{"id":"https://openalex.org/W4390992208","doi":"https://doi.org/10.1109/bibm58861.2023.10385876","title":"Parsing Clinical Trial Eligibility Criteria for Cohort Query by a Multi-Input Multi-Output Sequence Labeling Model","display_name":"Parsing Clinical Trial Eligibility Criteria for Cohort Query by a Multi-Input Multi-Output Sequence Labeling Model","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390992208","doi":"https://doi.org/10.1109/bibm58861.2023.10385876","pmid":"https://pubmed.ncbi.nlm.nih.gov/39015287"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10385876","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10385876","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11251129/pdf/nihms-2007993.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067851621","display_name":"Shubo Tian","orcid":"https://orcid.org/0000-0001-6415-1439"},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shubo Tian","raw_affiliation_strings":["Florida State University,Department of Statistics,Tallahassee,USA","Department of Statistics, Florida State University, Tallahassee, USA"],"affiliations":[{"raw_affiliation_string":"Florida State University,Department of Statistics,Tallahassee,USA","institution_ids":["https://openalex.org/I103163165"]},{"raw_affiliation_string":"Department of Statistics, Florida State University, Tallahassee, USA","institution_ids":["https://openalex.org/I103163165"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109541754","display_name":"Pengfei Yin","orcid":"https://orcid.org/0000-0001-8071-3120"},"institutions":[{"id":"https://openalex.org/I2800717037","display_name":"University of Florida Health","ror":"https://ror.org/04tk2gy88","country_code":"US","type":"education","lineage":["https://openalex.org/I2800717037"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pengfei Yin","raw_affiliation_strings":["University of Florida,Department of Health Outcomes and Biomedical Informatics,Gainesville,USA","Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, USA"],"affiliations":[{"raw_affiliation_string":"University of Florida,Department of Health Outcomes and Biomedical Informatics,Gainesville,USA","institution_ids":["https://openalex.org/I2800717037"]},{"raw_affiliation_string":"Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, USA","institution_ids":["https://openalex.org/I2800717037"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039891212","display_name":"Hansi Zhang","orcid":"https://orcid.org/0000-0003-4585-0888"},"institutions":[{"id":"https://openalex.org/I2800717037","display_name":"University of Florida Health","ror":"https://ror.org/04tk2gy88","country_code":"US","type":"education","lineage":["https://openalex.org/I2800717037"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hansi Zhang","raw_affiliation_strings":["University of Florida,Department of Health Outcomes and Biomedical Informatics,Gainesville,USA","Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, USA"],"affiliations":[{"raw_affiliation_string":"University of Florida,Department of Health Outcomes and Biomedical Informatics,Gainesville,USA","institution_ids":["https://openalex.org/I2800717037"]},{"raw_affiliation_string":"Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, USA","institution_ids":["https://openalex.org/I2800717037"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040418395","display_name":"Arslan Erdengasileng","orcid":"https://orcid.org/0000-0003-0905-3988"},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arslan Erdengasileng","raw_affiliation_strings":["Florida State University,Department of Statistics,Tallahassee,USA","Department of Statistics, Florida State University, Tallahassee, USA"],"affiliations":[{"raw_affiliation_string":"Florida State University,Department of Statistics,Tallahassee,USA","institution_ids":["https://openalex.org/I103163165"]},{"raw_affiliation_string":"Department of Statistics, Florida State University, Tallahassee, USA","institution_ids":["https://openalex.org/I103163165"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030951014","display_name":"Jiang Bian","orcid":"https://orcid.org/0000-0002-2238-5429"},"institutions":[{"id":"https://openalex.org/I2800717037","display_name":"University of Florida Health","ror":"https://ror.org/04tk2gy88","country_code":"US","type":"education","lineage":["https://openalex.org/I2800717037"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiang Bian","raw_affiliation_strings":["University of Florida,Department of Health Outcomes and Biomedical Informatics,Gainesville,USA","Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, USA"],"affiliations":[{"raw_affiliation_string":"University of Florida,Department of Health Outcomes and Biomedical Informatics,Gainesville,USA","institution_ids":["https://openalex.org/I2800717037"]},{"raw_affiliation_string":"Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, USA","institution_ids":["https://openalex.org/I2800717037"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047567293","display_name":"Zhe He","orcid":"https://orcid.org/0000-0003-3608-0244"},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhe He","raw_affiliation_strings":["Florida State University,School of Information,Tallahassee,USA","School of Information, Florida State University, Tallahassee, USA"],"affiliations":[{"raw_affiliation_string":"Florida State University,School of Information,Tallahassee,USA","institution_ids":["https://openalex.org/I103163165"]},{"raw_affiliation_string":"School of Information, Florida State University, Tallahassee, USA","institution_ids":["https://openalex.org/I103163165"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5067851621"],"corresponding_institution_ids":["https://openalex.org/I103163165"],"apc_list":null,"apc_paid":null,"fwci":0.3426,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.68185742,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"2023","issue":null,"first_page":"4426","last_page":"4430"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","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/T10028","display_name":"Topic Modeling","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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9987000226974487,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9957000017166138,"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":0.8029300570487976},{"id":"https://openalex.org/keywords/tuple","display_name":"Tuple","score":0.779466986656189},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.6926249265670776},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.6662853956222534},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.6199929118156433},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5914967060089111},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5723479390144348},{"id":"https://openalex.org/keywords/machine-translation","display_name":"Machine