{"id":"https://openalex.org/W2948196927","doi":"https://doi.org/10.18653/v1/w19-5028","title":"Clinical Concept Extraction for Document-Level Coding","display_name":"Clinical Concept Extraction for Document-Level Coding","publication_year":2019,"publication_date":"2019-01-01","ids":{"openalex":"https://openalex.org/W2948196927","doi":"https://doi.org/10.18653/v1/w19-5028","mag":"2948196927"},"language":"en","primary_location":{"id":"doi:10.18653/v1/w19-5028","is_oa":true,"landing_page_url":"http://doi.org/10.18653/v1/w19-5028","pdf_url":"https://www.aclweb.org/anthology/W19-5028.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 18th BioNLP Workshop and Shared Task","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.aclweb.org/anthology/W19-5028.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079108871","display_name":"Sarah Wiegreffe","orcid":null},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sarah Wiegreffe","raw_affiliation_strings":["Georgia Institute of Technology","#N#\u2021#N#Georgia Institute of Technology#N#"],"affiliations":[{"raw_affiliation_string":"Georgia Institute of Technology","institution_ids":["https://openalex.org/I130701444"]},{"raw_affiliation_string":"#N#\u2021#N#Georgia Institute of Technology#N#","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034622258","display_name":"Edward Choi","orcid":"https://orcid.org/0000-0002-5958-3509"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]},{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Edward Choi","raw_affiliation_strings":["Georgia Institute of Technology","Google,,,,,"],"affiliations":[{"raw_affiliation_string":"Georgia Institute of Technology","institution_ids":["https://openalex.org/I130701444"]},{"raw_affiliation_string":"Google,,,,,","institution_ids":["https://openalex.org/I1291425158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073544229","display_name":"Sherry Yan","orcid":null},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]},{"id":"https://openalex.org/I114073160","display_name":"Sutter Health","ror":"https://ror.org/0060avh92","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I114073160"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sherry Yan","raw_affiliation_strings":["Sutter Health * Current Affiliation: Google Inc","SUTTER HEALTH"],"affiliations":[{"raw_affiliation_string":"Sutter Health * Current Affiliation: Google Inc","institution_ids":["https://openalex.org/I114073160","https://openalex.org/I1291425158"]},{"raw_affiliation_string":"SUTTER HEALTH","institution_ids":["https://openalex.org/I114073160"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084279065","display_name":"Jimeng Sun","orcid":"https://orcid.org/0000-0003-1512-6426"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jimeng Sun","raw_affiliation_strings":["Georgia Institute of Technology","#N#\u2021#N#Georgia Institute of Technology#N#"],"affiliations":[{"raw_affiliation_string":"Georgia Institute of Technology","institution_ids":["https://openalex.org/I130701444"]},{"raw_affiliation_string":"#N#\u2021#N#Georgia Institute of Technology#N#","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047699861","display_name":"Jacob Eisenstein","orcid":null},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacob Eisenstein","raw_affiliation_strings":["Georgia Institute of Technology","#N#\u2021#N#Georgia Institute of Technology#N#"],"affiliations":[{"raw_affiliation_string":"Georgia Institute of Technology","institution_ids":["https://openalex.org/I130701444"]},{"raw_affiliation_string":"#N#\u2021#N#Georgia Institute of Technology#N#","institution_ids":["https://openalex.org/I130701444"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5079108871"],"corresponding_institution_ids":["https://openalex.org/I130701444"],"apc_list":null,"apc_paid":null,"fwci":0.10305101,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.45872656,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"261","last_page":"272"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9995999932289124,"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":0.9995999932289124,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9897000193595886,"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/T10028","display_name":"Topic Modeling","score":0.9825999736785889,"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":0.6694133877754211},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.6657185554504395},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.617591917514801},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.604812502861023},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.503485381603241},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4859672784805298},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.45572322607040405},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.0956108570098877},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08033093810081482}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6694133877754211},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.6657185554504395},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.617591917514801},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.604812502861023},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.503485381603241},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4859672784805298},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.45572322607040405},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0956108570098877},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08033093810081482},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.18653/v1/w19-5028","is_oa":true,"landing_page_url":"http://doi.org/10.18653/v1/w19-5028","pdf_url":"https://www.aclweb.org/anthology/W19-5028.