{"id":"https://openalex.org/W2611254939","doi":"https://doi.org/10.1109/jbhi.2017.2700722","title":"Deep Learning for Automated Extraction of Primary Sites From Cancer Pathology Reports","display_name":"Deep Learning for Automated Extraction of Primary Sites From Cancer Pathology Reports","publication_year":2017,"publication_date":"2017-05-03","ids":{"openalex":"https://openalex.org/W2611254939","doi":"https://doi.org/10.1109/jbhi.2017.2700722","mag":"2611254939","pmid":"https://pubmed.ncbi.nlm.nih.gov/28475069"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2017.2700722","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2017.2700722","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.osti.gov/biblio/1408007","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002942001","display_name":"John X. Qiu","orcid":null},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John X. Qiu","raw_affiliation_strings":["Health Data Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA","University of Tennessee, Knoxville, TN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Health Data Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"University of Tennessee, Knoxville, TN, USA","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054049458","display_name":"Hong\u2010Jun Yoon","orcid":"https://orcid.org/0000-0002-5450-5878"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hong-Jun Yoon","raw_affiliation_strings":["Biomedical Sciences, Engineering, and Computing Group, Computational Sciences and Engineering Division and the Health Data Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"raw_orcid":"https://orcid.org/0000-0002-5450-5878","affiliations":[{"raw_affiliation_string":"Biomedical Sciences, Engineering, and Computing Group, Computational Sciences and Engineering Division and the Health Data Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058728327","display_name":"Paul Fearn","orcid":null},"institutions":[{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul A. Fearn","raw_affiliation_strings":["National Cancer Institute, Surveillance Research Program, Bethesda, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Cancer Institute, Surveillance Research Program, Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210140884"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014968146","display_name":"Georgia D. Tourassi","orcid":"https://orcid.org/0000-0002-9418-9638"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Georgia D. Tourassi","raw_affiliation_strings":["Biomedical Sciences, Engineering, and Computing Group, Computational Sciences and Engineering Division and the Health Data Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"raw_orcid":"https://orcid.org/0000-0002-9418-9638","affiliations":[{"raw_affiliation_string":"Biomedical Sciences, Engineering, and Computing Group, Computational Sciences and Engineering Division and the Health Data Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5002942001"],"corresponding_institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I75027704"],"apc_list":null,"apc_paid":null,"fwci":7.9734,"has_fulltext":false,"cited_by_count":154,"citation_normalized_percentile":{"value":0.9823325,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"22","issue":"1","first_page":"244","last_page":"251"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9991000294685364,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9991000294685364,"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/T10028","display_name":"Topic Modeling","score":0.9987999796867371,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9954000115394592,"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/deep-learning","display_name":"Deep learning","score":0.822831928730011},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.7967357635498047},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7659144401550293},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.702349066734314},{"id":"https://openalex.org/keywords/transfer-of-learning","display_name":"Transfer of learning","score":0.6749744415283203},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4762965738773346},{"id":"https://openalex.org/keywords/abstraction","display_name":"Abstraction","score":0.44615134596824646},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.4124162197113037},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.40499019622802734},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3290918171405792}],"concepts":[{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.822831928730011},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7967357635498047},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7659144401550293},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.702349066734314},{"id":"https://openalex.org/C150899416","wikidata":"https://www.wikidata.org/wiki/Q1820378","display_name":"Transfer of