{"id":"https://openalex.org/W2100678627","doi":"https://doi.org/10.1186/2041-1480-5-3","title":"Detecting concept mentions in biomedical text using hidden Markov model: multiple concept types at once or one at a time?","display_name":"Detecting concept mentions in biomedical text using hidden Markov model: multiple concept types at once or one at a time?","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2100678627","doi":"https://doi.org/10.1186/2041-1480-5-3","mag":"2100678627","pmid":"https://pubmed.ncbi.nlm.nih.gov/24438362"},"language":"en","primary_location":{"id":"doi:10.1186/2041-1480-5-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-3","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-3","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028161578","display_name":"Manabu Torii","orcid":"https://orcid.org/0000-0002-4825-0696"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Manabu Torii","raw_affiliation_strings":["Department of Radiology, Georgetown University Medical Center, Washington, DC, USA. torii@udel.edu","Dept. of Radiology, Georgetown University Medical Center, Washington, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Radiology, Georgetown University Medical Center, Washington, DC, USA. torii@udel.edu","institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593"]},{"raw_affiliation_string":"Dept. of Radiology, Georgetown University Medical Center, Washington, USA","institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041082275","display_name":"Kavishwar B. Wagholikar","orcid":"https://orcid.org/0000-0002-6219-861X"},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kavishwar Wagholikar","raw_affiliation_strings":["Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA","Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723"]},{"raw_affiliation_string":"Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, USA","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101585391","display_name":"Hongfang Liu","orcid":"https://orcid.org/0000-0003-2570-3741"},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hongfang Liu","raw_affiliation_strings":["Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA","Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723"]},{"raw_affiliation_string":"Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, USA","institution_ids":["https://openalex.org/I1330342723"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5028161578"],"corresponding_institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593"],"apc_list":{"value":1340,"currency":"USD","value_usd":1340},"apc_paid":{"value":1340,"currency":"USD","value_usd":1340},"fwci":0.9097,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.73301892,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"5","issue":"1","first_page":"3","last_page":"3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9323999881744385,"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":0.9323999881744385,"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":0.024700000882148743,"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.008500000461935997,"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":0.811336874961853},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6765122413635254},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5967505574226379},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.46244436502456665},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.4590628743171692},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.44870275259017944},{"id":"https://openalex.org/keywords/confusion","display_name":"Confusion","score":0.4485378563404083},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4363166391849518},{"id":"https://openalex.org/keywords/concept-drift","display_name":"Concept drift","score":0.4271022081375122},{"id":"https://openalex.org/keywords/sentence","display_name":"Sentence","score":0.41938668489456177},{"id":"https://openalex.org/keywords/type","display_name":"Type (biology)","score":0.4187489151954651}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.811336874961853},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6765122413635254},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5967505574226379},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.46244436502456665},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.4590628743171692},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.44870275259017944},{"id":"https://openalex.org/C2781140086","wikidata":"https://www.wikidata.org/wiki/Q557945","display_name":"Confusion","level":2,"score":0.4485378563404083},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4363166391849518},{"id":"https://openalex.org/C60777511","wikidata":"https://www.wikidata.org/wiki/Q3045002","display_name":"Concept drift","level":3,"score":0.4271022081375122},{"id":"https://openalex.org/C2777530160","wikidata":"https://www.wikidata.org/wiki/Q41796","display_name":"Sentence","level":2,"score":0.41938668489456177},{"id":"https://openalex.org/C2777299769","wikidata":"https://www.wikidata.org/wiki/Q3707858","display_name":"Type (biology)","level":2,"score":0.4187489151954651},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C11171543","wikidata":"https://www.wikidata.org/wiki/Q41630","display_name":"Psychoanalysis","level":1,"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/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C89198739","wikidata":"https://www.wikidata.org/wiki/Q3079880","display_name":"Data