{"id":"https://openalex.org/W4393076162","doi":"https://doi.org/10.1158/1538-7445.am2024-7402","title":"Abstract 7402: Foundation AI models predict molecular measurements of tumor purity","display_name":"Abstract 7402: Foundation AI models predict molecular measurements of tumor purity","publication_year":2024,"publication_date":"2024-03-22","ids":{"openalex":"https://openalex.org/W4393076162","doi":"https://doi.org/10.1158/1538-7445.am2024-7402"},"language":"en","primary_location":{"id":"doi:10.1158/1538-7445.am2024-7402","doi":"https://doi.org/10.1158/1538-7445.am2024-7402","is_oa":false,"landing_page_url":"https://doi.org/10.1158/1538-7445.am2024-7402","pdf_url":null,"source":{"id":"https://openalex.org/S168522863","display_name":"Cancer Research","issn_l":"0008-5472","issn":["0008-5472","1538-7445"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320273","host_organization_name":"American Association for Cancer Research","host_organization_lineage":["https://openalex.org/P4310320273"],"host_organization_lineage_names":["American Association for Cancer Research"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cancer Research","raw_type":"journal-article"},"volume":null,"type":"conference-abstract","is_traditional":false,"indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075122631","display_name":"Ylaine Gerardin","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210138410","display_name":"PathAI (United States)","ror":"https://ror.org/04eb71689","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ylaine Gerardin","raw_affiliation_strings":["1PathAI, Inc., Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1PathAI, Inc., Boston, MA","institution_ids":["https://openalex.org/I4210138410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008540053","display_name":"Daniel Shenker","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210138410","display_name":"PathAI (United States)","ror":"https://ror.org/04eb71689","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Shenker","raw_affiliation_strings":["1PathAI, Inc., Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1PathAI, Inc., Boston, MA","institution_ids":["https://openalex.org/I4210138410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103964529","display_name":"Jennifer Hipp","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210138410","display_name":"PathAI (United States)","ror":"https://ror.org/04eb71689","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jennifer Hipp","raw_affiliation_strings":["1PathAI, Inc., Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1PathAI, Inc., Boston, MA","institution_ids":["https://openalex.org/I4210138410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082158401","display_name":"Natalia Harguindeguy","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210138410","display_name":"PathAI (United States)","ror":"https://ror.org/04eb71689","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Natalia Harguindeguy","raw_affiliation_strings":["1PathAI, Inc., Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1PathAI, Inc., Boston, MA","institution_ids":["https://openalex.org/I4210138410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019438937","display_name":"Dinkar Juyal","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210138410","display_name":"PathAI (United States)","ror":"https://ror.org/04eb71689","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dinkar Juyal","raw_affiliation_strings":["1PathAI, Inc., Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1PathAI, Inc., Boston, MA","institution_ids":["https://openalex.org/I4210138410"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Chintan Shah","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210138410","display_name":"PathAI (United States)","ror":"https://ror.org/04eb71689","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chintan Shah","raw_affiliation_strings":["1PathAI, Inc., Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1PathAI, Inc., Boston, MA","institution_ids":["https://openalex.org/I4210138410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052055737","display_name":"Syed Ashar