{"id":"https://openalex.org/W7129451179","doi":"https://doi.org/10.48550/arxiv.2602.14177","title":"Towards Spatial Transcriptomics-driven Pathology Foundation Models","display_name":"Towards Spatial Transcriptomics-driven Pathology Foundation Models","publication_year":2026,"publication_date":"2026-02-15","ids":{"openalex":"https://openalex.org/W7129451179","doi":"https://doi.org/10.48550/arxiv.2602.14177"},"language":null,"primary_location":{"id":"pmh:doi:10.48550/arxiv.2602.14177","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":null,"license_id":null,"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/A5069476972","display_name":"Konstantin Hemker","orcid":"https://orcid.org/0009-0008-6414-0551"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Hemker, Konstantin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066569995","display_name":"Andrew H. Song","orcid":"https://orcid.org/0000-0001-9356-9156"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Song, Andrew H.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126173158","display_name":"Cristina Almagro-P\u00e9rez","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Almagro-P\u00e9rez, Cristina","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078448683","display_name":"Guillaume Jaume","orcid":"https://orcid.org/0000-0002-3832-1390"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jaume, Guillaume","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Wagner, Sophia J.","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wagner, Sophia J.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023061511","display_name":"Anurag Vaidya","orcid":"https://orcid.org/0000-0001-6378-6010"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Vaidya, Anurag","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003682166","display_name":"Nikola Simidjievski","orcid":"https://orcid.org/0000-0003-3948-6370"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Simidjievski, Nikola","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036018012","display_name":"Mateja Jamnik","orcid":"https://orcid.org/0000-0003-2772-2532"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jamnik, Mateja","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5126181496","display_name":"Faisal Mahmood","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mahmood, Faisal","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5069476972"],"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":0.9710000157356262,"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":0.9710000157356262,"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":0.014600000344216824,"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/T11307","display_name":"Domain Adaptation and Few-Shot Learning","score":0.003100000089034438,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/foundation","display_name":"Foundation (evidence)","score":0.6546000242233276},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.498199999332428},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.4867999851703644},{"id":"https://openalex.org/keywords/seal","display_name":"Seal (emblem)","score":0.4178999960422516},{"id":"https://openalex.org/keywords/modalities","display_name":"Modalities","score":0.3785000145435333},{"id":"https://openalex.org/keywords/molecular-pathology","display_name":"Molecular pathology","score":0.35420000553131104},{"id":"https://openalex.org/keywords/human-disease","display_name":"Human disease","score":0.3467000126838684}],"concepts":[{"id":"https://openalex.org/C2780966255","wikidata":"https://www.wikidata.org/wiki/Q5474306","display_name":"Foundation (evidence)","level":2,"score":0.6546000242233276},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5730999708175659},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5493000149726868},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.498199999332428},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.4867999851703644},{"id":"https://openalex.org/C2777755289","wikidata":"https://www.wikidata.org/wiki/Q162919","display_name":"Seal (emblem)","level":2,"score":0.4178999960422516},{"id":"https://openalex.org/C2779903281","wikidata":"https://www.wikidata.org/wiki/Q6888026","display_name":"Modalities","level":2,"score":0.3785000145435333},{"id":"https://openalex.org/C74092355","wikidata":"https://www.wikidata.org/wiki/Q1056943","display_name":"Molecular pathology","level":3,"score":0.35420000553131104},{"id":"https://openalex.org/C2988867146","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Human disease","level":3,"score":0.3467000126838684},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.3402000069618225},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33469998836517334},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.29670000076293945},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.27559998631477356},{"id":"https://openalex.org/C2777522853","wikidata":"https://www.wikidata.org/wiki/Q5276128","display_name":"Digital pathology","level":2,"score":0.26499998569488525},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.26089999079704285},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.2567000091075897},{"id":"https://openalex.org/C136339569","wikidata":"https://www.wikidata.org/wiki/Q1142297","display_name":"Molecular imaging","level":3,"score":0.2533000111579895},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.25200000405311584},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.25110000371932983}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:doi:10.48550/arxiv.2602.14177","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"doi:10.48550/arxiv.2602.14177","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2602.14177","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":"pmh:doi:10.48550/arxiv.2602.14177","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.5193426609039307}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Spatial":[0,66],"transcriptomics":[1],"(ST)":[2],"provides":[3,143],"spatially":[4],"resolved":[5],"measurements":[6],"of":[7,12,16,36,209],"gene":[8,120,177],"expression,":[9],"enabling":[10],"characterization":[11],"the":[13,34],"molecular":[14,78,165,220],"landscape":[15],"human":[17],"tissue":[18],"beyond":[19],"histological":[20,61],"assessment":[21],"as":[22,24,94,173,175,197],"well":[23,174],"localized":[25,77,219],"readouts":[26],"that":[27,40,47,75,100,151,214],"can":[28,55,101],"be":[29,56,102],"aligned":[30],"with":[31,43,218],"morphology.":[32],"Concurrently,":[33],"success":[35],"multimodal":[37],"foundation":[38,109,149,211],"models":[39,150,217],"integrate":[41],"vision":[42,82],"complementary":[44],"modalities":[45],"suggests":[46],"morphomolecular":[48],"coupling":[49],"between":[50],"local":[51],"expression":[52,121,178],"and":[53,127,137,159,169,191,225,232],"morphology":[54],"systematically":[57],"used":[58,107,157],"to":[59,105],"improve":[60],"representations":[62,231],"themselves.":[63],"We":[64,111],"introduce":[65],"Expression-Aligned":[67],"Learning":[68],"(SEAL),":[69],"a":[70,95,144,203],"vision-omics":[71,97],"self-supervised":[72],"learning":[73],"framework":[74,205],"infuses":[76],"information":[79],"into":[80],"pathology":[81,108,148,210],"encoders.":[83],"Rather":[84],"than":[85],"training":[86,115],"new":[87,193],"encoders":[88,183],"from":[89,130],"scratch,":[90],"SEAL":[91,113,142,182],"is":[92,222],"designed":[93],"parameter-efficient":[96],"finetuning":[98,208],"method":[99],"flexibly":[103],"applied":[104],"widely":[106,156],"models.":[110],"instantiate":[112],"by":[114],"on":[116,163,188],"over":[117,155],"700,000":[118],"paired":[119],"spot-tissue":[122],"region":[123],"examples":[124],"spanning":[125],"tumor":[126],"normal":[128],"samples":[129],"14":[131],"organs.":[132],"Tested":[133],"across":[134],"38":[135],"slide-level":[136,164],"15":[138],"patch-level":[139,176],"downstream":[140],"tasks,":[141],"drop-in":[145],"replacement":[146],"for":[147,206,228],"consistently":[152],"improves":[153],"performance":[154],"vision-only":[158],"ST":[160],"prediction":[161,179],"baselines":[162],"status,":[166],"pathway":[167],"activity,":[168],"treatment":[170],"response":[171],"prediction,":[172],"tasks.":[180],"Additionally,":[181],"exhibit":[184],"robust":[185],"domain":[186],"generalization":[187],"out-of-distribution":[189],"evaluations":[190],"enable":[192],"cross-modal":[194,235],"capabilities":[195],"such":[196],"gene-to-image":[198],"retrieval.":[199],"Our":[200],"work":[201],"proposes":[202],"general":[204],"ST-guided":[207],"models,":[212],"showing":[213],"augmenting":[215],"existing":[216],"supervision":[221],"an":[223],"effective":[224],"practical":[226],"step":[227],"improving":[229],"visual":[230],"expanding":[233],"their":[234],"utility.":[236]},"counts_by_year":[],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2026-02-18T00:00:00"}