learning","level":2,"score":0.6749744415283203},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4762965738773346},{"id":"https://openalex.org/C124304363","wikidata":"https://www.wikidata.org/wiki/Q673661","display_name":"Abstraction","level":2,"score":0.44615134596824646},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.4124162197113037},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.40499019622802734},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3290918171405792},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003936","descriptor_name":"Diagnosis, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003936","descriptor_name":"Diagnosis, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003936","descriptor_name":"Diagnosis, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","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":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","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":"Q000175","qualifier_name":"diagnosis","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":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/jbhi.2017.2700722","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2017.2700722","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:28475069","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28475069","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":"IEEE journal of biomedical and health informatics","raw_type":null},{"id":"pmh:oai:osti.gov:1408007","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1408007","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null}],"best_oa_location":{"id":"pmh:oai:osti.gov:1408007","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1408007","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/8","score":0.5400000214576721,"display_name":"Decent work and economic growth"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W45867036","https://openalex.org/W168564468","https://openalex.org/W179875071","https://openalex.org/W182110599","https://openalex.org/W1557757161","https://openalex.org/W1662133657","https://openalex.org/W1832693441","https://openalex.org/W1994863727","https://openalex.org/W2036705578","https://openalex.org/W2094937180","https://openalex.org/W2112796928","https://openalex.org/W2131744502","https://openalex.org/W2149527488","https://openalex.org/W2153579005","https://openalex.org/W2158922990","https://openalex.org/W2214674395","https://openalex.org/W2215206286","https://openalex.org/W2283041611","https://openalex.org/W2322570510","https://openalex.org/W2328399960","https://openalex.org/W2345723683","https://openalex.org/W2493134281","https://openalex.org/W2952230511","https://openalex.org/W2963083845","https://openalex.org/W4294170691","https://openalex.org/W6601805350","https://openalex.org/W6606906144","https://openalex.org/W6607333740","https://openalex.org/W6607438652","https://openalex.org/W6638733343","https://openalex.org/W6679775712","https://openalex.org/W6682691769","https://openalex.org/W6683738474","https://openalex.org/W6688533166","https://openalex.org/W6688598427","https://openalex.org/W6702009625"],"related_works":["https://openalex.org/W2669956259","https://openalex.org/W4249005693","https://openalex.org/W4392946183","https://openalex.org/W3088732000","https://openalex.org/W4226493464","https://openalex.org/W3133861977","https://openalex.org/W3183901164","https://openalex.org/W4206357785","https://openalex.org/W4281381188","https://openalex.org/W2951211570"],"abstract_inverted_index":{"Pathology":[0],"reports":[1,17,92],"are":[2],"a":[3,24,36,47,61,64,87,106,157,170],"primary":[4],"source":[5],"of":[6,15,49,75,89,138,160,198,204],"information":[7],"for":[8,41,176,201],"cancer":[9,53,190],"registries":[10],"which":[11],"process":[12],"high":[13],"volumes":[14],"free-text":[16],"annually.":[18],"Information":[19],"extraction":[20],"and":[21,35,51,63,78,134,142,189],"coding":[22],"is":[23],"manual,":[25],"labor-intensive":[26],"process.":[27],"In":[28],"this":[29],"study,":[30],"we":[31],"investigated":[32],"deep":[33,118,178,199],"learning":[34,119,168,179,200],"convolutional":[37],"neural":[38],"network":[39],"(CNN),":[40],"extracting":[42],"ICD-O-3":[43,164],"topographic":[44],"codes":[45],"from":[46],"corpus":[48],"breast":[50],"lung":[52],"pathology":[54,91,205],"reports.":[55,206],"We":[56,114],"performed":[57],"two":[58],"experiments,":[59],"using":[60],"CNN":[62,101,155,187],"more":[65,107],"conventional":[66,108,124],"term":[67,109],"frequency":[68,110],"vector":[69,111],"approach,":[70],"to":[71,140],"assess":[72],"the":[73,98,117,123,127,152,177,186,196],"effects":[74],"class":[76,128,146],"prevalence":[77,129],"inter-class":[79],"transfer":[80],"learning.":[81],"The":[82],"experiments":[83],"were":[84,148,183],"based":[85],"on":[86,185],"set":[88],"942":[90],"with":[93],"human":[94],"expert":[95],"annotations":[96],"as":[97],"gold":[99],"standard.":[100],"performance":[102,174],"was":[103],"compared":[104],"against":[105],"space":[112],"approach.":[113],"observed":[115],"that":[116],"models":[120],"consistently":[121],"outperformed":[122],"approaches":[125],"in":[126,132],"experiment,":[130],"resulting":[131],"micro-":[133],"macro-F":[135],"score":[136,159],"increases":[137],"up":[139],"0.132":[141],"0.226,":[143],"respectively,":[144],"when":[145],"labels":[147],"well":[149],"populated.":[150],"Specifically,":[151],"best":[153],"performing":[154],"achieved":[156],"micro-F":[158],"0.722":[161],"over":[162],"12":[163],"topography":[165],"codes.":[166],"Transfer":[167],"provided":[169],"consistent":[171],"but":[172,181],"modest":[173],"boost":[175],"methods":[180],"trends":[182],"contingent":[184],"method":[188],"site.":[191],"These":[192],"encouraging":[193],"results":[194],"demonstrate":[195],"potential":[197],"automated":[202],"abstraction":[203]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":19},{"year":2021,"cited_by_count":26},{"year":2020,"cited_by_count":18},{"year":2019,"cited_by_count":35},{"year":2018,"cited_by_count":15},{"year":2017,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