Javed","orcid":"https://orcid.org/0009-0001-7838-3027","observed_orcids":["https://orcid.org/0009-0001-7838-3027"]},"institutions":[{"id":"https://openalex.org/I4210138410","display_name":"PathAI (United States)","ror":"https://ror.org/04eb71689","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Syed Ashar Javed","raw_affiliation_strings":["1PathAI, Inc., Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1PathAI, Inc., Boston, MA","institution_ids":["https://openalex.org/I4210138410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111988313","display_name":"Marc Thibault","orcid":"https://orcid.org/0000-0002-4790-7537","observed_orcids":["https://orcid.org/0000-0002-4790-7537"]},"institutions":[{"id":"https://openalex.org/I4210138410","display_name":"PathAI (United States)","ror":"https://ror.org/04eb71689","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marc Thibault","raw_affiliation_strings":["1PathAI, Inc., Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1PathAI, Inc., Boston, MA","institution_ids":["https://openalex.org/I4210138410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033090697","display_name":"Michael Nercessian","orcid":"https://orcid.org/0009-0003-4315-3031","observed_orcids":["https://orcid.org/0009-0003-4315-3031"]},"institutions":[{"id":"https://openalex.org/I4210138410","display_name":"PathAI (United States)","ror":"https://ror.org/04eb71689","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Nercessian","raw_affiliation_strings":["1PathAI, Inc., Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1PathAI, Inc., Boston, MA","institution_ids":["https://openalex.org/I4210138410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091338037","display_name":"Darpan Sanghavi","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210138410","display_name":"PathAI (United States)","ror":"https://ror.org/04eb71689","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Darpan Sanghavi","raw_affiliation_strings":["1PathAI, Inc., Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1PathAI, Inc., Boston, MA","institution_ids":["https://openalex.org/I4210138410"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Benjamin Trotter","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210138410","display_name":"PathAI (United States)","ror":"https://ror.org/04eb71689","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin Trotter","raw_affiliation_strings":["1PathAI, Inc., Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1PathAI, Inc., Boston, MA","institution_ids":["https://openalex.org/I4210138410"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029374555","display_name":"Ryan Y. Leung","orcid":"https://orcid.org/0000-0002-5723-4364","observed_orcids":["https://orcid.org/0000-0002-5723-4364"]},"institutions":[{"id":"https://openalex.org/I4210138410","display_name":"PathAI (United States)","ror":"https://ror.org/04eb71689","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan Leung","raw_affiliation_strings":["1PathAI, Inc., Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1PathAI, Inc., Boston, MA","institution_ids":["https://openalex.org/I4210138410"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210138410"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"84","issue":"6_Supplement","first_page":"7402","last_page":"7402"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.9994999766349792,"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"}},{"id":"https://openalex.org/T12422","display_name":"Radiomics and Machine Learning in Medical Imaging","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11636","display_name":"Artificial Intelligence in Healthcare and Education","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/tumor-purity","display_name":"tumor purity","score":0.8109999895095825},{"id":"https://openalex.org/keywords/whole-slide-images","display_name":"whole slide images","score":0.6420000195503235},{"id":"https://openalex.org/keywords/h-e-staining","display_name":"H&E staining","score":0.8059999942779541},{"id":"https://openalex.org/keywords/tissue-quality-assessment","display_name":"tissue quality assessment","score":0.6570000052452087},{"id":"https://openalex.org/keywords/colon-adenocarcinoma","display_name":"colon