{"id":"https://openalex.org/W4404649999","doi":"https://doi.org/10.48550/arxiv.2411.13623","title":"Unsupervised Foundation Model-Agnostic Slide-Level Representation Learning","display_name":"Unsupervised Foundation Model-Agnostic Slide-Level Representation Learning","publication_year":2024,"publication_date":"2024-11-20","ids":{"openalex":"https://openalex.org/W4404649999","doi":"https://doi.org/10.48550/arxiv.2411.13623"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2411.13623","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2411.13623","pdf_url":"https://arxiv.org/pdf/2411.13623","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2411.13623","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113076192","display_name":"Tim Lenz","orcid":"https://orcid.org/0000-0002-9034-2535"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Lenz, Tim","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107077385","display_name":"Peter Neidlinger","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Neidlinger, Peter","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056339832","display_name":"Marta Ligero","orcid":"https://orcid.org/0000-0001-9824-7316"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ligero, Marta","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056031179","display_name":"Georg W\u00f6lflein","orcid":"https://orcid.org/0000-0002-0407-7617"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"W\u00f6lflein, Georg","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034336361","display_name":"Marko van Treeck","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"van Treeck, Marko","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5073483894","display_name":"Jakob Nikolas Kather","orcid":"https://orcid.org/0000-0002-3730-5348"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kather, Jakob Nikolas","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5113076192"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":2,"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/T14510","display_name":"Medical Imaging and Analysis","score":0.39329999685287476,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T14510","display_name":"Medical Imaging and Analysis","score":0.39329999685287476,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13702","display_name":"Machine Learning in Healthcare","score":0.3804999887943268,"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":0.8360068202018738},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6585344076156616},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5658128261566162},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5123923420906067},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.4229016602039337},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.35692262649536133},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.08962243795394897},{"id":"https://openalex.org/keywords/political-science","display_name":"Political science","score":0.05172300338745117}],"concepts":[{"id":"https://openalex.org/C2780966255","wikidata":"https://www.wikidata.org/wiki/Q5474306","display_name":"Foundation (evidence)","level":2,"score":0.8360068202018738},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6585344076156616},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5658128261566162},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5123923420906067},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.4229016602039337},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35692262649536133},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.08962243795394897},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.05172300338745117},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2411.13623","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2411.13623","pdf_url":"https://arxiv.org/pdf/2411.13623","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2411.13623","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2411.13623","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:oai:arXiv.org:2411.13623","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2411.13623","pdf_url":"https://arxiv.org/pdf/2411.13623","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1146481553","display_name":"How the brain codes the past to predict the future","funder_award_id":"263318","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G1949475607","display_name":null,"funder_award_id":"NIHR203331","funder_id":"https://openalex.org/F4320336708","funder_display_name":"Leeds Biomedical Research Centre"},{"id":"https://openalex.org/G2199214065","display_name":null,"funder_award_id":"PEARL","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G2341156914","display_name":null,"funder_award_id":"01EO2101","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G2654538971","display_name":null,"funder_award_id":"101057091","funder_id":"https://openalex.org/F4320334322","funder_display_name":"HORIZON EUROPE Framework Programme"},{"id":"https://openalex.org/G2669879858","display_name":null,"funder_award_id":"01VSF21048","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G2820917408","display_name":null,"funder_award_id":"01VSF21048","funder_id":"https://openalex.org/F4320328691","funder_display_name":"Gemeinsame Bundesausschuss"},{"id":"https://openalex.org/G3332309157","display_name":null,"funder_award_id":"ODELIA","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3378117337","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320319990","funder_display_name":"National Institute for Health and Care Research"},{"id":"https://openalex.org/G3512296018","display_name":null,"funder_award_id":"101096312","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3514550006","display_name":null,"funder_award_id":"Centre","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3848825097","display_name":null,"funder_award_id":"70115166","funder_id":"https://openalex.org/F4320323556","funder_display_name":"Deutsche Krebshilfe"},{"id":"https://openalex.org/G4243001891","display_name":"New directions for