{"id":"https://openalex.org/W4225107780","doi":"https://doi.org/10.1093/bib/bbac294","title":"Contrastive learning-based computational histopathology predict differential expression of cancer driver genes","display_name":"Contrastive learning-based computational histopathology predict differential expression of cancer driver genes","publication_year":2022,"publication_date":"2022-07-28","ids":{"openalex":"https://openalex.org/W4225107780","doi":"https://doi.org/10.1093/bib/bbac294","pmid":"https://pubmed.ncbi.nlm.nih.gov/35901472"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac294","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac294","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"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/A5101566735","display_name":"Haojie Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haojie Huang","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , 410075, Changsha , China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , 410075, Changsha , China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101154024","display_name":"Zhou Gong-ming","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gongming Zhou","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , 410075, Changsha , China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , 410075, Changsha , China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113657781","display_name":"Xuejun Liu","orcid":"https://orcid.org/0009-0005-0130-9952"},"institutions":[{"id":"https://openalex.org/I134687103","display_name":"Nanjing Tech University","ror":"https://ror.org/03sd35x91","country_code":"CN","type":"education","lineage":["https://openalex.org/I134687103"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuejun Liu","raw_affiliation_strings":["School of Computer Science and Technology, Nanjing Tech University , 211816, Nanjing , China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Nanjing Tech University , 211816, Nanjing , China","institution_ids":["https://openalex.org/I134687103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076784576","display_name":"Lei Deng","orcid":"https://orcid.org/0000-0003-2647-4610"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Deng","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , 410075, Changsha , China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , 410075, Changsha , China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100329153","display_name":"Wu Chen","orcid":"https://orcid.org/0000-0002-1787-5191"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chen Wu","raw_affiliation_strings":["The third affiliated hospital of Soochow University , 213100, Changzhou , China"],"affiliations":[{"raw_affiliation_string":"The third affiliated hospital of Soochow University , 213100, Changzhou , China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101469519","display_name":"Dachuan Zhang","orcid":"https://orcid.org/0000-0002-9778-3456"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Dachuan Zhang","raw_affiliation_strings":["The third affiliated hospital of Soochow University , 213100, Changzhou , China"],"affiliations":[{"raw_affiliation_string":"The third affiliated hospital of Soochow University , 213100, Changzhou , China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100387512","display_name":"Hui Liu","orcid":"https://orcid.org/0000-0001-7158-913X"},"institutions":[{"id":"https://openalex.org/I134687103","display_name":"Nanjing Tech University","ror":"https://ror.org/03sd35x91","country_code":"CN","type":"education","lineage":["https://openalex.org/I134687103"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hui Liu","raw_affiliation_strings":["School of Computer Science and Technology, Nanjing Tech University , 211816, Nanjing , China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Nanjing Tech University , 211816, Nanjing , China","institution_ids":["https://openalex.org/I134687103"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5100387512","https://openalex.org/A5101469519"],"corresponding_institution_ids":["https://openalex.org/I134687103","https://openalex.org/I3923682"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.9893,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.88109241,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"23","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.9997000098228455,"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":0.9997000098228455,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.996399998664856,"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/T12874","display_name":"Digital Imaging for Blood Diseases","score":0.9814000129699707,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/digital-pathology","display_name":"Digital pathology","score":0.6894552707672119},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5725617408752441},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5699655413627625},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4801604151725769},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46953997015953064},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.438078910112381},{"id":"https://openalex.org/keywords/pathological","display_name":"Pathological","score":0.43793055415153503},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.33800244331359863},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3194928467273712},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.2999638020992279},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.10604184865951538},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1043194830417633}],"concepts":[{"id":"https://openalex.org/C2777522853","wikidata":"https://www.wikidata.org/wiki/Q5276128","display_name":"Digital