{"id":"https://openalex.org/W4317951337","doi":"https://doi.org/10.48550/arxiv.2301.09617","title":"Fully transformer-based biomarker prediction from colorectal cancer histology: a large-scale multicentric study","display_name":"Fully transformer-based biomarker prediction from colorectal cancer histology: a large-scale multicentric study","publication_year":2023,"publication_date":"2023-01-23","ids":{"openalex":"https://openalex.org/W4317951337","doi":"https://doi.org/10.48550/arxiv.2301.09617"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2301.09617","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2301.09617","pdf_url":"https://arxiv.org/pdf/2301.09617","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":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2301.09617","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000341866","display_name":"Sophia J. Wagner","orcid":"https://orcid.org/0000-0003-3763-2282"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Wagner, Sophia J.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024474789","display_name":"Daniel Reisenb\u00fcchler","orcid":"https://orcid.org/0000-0001-8820-0530"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Reisenb\u00fcchler, Daniel","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045885712","display_name":"Nicholas P. West","orcid":"https://orcid.org/0000-0002-0346-6709"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"West, Nicholas P.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039656339","display_name":"Jan Niehues","orcid":"https://orcid.org/0000-0003-4016-9129"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Niehues, Jan Moritz","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012440991","display_name":"Gregory Patrick Veldhuizen","orcid":"https://orcid.org/0000-0001-7364-8498"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Veldhuizen, Gregory Patrick","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056121788","display_name":"Philip Quirke","orcid":"https://orcid.org/0000-0002-3597-5444"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Quirke, Philip","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019453132","display_name":"Heike I. Grabsch","orcid":"https://orcid.org/0000-0001-9520-6228"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Grabsch, Heike I.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001404405","display_name":"Piet A. van den Brandt","orcid":"https://orcid.org/0000-0001-8781-8099"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Brandt, Piet A. van den","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054579793","display_name":"Gordon Hutchins","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hutchins, Gordon G. A.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023175702","display_name":"Susan D. Richman","orcid":"https://orcid.org/0000-0003-3993-5041"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Richman, Susan D.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010589327","display_name":"Tanwei Yuan","orcid":"https://orcid.org/0000-0001-7387-6327"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yuan, Tanwei","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091797746","display_name":"Rupert Langer","orcid":"https://orcid.org/0000-0001-9491-3609"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Langer, Rupert","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026134593","display_name":"Josien Christina Anna Jenniskens","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jenniskens, Josien Christina Anna","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040944112","display_name":"Kelly Offermans","orcid":"https://orcid.org/0000-0001-6842-4887"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Offermans, Kelly","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011388557","display_name":"Wolfram Mueller","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mueller, Wolfram","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077385319","display_name":"Richard Gray","orcid":"https://orcid.org/0000-0001-9694-4206"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gray, Richard","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070703103","display_name":"Stephen B. Gruber","orcid":"https://orcid.org/0000-0001-8656-7822"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gruber, Stephen B.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085891308","display_name":"Joel K. Greenson","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Greenson, Joel K.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082547550","display_name":"Gad Rennert","orcid":"https://orcid.org/0000-0002-8512-068X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rennert, Gad","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042231024","display_name":"Joseph D. Bonner","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bonner, Joseph D.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113922807","display_name":"Daniel Schmolze","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Schmolze, Daniel","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053522042","display_name":"Jacqueline A. James","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"James, Jacqueline A.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070895143","display_name":"Maurice B. Loughrey","orcid":"https://orcid.org/0000-0001-8424-1765"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Loughrey, Maurice B.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045420024","display_name":"Manuel Salto\u2010Tellez","orcid":"https://orcid.org/0000-0001-8586-282X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Salto-Tellez, Manuel","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077206620","display_name":"Hermann Brenner","orcid":"https://orcid.org/0000-0002-6129-1572"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Brenner, Hermann","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036777611","display_name":"Michael Hoffmeister","orcid":"https://orcid.org/0000-0002-8307-3197"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hoffmeister, Michael","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016512818","display_name":"Daniel Truhn","orcid":"https://orcid.org/0000-0002-9605-0728"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Truhn, Daniel","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019012882","display_name":"Julia A. Schnabel","orcid":"https://orcid.org/0000-0001-6107-3009"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Schnabel, Julia A.