adenocarcinoma","score":0.8410000205039978},{"id":"https://openalex.org/keywords/melanoma","display_name":"melanoma","score":0.996999979019165},{"id":"https://openalex.org/keywords/prostate-cancer","display_name":"prostate cancer","score":0.9919999837875366},{"id":"https://openalex.org/keywords/non-small-cell-lung-cancer","display_name":"non-small cell lung cancer","score":1.0},{"id":"https://openalex.org/keywords/absolute","display_name":"absolute","score":0.765999972820282},{"id":"https://openalex.org/keywords/estimates","display_name":"estimates","score":0.8109999895095825},{"id":"https://openalex.org/keywords/lumps","display_name":"lumps","score":0.9089999794960022},{"id":"https://openalex.org/keywords/dna-copy-number","display_name":"DNA copy number","score":0.6240000128746033},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.8790000081062317},{"id":"https://openalex.org/keywords/gene-expression","display_name":"gene expression","score":0.8339999914169312},{"id":"https://openalex.org/keywords/tumor-segmentation","display_name":"tumor segmentation","score":0.4309999942779541},{"id":"https://openalex.org/keywords/concordance","display_name":"concordance","score":0.4959999918937683}],"concepts":[{"id":"https://openalex.org/C2780966255","wikidata":"https://www.wikidata.org/wiki/Q5474306","display_name":"Foundation (evidence)","level":2,"score":0.6698899269104004},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.4298032820224762},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36263126134872437},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2338351607322693},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.1307767927646637},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.09908819198608398}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1158/1538-7445.am2024-7402","doi":"https://doi.org/10.1158/1538-7445.am2024-7402","is_oa":false,"landing_page_url":"https://doi.org/10.1158/1538-7445.am2024-7402","pdf_url":null,"source":{"id":"https://openalex.org/S168522863","display_name":"Cancer Research","issn_l":"0008-5472","issn":["0008-5472","1538-7445"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320273","host_organization_name":"American Association for Cancer Research","host_organization_lineage":["https://openalex.org/P4310320273"],"host_organization_lineage_names":["American Association for Cancer Research"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cancer Research","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.9074000120162964,"display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4295836817","https://openalex.org/W4393090194","https://openalex.org/W4281614882","https://openalex.org/W4407001204","https://openalex.org/W4225982186","https://openalex.org/W7164405006","https://openalex.org/W7165633104","https://openalex.org/W4388089640","https://openalex.org/W4399088283","https://openalex.org/W7207627202"],"abstract_inverted_index":{"Abstract":[0],"Background:":[1],"Molecular":[2],"assays,":[3],"such":[4],"as":[5,185],"comprehensive":[6],"genomic":[7],"profiling,":[8],"play":[9],"a":[10,195,339],"critical":[11],"role":[12],"in":[13,21,29,251,292,302,310,349,375,399],"characterizing":[14],"patient":[15],"disease":[16],"and":[17,37,43,78,86,94,101,123,126,153,171,215,225,273,288,312,327,360,368,394],"guiding":[18],"treatment":[19],"selection":[20],"oncology":[22],"but":[23],"require":[24],"sufficient":[25],"tumor":[26,44,88,169,181,192,199,227,249,333,347,357,366,446],"nucleic":[27],"acids":[28],"tissue":[30,41,63,77,193,358],"samples":[31],"for":[32,52,165,176,343,364,455],"reliable":[33],"results.":[34],"Automated,":[35],"accurate":[36],"reproducible":[38],"quantification":[39,345],"of":[40,59,134,142,168,173,179,188,248,346,384,391,445,451],"area":[42],"nuclei":[45],"from":[46,118,160],"H&E":[47,82,140],"slides":[48],"to":[49,75,91],"determine":[50],"suitability":[51],"molecular":[53,93,246,289,325,373,392,443],"testing":[54,393],"could":[55,387],"reduce":[56],"the":[57,166,177,186,233,260,280,298,318,322,344,389,452],"amount":[58],"time":[60],"spent":[61],"assessing":[62],"quality.":[64],"To":[65],"address":[66],"this":[67],"need,":[68],"we":[69,337],"developed":[70],"pan-indication":[71,340],"foundation":