deep learning in cancer research through concept explainability and virtual experimentation.","funder_award_id":"101114631","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4281281669","display_name":null,"funder_award_id":"R01 CA263318","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4447653093","display_name":null,"funder_award_id":"Network","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G451588841","display_name":null,"funder_award_id":"101057091","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4712284355","display_name":null,"funder_award_id":"57616814","funder_id":"https://openalex.org/F4320320875","funder_display_name":"Deutscher Akademischer Austauschdienst"},{"id":"https://openalex.org/G5016914395","display_name":null,"funder_award_id":"SECAI","funder_id":"https://openalex.org/F4320320875","funder_display_name":"Deutscher Akademischer Austauschdienst"},{"id":"https://openalex.org/G5109404045","display_name":null,"funder_award_id":"NADIR","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6098565189","display_name":null,"funder_award_id":"57616814","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G6345853531","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6425104771","display_name":null,"funder_award_id":"DEEP-HCC","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G6697820746","display_name":null,"funder_award_id":"NIHR203331","funder_id":"https://openalex.org/F4320319990","funder_display_name":"National Institute for Health and Care Research"},{"id":"https://openalex.org/G6777017359","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320320875","funder_display_name":"Deutscher Akademischer Austauschdienst"},{"id":"https://openalex.org/G7282467613","display_name":null,"funder_award_id":"ODELIA","funder_id":"https://openalex.org/F4320334322","funder_display_name":"HORIZON EUROPE Framework Programme"},{"id":"https://openalex.org/G826797920","display_name":null,"funder_award_id":"01KD2104C","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8311021456","display_name":null,"funder_award_id":"031L0312A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8318064016","display_name":null,"funder_award_id":"Horizon","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8729913089","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320321613","funder_display_name":"Technische Universit\u00e4t Dresden"},{"id":"https://openalex.org/G914080343","display_name":null,"funder_award_id":"203331","funder_id":"https://openalex.org/F4320336708","funder_display_name":"Leeds Biomedical Research Centre"}],"funders":[{"id":"https://openalex.org/F4320319990","display_name":"National Institute for Health and Care Research","ror":"https://ror.org/0187kwz08"},{"id":"https://openalex.org/F4320319994","display_name":"Department of Health and Social Care","ror":"https://ror.org/03sbpja79"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320875","display_name":"Deutscher Akademischer Austauschdienst","ror":"https://ror.org/039djdh30"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320321613","display_name":"Technische Universit\u00e4t Dresden","ror":"https://ror.org/042aqky30"},{"id":"https://openalex.org/F4320323556","display_name":"Deutsche Krebshilfe","ror":"https://ror.org/01wxdd722"},{"id":"https://openalex.org/F4320328691","display_name":"Gemeinsame Bundesausschuss","ror":"https://ror.org/008c2qm47"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334322","display_name":"HORIZON EUROPE Framework Programme","ror":null},{"id":"https://openalex.org/F4320336708","display_name":"Leeds Biomedical Research Centre","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4404649999.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"Representation":[0],"learning":[1,32,62,71],"of":[2,66,79,128],"pathology":[3],"whole-slide":[4],"images":[5],"(WSIs)":[6],"has":[7,34],"primarily":[8],"relied":[9],"on":[10,123,132,143,154],"weak":[11],"supervision":[12],"with":[13,171],"Multiple":[14],"Instance":[15],"Learning":[16],"(MIL).":[17],"This":[18],"approach":[19],"leads":[20],"to":[21,26,38,72],"slide":[22,52,60,81,108,130],"representations":[23],"highly":[24],"tailored":[25],"a":[27,96],"specific":[28],"clinical":[29],"task.":[30],"Self-supervised":[31],"(SSL)":[33],"been":[35],"successfully":[36],"applied":[37],"train":[39],"histopathology":[40],"foundation":[41],"models":[42],"(FMs)":[43],"for":[44,59],"patch":[45,69],"embedding":[46],"generation.":[47],"However,":[48],"generating":[49],"patient":[50],"or":[51,82],"level":[53,70],"embeddings":[54,90],"remains":[55],"challenging.":[56],"Existing":[57],"approaches":[58],"representation":[61],"extend":[63],"the":[64,80],"principles":[65],"SSL":[67,100],"from":[68,91,157],"entire":[73],"slides":[74],"by":[75,83,145],"aligning":[76],"different":[77,134],"augmentations":[78],"utilizing":[84],"multimodal":[85],"data.":[86],"By":[87],"integrating":[88],"tile":[89],"multiple":[92,117],"FMs,":[93],"we":[94],"propose":[95],"new":[97],"single":[98],"modality":[99],"method":[101],"in":[102],"feature":[103,174],"space":[104],"that":[105],"generates":[106],"useful":[107],"representations.":[109],"Our":[110],"contrastive":[111],"pretraining":[112],"strategy,":[113],"called":[114],"COBRA,":[115],"employs":[116],"FMs":[118],"and":[119],"an":[120],"architecture":[121],"based":[122],"Mamba-2.":[124],"COBRA":[125,164],"exceeds":[126],"performance":[127],"state-of-the-art":[129],"encoders":[131],"four":[133],"public":[135],"Clinical":[136],"Protemic":[137],"Tumor":[138],"Analysis":[139],"Consortium":[140],"(CPTAC)":[141],"cohorts":[142],"average":[144],"at":[146,168,178],"least":[147],"+4.4%":[148],"AUC,":[149],"despite":[150],"only":[151],"being":[152],"pretrained":[153],"3048":[155],"WSIs":[156],"The":[158],"Cancer":[159],"Genome":[160],"Atlas":[161],"(TCGA).":[162],"Additionally,":[163],"is":[165],"readily":[166],"compatible":[167],"inference":[169],"time":[170],"previously":[172],"unseen":[173],"extractors.":[175],"Code":[176],"available":[177],"https://github.com/KatherLab/COBRA.":[179]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}