pathology","level":2,"score":0.6894552707672119},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5725617408752441},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5699655413627625},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4801604151725769},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46953997015953064},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.438078910112381},{"id":"https://openalex.org/C207886595","wikidata":"https://www.wikidata.org/wiki/Q1456138","display_name":"Pathological","level":2,"score":0.43793055415153503},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.33800244331359863},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3194928467273712},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.2999638020992279},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.10604184865951538},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1043194830417633}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac294","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac294","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35901472","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35901472","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5699999928474426,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G3638561661","display_name":null,"funder_award_id":"62072058","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4765830214","display_name":null,"funder_award_id":"61972422","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1967520584","https://openalex.org/W1977653087","https://openalex.org/W2030093162","https://openalex.org/W2042790153","https://openalex.org/W2066311574","https://openalex.org/W2113727201","https://openalex.org/W2133059825","https://openalex.org/W2149622904","https://openalex.org/W2339885376","https://openalex.org/W2344657883","https://openalex.org/W2533788982","https://openalex.org/W2760946358","https://openalex.org/W2761668583","https://openalex.org/W2794616003","https://openalex.org/W2796409016","https://openalex.org/W2799615997","https://openalex.org/W2810797885","https://openalex.org/W2913510405","https://openalex.org/W2914568698","https://openalex.org/W2948930564","https://openalex.org/W2954499361","https://openalex.org/W2956228567","https://openalex.org/W2964879311","https://openalex.org/W2999399991","https://openalex.org/W3007100994","https://openalex.org/W3018295606","https://openalex.org/W3036122989","https://openalex.org/W3043835773","https://openalex.org/W3044996171","https://openalex.org/W3046305306","https://openalex.org/W3047825284","https://openalex.org/W3083699157","https://openalex.org/W3084161163","https://openalex.org/W3099287508","https://openalex.org/W3113328935","https://openalex.org/W3115168802","https://openalex.org/W3133711868","https://openalex.org/W3156270925","https://openalex.org/W3206417123","https://openalex.org/W3213145260","https://openalex.org/W4232452103","https://openalex.org/W4236965008","https://openalex.org/W6750555868","https://openalex.org/W6752990288","https://openalex.org/W6766746495","https://openalex.org/W6783001986"],"related_works":["https://openalex.org/W2365243064","https://openalex.org/W1975767702","https://openalex.org/W2386699790","https://openalex.org/W2063918854","https://openalex.org/W2373252393","https://openalex.org/W2352462806","https://openalex.org/W2373002487","https://openalex.org/W2368418853","https://openalex.org/W3128797991","https://openalex.org/W2370819194"],"abstract_inverted_index":{"In":[0],"this":[1],"paper,":[2],"we":[3,74,99],"propose":[4],"a":[5],"self-supervised":[6],"contrastive":[7,23],"learning":[8,24],"framework,":[9],"HistCode,":[10],"to":[11,29,41,92],"infer":[12],"differential":[13,70],"gene":[14,71,136],"expression":[15,137],"from":[16,96],"whole":[17],"slide":[18],"images":[19],"(WSIs).":[20],"We":[21,112],"leveraged":[22],"on":[25],"large-scale":[26],"unannotated":[27],"WSIs":[28,103],"derive":[30],"slide-level":[31],"histopathological":[32],"features":[33,95],"in":[34,62],"latent":[35],"space,":[36],"and":[37,44,66,117],"then":[38],"transfer":[39],"it":[40],"tumor":[42,63,116],"diagnosis":[43,64],"prediction":[45],"of":[46,109,126],"differentially":[47],"expressed":[48],"cancer":[49],"driver":[50],"genes.":[51],"Our":[52],"experiments":[53],"showed":[54],"that":[55,114],"our":[56],"method":[57],"outperformed":[58],"other":[59],"state-of-the-art":[60],"models":[61],"tasks,":[65],"also":[67,140],"effectively":[68],"predicted":[69],"expression.":[72],"Interestingly,":[73],"found":[75,113],"the":[76,90,102,106,115,124,130,143],"genes":[77],"with":[78,123,142],"higher":[79],"fold":[80],"change":[81],"can":[82],"be":[83],"more":[84],"precisely":[85],"predicted.":[86],"To":[87],"intuitively":[88],"illustrate":[89],"ability":[91],"extract":[93],"informative":[94],"pathological":[97],"images,":[98],"spatially":[100],"visualized":[101],"colored":[104],"by":[105,134],"attention":[107],"scores":[108],"image":[110],"tiles.":[111],"necrosis":[118],"areas":[119],"were":[120],"highly":[121],"consistent":[122,141],"annotations":[125],"experienced":[127],"pathologists.":[128],"Moreover,":[129],"spatial":[131],"heatmap":[132],"generated":[133],"lymphocyte-specific":[135],"patterns":[138],"was":[139],"manually":[144],"labeled":[145],"WSIs.":[146]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":4}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}