stream mining","level":2,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/2041-1480-5-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-3","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-3","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},{"id":"pmid:24438362","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24438362","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":"Journal of biomedical semantics","raw_type":null},{"id":"pmh:oai:europepmc.org:2896435","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3908466","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"pmh:oai:pubmedcentral.nih.gov:3908466","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3908466","pdf_url":null,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Biomed Semantics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/2041-1480-5-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-3","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-3","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.8100000023841858,"display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G5387631503","display_name":"CAREER:  Natural Language Processing for Biological Knowledge Management","funder_award_id":"0845523","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7999594839","display_name":null,"funder_award_id":"R01 GM102282","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309644","display_name":"State University of New York","ror":"https://ror.org/01q1z8k08"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2100678627.pdf","grobid_xml":"https://content.openalex.org/works/W2100678627.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1524642381","https://openalex.org/W1623072288","https://openalex.org/W2021331223","https://openalex.org/W2047782770","https://openalex.org/W2048140075","https://openalex.org/W2104381725","https://openalex.org/W2111437636","https://openalex.org/W2114039834","https://openalex.org/W2138482836","https://openalex.org/W2163107094","https://openalex.org/W2168041406","https://openalex.org/W2179276135"],"related_works":["https://openalex.org/W2990081132","https://openalex.org/W4296984035","https://openalex.org/W3127121676","https://openalex.org/W3108206468","https://openalex.org/W2053269318","https://openalex.org/W3091433184","https://openalex.org/W2364370872","https://openalex.org/W2902096670","https://openalex.org/W2931947761","https://openalex.org/W2025614924"],"abstract_inverted_index":{"BACKGROUND:":[0],"Identifying":[1],"phrases":[2,202],"that":[3,125,198,215],"refer":[4],"to":[5,46,74,160,168,235,242],"particular":[6],"concept":[7,99,111,130,142,178,201,210,220,248],"types":[8,49,63,100,112,131,221,249],"is":[9,71,233],"a":[10,34,60,65,93,104,140,224],"critical":[11],"step":[12],"in":[13,222,238],"extracting":[14],"information":[15],"from":[16],"documents.":[17],"Provided":[18],"with":[19,97,109],"annotated":[20,96,108],"documents":[21],"as":[22],"training":[23],"data,":[24],"supervised":[25],"machine":[26,35,228],"learning":[27,36,229],"can":[28],"automate":[29],"this":[30,39],"process.":[31],"When":[32],"building":[33],"model":[37,42],"for":[38,57,128,139,146,155,189,227],"task,":[40],"the":[41,87,121,147,156,163,171,176,190,239],"may":[43,54],"be":[44,55,204],"built":[45,56],"detect":[47],"all":[48],"simultaneously":[50,207],"(all-types-at-once)":[51],"or":[52,59,68],"it":[53],"one":[58],"few":[61],"selected":[62],"at":[64],"time":[66],"(one-type-":[67],"a-few-types-at-a-time).":[69],"It":[70],"of":[72,200],"interest":[73],"investigate":[75],"which":[76],"strategy":[77],"yields":[78],"better":[79,134],"detection":[80,182,199],"performance.":[81],"RESULTS:":[82],"Hidden":[83],"Markov":[84],"models":[85,126],"using":[86],"different":[88],"strategies":[89,149],"were":[90,118,150,187],"evaluated":[91],"on":[92,162,170,175],"clinical":[94],"corpus":[95,107,165,226],"three":[98],"(i2b2/VA":[101],"corpus)":[102],"and":[103,120,166,183],"biology":[105],"literature":[106],"five":[110],"(JNLPBA":[113],"corpus).":[114],"Ten-fold":[115],"cross-validation":[116],"tests":[117],"conducted":[119],"experimental":[122],"results":[123,196],"showed":[124],"trained":[127,138],"multiple":[129,209,219,247],"consistently":[132],"yielded":[133],"performance":[135,245],"than":[136,152],"those":[137,153],"single":[141],"type.":[143],"F-scores":[144],"observed":[145,154,188],"former":[148],"higher":[151],"latter":[157],"by":[158,206],"0.9":[159],"2.6%":[161],"i2b2/VA":[164],"1.4":[167],"10.1%":[169],"JNLPBA":[172],"corpus,":[173],"depending":[174],"target":[177],"types.":[179,211],"Improved":[180],"boundary":[181],"reduced":[184],"type":[185],"confusion":[186],"all-types-at-once":[191],"strategy.":[192],"CONCLUSIONS:":[193],"The":[194],"current":[195],"suggest":[197],"could":[203],"improved":[205],"tackling":[208],"This":[212],"also":[213],"suggests":[214],"we":[216],"should":[217],"annotate":[218],"developing":[223],"new":[225],"models.":[230],"Further":[231],"investigation":[232],"expected":[234],"gain":[236],"insights":[237],"underlying":[240],"mechanism":[241],"achieve":[243],"good":[244],"when":[246],"are":[250],"considered.":[251]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