[72,135],"AI":[73,222,239,255,285,314,353,386,440],"models":[74,103,136,354,441],"quantify":[76],"cell":[79,102,155],"features":[80,348],"within":[81,191],"whole-slide":[83],"images":[84],"(WSI)":[85],"compared":[87],"purity":[89,182,200,228,250,257,447],"estimates":[90],"orthogonal":[92,245],"manual":[95,216,328],"methods.":[96],"Methods:":[97],"Pan-indication":[98],"artifact,":[99],"tissue,":[100],"were":[104,218,242],"each":[105],"trained":[106],"using":[107,232],"at":[108],"least":[109],"2.8":[110],"million":[111],"pathologist":[112,129],"annotations":[113],"across":[114],"over":[115],"100,000":[116],"WSI":[117],"14":[119],"stains,":[120],"25":[121],"organs,":[122],"9":[124],"scanners":[125],"validated":[127],"against":[128,308],"ground-truth":[130],"labels.":[131],"This":[132,379],"suite":[133],"was":[137,230,291,301],"deployed":[138],"on":[139,194,204],"WSIs":[141],"colon":[143],"adenocarcinoma":[144],"(COAD;":[145],"N=442),":[146],"melanoma":[147,293],"(N=363),":[148],"prostate":[149],"cancer":[150,157,174,189,362,377],"(PRAD;":[151],"N=490),":[152],"non-small":[154],"lung":[156],"(NSCLC;":[158],"N=996)":[159],"TCGA1.":[161],"Model":[162],"outputs":[163],"allowed":[164],"segmentation":[167],"regions":[170,359],"enumeration":[172],"cells":[175,190,363],"purpose":[178],"determining":[180,365],"scores,":[183],"calculated":[184],"fraction":[187],"WSI.":[196,351],"For":[197],"comparison,":[198],"values":[201,229],"determined":[202],"based":[203],"DNA":[205,212],"copy":[206],"number":[207],"(ABSOLUTE),":[208],"gene":[209],"expression":[210],"(ESTIMATE),":[211],"methylation":[213],"(LUMP)":[214],"assessment2":[217],"obtained.":[219],"Concordance":[220],"between":[221,284],"model":[223,240,256,286,315],"scores":[224,241,258,287,316],"other":[226,323],"assessed":[231],"intraclass":[234],"correlation":[235],"coefficient,":[236],"ICC(2,1).":[237],"Results:":[238],"correlated":[243],"with":[244,262,372],"measures":[247],"all":[252,330],"four":[253,376],"indications.":[254,378],"corresponded":[259],"most":[261],"ABSOLUTE":[263,309,332],"(ICC":[264,270,275,294,304],"range:":[265,271,276,295,305],"0.22-0.46),":[266],"followed":[267],"by":[268],"LUMP":[269],"0.02-0.50)":[272],"ESTIMATE":[274],"0.03-0.34).":[277],"Across":[278],"indications,":[279],"highest":[281,319],"agreement":[282,300],"observed":[283],"methods":[290,326],"0.34-0.50),":[296],"while":[297,321],"lowest":[299],"PRAD":[303],"0.02-0.22).":[306],"Compared":[307],"NSCLC":[311],"PRAD,":[313],"showed":[317],"concordance,":[320],"two":[324],"assessment":[329],"overestimated":[331],"purity.":[334],"Conclusions:":[335],"Here,":[336],"describe":[338],"AI-based":[341],"approach":[342],"H&E-stained":[350],"Foundation":[352,439],"successfully":[355],"segment":[356],"enumerate":[361],"purity,":[367],"these":[369],"predictions":[370],"correlate":[371],"metrics":[374],"work":[380],"provides":[381],"further":[382],"evidence":[383],"how":[385],"improve":[388],"efficiency":[390],"enhance":[395],"precision":[396],"medicine":[397],"approaches":[398],"oncology.":[400],"References:":[401],"1TCGA":[402],"https://gdc.cancer.gov/about-data/publications/pancanatlas;":[403],"2Aran,":[404],"D.":[405],"et":[406],"al.":[407],"Nat":[408],"Comms":[409],"6:8971":[410],"(2015)":[411],"Citation":[412],"Format:":[413],"Ylaine":[414],"Gerardin,":[415],"Daniel":[416],"Shenker,":[417],"Jennifer":[418],"Hipp,":[419],"Natalia":[420],"Harguindeguy,":[421],"Dinkar":[422],"Juyal,":[423],"Chintan":[424],"Shah,":[425],"Syed":[426],"Ashar":[427],"Javed,":[428],"Marc":[429],"Thibault,":[430],"Michael":[431],"Nercessian,":[432],"Darpan":[433],"Sanghavi,":[434],"Benjamin":[435],"Trotter,":[436],"Ryan":[437],"Leung.":[438],"predict":[442],"measurements":[444],"[abstract].":[448],"In:":[449],"Proceedings":[450],"American":[453],"Association":[454],"Cancer":[456,474],"Research":[457],"Annual":[458],"Meeting":[459],"2024;":[460],"Part":[461],"1":[462],"(Regular":[463],"Abstracts);":[464],"2024":[465],"Apr":[466],"5-10;":[467],"San":[468],"Diego,":[469],"CA.":[470],"Philadelphia":[471],"(PA):":[472],"AACR;":[473],"Res":[475],"2024;84(6_Suppl):Abstract":[476],"nr":[477],"7402.":[478]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2024-03-23T00:00:00"}