translation","score":0.47508755326271057},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.468436062335968},{"id":"https://openalex.org/keywords/sequence-labeling","display_name":"Sequence labeling","score":0.46019792556762695},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.4281330108642578},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3884662389755249},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3348395824432373},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.20200392603874207},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11315414309501648}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8029300570487976},{"id":"https://openalex.org/C118930307","wikidata":"https://www.wikidata.org/wiki/Q600590","display_name":"Tuple","level":2,"score":0.779466986656189},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.6926249265670776},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.6662853956222534},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.6199929118156433},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5914967060089111},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5723479390144348},{"id":"https://openalex.org/C203005215","wikidata":"https://www.wikidata.org/wiki/Q79798","display_name":"Machine translation","level":2,"score":0.47508755326271057},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.468436062335968},{"id":"https://openalex.org/C35639132","wikidata":"https://www.wikidata.org/wiki/Q7452468","display_name":"Sequence labeling","level":3,"score":0.46019792556762695},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.4281330108642578},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3884662389755249},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3348395824432373},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.20200392603874207},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11315414309501648},{"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},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/bibm58861.2023.10385876","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10385876","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmid:39015287","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39015287","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":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11251129","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11251129","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11251129/pdf/nihms-2007993.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proceedings (IEEE Int Conf Bioinformatics Biomed)","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:11251129","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11251129","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11251129/pdf/nihms-2007993.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proceedings (IEEE Int Conf Bioinformatics Biomed)","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.8199999928474426,"display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G2417061327","display_name":null,"funder_award_id":"UL1TR0014","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3328176752","display_name":null,"funder_award_id":"UL1TR00142","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3497591915","display_name":null,"funder_award_id":"(NIH)","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3747674280","display_name":null,"funder_award_id":"R21CA253394","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3752933254","display_name":null,"funder_award_id":"R21AG068717","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4818037007","display_name":null,"funder_award_id":"TR001427","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4923956253","display_name":null,"funder_award_id":"R21AG061431","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7211153767","display_name":null,"funder_award_id":"UL1TR001427","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390992208.pdf"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W2111678566","https://openalex.org/W2114847203","https://openalex.org/W2165067209","https://openalex.org/W2194775991","https://openalex.org/W2292790679","https://openalex.org/W2396881363","https://openalex.org/W2604410201","https://openalex.org/W2804778516","https://openalex.org/W2896457183","https://openalex.org/W2911661483","https://openalex.org/W2965373594","https://openalex.org/W2970224261","https://openalex.org/W3006162251","https://openalex.org/W3081304278","https://openalex.org/W3191402931","https://openalex.org/W4242781527","https://openalex.org/W6755207826","https://openalex.org/W6766673545"],"related_works":["https://openalex.org/W4245395944","https://openalex.org/W3115565094","https://openalex.org/W4288558800","https://openalex.org/W2953770453","https://openalex.org/W3097570857","https://openalex.org/W4287623157","https://openalex.org/W3104108644","https://openalex.org/W4287654226","https://openalex.org/W2179743027","https://openalex.org/W3042366391"],"abstract_inverted_index":{"To":[0],"enable":[1],"electronic":[2],"screening":[3],"of":[4,53,72,90,111],"eligible":[5],"patients":[6],"for":[7],"clinical":[8,11],"trials,":[9],"free-text":[10],"trial":[12],"eligibility":[13,49,98],"criteria":[14,50,99],"should":[15],"be":[16],"translated":[17],"to":[18,30,47],"a":[19,39,61,77],"computable":[20],"format.":[21],"Natural":[22],"language":[23],"processing":[24],"(NLP)":[25],"techniques":[26],"have":[27],"the":[28,70,73,82,93],"potential":[29],"automate":[31],"this":[32,35],"process.":[33],"In":[34],"study,":[36],"we":[37],"explored":[38],"supervised":[40],"multi-input":[41],"multi-output":[42],"(MIMO)":[43],"sequence":[44],"labelling":[45],"model":[46],"parse":[48],"into":[51,100,114],"combinations":[52],"fact":[54],"and":[55,102],"condition":[56],"tuples.":[57],"Our":[58],"experiments":[59],"on":[60],"small":[62],"manually":[63],"annotated":[64],"training":[65],"dataset":[66],"showed":[67],"that":[68,69],"performance":[71,94],"MIMO":[74],"framework":[75],"with":[76],"BERT-based":[78],"encoder":[79],"using":[80],"all":[81],"input":[83],"sequences":[84],"achieved":[85],"an":[86],"overall":[87],"lenient-level":[88],"AUROC":[89],"0.61.":[91],"Although":[92],"is":[95],"suboptimal,":[96],"representing":[97],"logical":[101],"semantically":[103],"clear":[104],"tuples":[105,113],"can":[106],"potentially":[107],"make":[108],"subsequent":[109],"translation":[110],"these":[112],"database":[115],"queries":[116],"more":[117],"reliable.":[118]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