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004138391","display_name":"Melanie Boxberg","orcid":"https://orcid.org/0000-0001-5989-7922"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Boxberg, Melanie","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070636207","display_name":"Tingying Peng","orcid":"https://orcid.org/0000-0002-7881-1749"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Peng, Tingying","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":31,"corresponding_author_ids":["https://openalex.org/A5000341866"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":5,"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/T12422","display_name":"Radiomics and Machine Learning in Medical Imaging","score":0.989799976348877,"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"}},"topics":[{"id":"https://openalex.org/T12422","display_name":"Radiomics and Machine Learning in Medical Imaging","score":0.989799976348877,"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/T10552","display_name":"Colorectal Cancer Screening and Detection","score":0.982699990272522,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"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/T10862","display_name":"AI in cancer detection","score":0.9735000133514404,"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/computer-science","display_name":"Computer science","score":0.5194701552391052},{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.5153124332427979},{"id":"https://openalex.org/keywords/biomarker","display_name":"Biomarker","score":0.4757746756076813},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4610874056816101},{"id":"https://openalex.org/keywords/generalizability-theory","display_name":"Generalizability theory","score":0.4410404860973358},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.3977629542350769},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3818127512931824},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07728084921836853}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5194701552391052},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.5153124332427979},{"id":"https://openalex.org/C2781197716","wikidata":"https://www.wikidata.org/wiki/Q864574","display_name":"Biomarker","level":2,"score":0.4757746756076813},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4610874056816101},{"id":"https://openalex.org/C27158222","wikidata":"https://www.wikidata.org/wiki/Q5532422","display_name":"Generalizability theory","level":2,"score":0.4410404860973358},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3977629542350769},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3818127512931824},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07728084921836853},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2301.09617","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2301.09617","pdf_url":"https://arxiv.org/pdf/2301.09617","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":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2301.09617","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2301.09617","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:2301.09617","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2301.09617","pdf_url":"https://arxiv.org/pdf/2301.09617","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":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4317951337.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4378220270","https://openalex.org/W1986582023","https://openalex.org/W2883749686","https://openalex.org/W2961085424","https://openalex.org/W2966829450","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W3170094116","https://openalex.org/W4386462264"],"abstract_inverted_index":{"Background:":[0],"Deep":[1],"learning":[2],"(DL)":[3],"can":[4],"extract":[5],"predictive":[6,177],"and":[7,49,111,122,153,231],"prognostic":[8],"biomarkers":[9],"from":[10,102,136],"routine":[11],"pathology":[12,103,220],"slides":[13,221],"in":[14,29,34,53,64],"colorectal":[15,138],"cancer.":[16],"For":[17],"example,":[18],"a":[19,67,93,107,112,164,170,175,206],"DL":[20,73],"test":[21],"for":[22,61,98,115,181,190,225],"the":[23,148,191],"diagnosis":[24],"of":[25,119,172,179,219],"microsatellite":[26],"instability":[27],"(MSI)":[28],"CRC":[30],"has":[31],"been":[32,59,76],"approved":[33],"2022.":[35],"Current":[36],"approaches":[37,74],"rely":[38],"on":[39,78,132,163,184,201,217,228],"convolutional":[40],"neural":[41],"networks":[42,45],"(CNNs).":[43],"Transformer":[44],"are":[46,50,236],"outperforming":[47],"CNNs":[48],"replacing":[51],"them":[52],"many":[54],"applications,":[55],"but":[56],"have":[57,75],"not":[58],"used":[60],"biomarker":[62,100,226],"prediction":[63,101,124,183,227],"cancer":[65,139],"at":[66,125],"large":[68,165],"scale.":[69],"In":[70,88],"addition,":[71],"most":[72],"trained":[77,216],"small":[79],"patient":[80,126],"cohorts,":[81],"which":[82],"limits":[83],"their":[84],"clinical":[85],"utility.":[86],"Methods:":[87],"this":[89],"study,":[90],"we":[91,168],"developed":[92],"new":[94,234],"fully":[95,143,212],"transformer-based":[96,144,213],"pipeline":[97,131,215],"end-to-end":[99,214],"slides.":[104],"We":[105,128,188],"combine":[106],"pre-trained":[108],"transformer":[109,113],"encoder":[110],"network":[114],"patch":[116],"aggregation,":[117],"capable":[118],"yielding":[120],"single":[121],"multi-target":[123],"level.":[127],"train":[129],"our":[130],"over":[133],"9,000":[134],"patients":[135],"10":[137],"cohorts.":[140],"Results:":[141],"A":[142,211],"approach":[145],"massively":[146],"improves":[147],"performance,":[149],"generalizability,":[150],"data":[151],"efficiency,":[152],"interpretability":[154],"as":[155],"compared":[156],"with":[157,174],"current":[158],"state-of-the-art":[159],"algorithms.":[160],"After":[161],"training":[162,197],"multicenter":[166],"cohort,":[167],"achieve":[169],"sensitivity":[171],"0.97":[173],"negative":[176],"value":[178],"0.99":[180],"MSI":[182],"surgical":[185,229],"resection":[186,195],"specimens.":[187],"demonstrate":[189],"first":[192],"time":[193],"that":[194],"specimen-only":[196],"reaches":[198],"clinical-grade":[199,223],"performance":[200,224],"endoscopic":[202],"biopsy":[203],"tissue,":[204],"solving":[205],"long-standing":[207],"diagnostic":[208],"problem.":[209],"Interpretation:":[210],"thousands":[218],"yields":[222],"resections":[230],"biopsies.":[232],"Our":[233],"methods":[235],"freely":[237],"available":[238],"under":[239],"an":[240],"open":[241],"source":[242],"license.":[243]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3}],"updated_date":"2026-02-09T09:26:11.010843","created_date":"2025-10-10T00:00:00"}