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 18th BioNLP Workshop and Shared Task","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:1906.03380","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1906.03380","pdf_url":"https://arxiv.org/pdf/1906.03380","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"mag:2948196927","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1906.03380","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.1906.03380","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1906.03380","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.18653/v1/w19-5028","is_oa":true,"landing_page_url":"http://doi.org/10.18653/v1/w19-5028","pdf_url":"https://www.aclweb.org/anthology/W19-5028.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 18th BioNLP Workshop and Shared Task","raw_type":"proceedings-article"},"sustainable_development_goals":[{"score":0.5600000023841858,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309321","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44"},{"id":"https://openalex.org/F4320314206","display_name":"Sutter Health","ror":"https://ror.org/0060avh92"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2948196927.pdf","grobid_xml":"https://content.openalex.org/works/W2948196927.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1550258693","https://openalex.org/W1637593105","https://openalex.org/W1966716734","https://openalex.org/W1976526581","https://openalex.org/W2109977485","https://openalex.org/W2146089916","https://openalex.org/W2162311237","https://openalex.org/W2404369708","https://openalex.org/W2508848934","https://openalex.org/W2557074642","https://openalex.org/W2624871570","https://openalex.org/W2732371337","https://openalex.org/W2768488789","https://openalex.org/W2772121968","https://openalex.org/W2772765860","https://openalex.org/W2793265220","https://openalex.org/W2803118636","https://openalex.org/W2888882903","https://openalex.org/W2889577585","https://openalex.org/W2889869899","https://openalex.org/W2898355739","https://openalex.org/W2905273891","https://openalex.org/W2951560156","https://openalex.org/W2955483668","https://openalex.org/W2962912956","https://openalex.org/W2963427391","https://openalex.org/W2964142373","https://openalex.org/W2964308564"],"related_works":["https://openalex.org/W2970971588","https://openalex.org/W2605191883","https://openalex.org/W2941310691","https://openalex.org/W2467816047","https://openalex.org/W3006779453","https://openalex.org/W3005971956","https://openalex.org/W2025428542","https://openalex.org/W2538256802","https://openalex.org/W2189067371","https://openalex.org/W1539773714","https://openalex.org/W2292429631","https://openalex.org/W2767908683","https://openalex.org/W2902270739","https://openalex.org/W2295390119","https://openalex.org/W3011047319","https://openalex.org/W2979647235","https://openalex.org/W2966605532","https://openalex.org/W1535212002","https://openalex.org/W874670514","https://openalex.org/W3046189927"],"abstract_inverted_index":{"The":[0],"text":[1,31,58,90],"of":[2,10,30,46,59,91,108],"clinical":[3,14,22,60,123],"notes":[4,23],"can":[5],"be":[6],"a":[7,35,105],"valuable":[8],"source":[9],"patient":[11],"information":[12,26],"and":[13,130],"assessments.":[15],"Historically,":[16],"the":[17,44,56,66,69,89,92,109,112,121],"primary":[18],"approach":[19],"for":[20],"exploiting":[21],"has":[24,42],"been":[25],"extraction:":[27],"linking":[28],"spans":[29],"to":[32,50,64,85,103],"concepts":[33,79,97,114],"in":[34],"detailed":[36],"domain":[37],"ontology.":[38],"However,":[39],"recent":[40],"work":[41],"demonstrated":[43],"potential":[45],"supervised":[47],"machine":[48],"learning":[49],"extract":[51],"document-level":[52,122],"codes":[53],"directly":[54],"from":[55],"raw":[57],"notes.":[61],"We":[62,126],"propose":[63],"bridge":[65],"gap":[67],"between":[68],"two":[70,73],"approaches":[71],"with":[72],"novel":[74],"syntheses:":[75],"(1)":[76],"treating":[77,95],"extracted":[78,96],"as":[80,98],"features,":[81],"which":[82,100],"are":[83,101],"used":[84,102],"supplement":[86],"or":[87],"replace":[88],"note;":[93],"(2)":[94],"labels,":[99],"learn":[104],"better":[106],"representation":[107],"text.":[110],"Unfortunately,":[111],"resulting":[113],"do":[115],"not":[116],"yield":[117],"performance":[118],"gains":[119],"on":[120],"coding":[124],"task.":[125],"explore":[127],"possible":[128],"explanations":[129],"future":[131],"research":[132],"directions.":[133]},"counts_by_year":[{"year":2020,"cited_by_count":1}],"updated_date":"2026-02-09T09:26:11.010843","created_date":"2025-10-10T00:00:00"}
