.2736999988555908},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.26969999074935913},{"id":"https://openalex.org/C105306849","wikidata":"https://www.wikidata.org/wiki/Q81054","display_name":"Storm","level":2,"score":0.2667999863624573}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2604.03630","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.03630","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2604.03630","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.03630","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":null,"license_id":null,"version":null,"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":{"Spatial":[0],"transcriptomics":[1],"(ST)":[2],"enables":[3],"gene":[4,60,91],"expression":[5,92],"mapping":[6],"within":[7],"anatomical":[8],"context":[9],"but":[10],"remains":[11],"costly":[12],"and":[13,16,32,62,68,84,111,127,140],"low-throughput.":[14],"Hematoxylin":[15],"eosin":[17],"(H\\&E)":[18],"staining":[19],"offers":[20],"rich":[21],"morphology":[22],"yet":[23],"lacks":[24],"molecular":[25],"resolution.":[26],"We":[27],"present":[28],"\\textbf{\\ours}":[29],"(\\textbf{S}patial":[30],"\\textbf{T}ranscriptomics":[31],"hist\\textbf{O}logy":[33],"\\textbf{R}epresentation":[34],"\\textbf{M}odel),":[35],"a":[36,54,133],"foundation":[37],"model":[38,101],"trained":[39],"on":[40],"1.2":[41],"million":[42],"spatially":[43,137],"resolved":[44],"transcriptomic":[45],"profiles":[46],"with":[47],"matched":[48],"histology":[49],"across":[50,96,106],"18":[51],"organs.":[52],"Using":[53],"hierarchical":[55],"architecture":[56],"integrating":[57],"morphological":[58],"features,":[59],"expression,":[61],"spatial":[63,76,90],"context,":[64],"STORM":[65,74,121],"bridges":[66],"imaging":[67],"omics":[69],"through":[70],"robust":[71],"molecular--morphological":[72],"representations.":[73],"enhances":[75],"domain":[77],"discovery,":[78],"producing":[79],"biologically":[80],"coherent":[81],"tissue":[82],"maps,":[83],"outperforms":[85],"existing":[86],"methods":[87],"in":[88],"predicting":[89],"from":[93],"H\\&E":[94],"images":[95],"11":[97],"tumor":[98],"types.":[99],"The":[100],"is":[102],"platform-agnostic,":[103],"performing":[104],"consistently":[105],"Visium,":[107],"Xenium,":[108],"Visium":[109],"HD,":[110],"CosMx.":[112],"Applied":[113],"to":[114],"23":[115],"independent":[116],"cohorts":[117],"comprising":[118],"7,245":[119],"patients,":[120],"significantly":[122],"improves":[123],"immunotherapy":[124],"response":[125],"prediction":[126],"prognostication":[128],"over":[129],"established":[130],"biomarkers,":[131],"providing":[132],"scalable":[134],"framework":[135],"for":[136],"informed":[138],"discovery":[139],"clinical":[141],"precision":[142],"medicine.":[143]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2026-04-08T00:00:00"}