{"id":"https://openalex.org/W4389543231","doi":"https://doi.org/10.1109/embc40787.2023.10340998","title":"Automatic Annotation of PubMed Articles with MeSH Qualifiers*","display_name":"Automatic Annotation of PubMed Articles with MeSH Qualifiers*","publication_year":2023,"publication_date":"2023-07-24","ids":{"openalex":"https://openalex.org/W4389543231","doi":"https://doi.org/10.1109/embc40787.2023.10340998","pmid":"https://pubmed.ncbi.nlm.nih.gov/38082894"},"language":"en","primary_location":{"id":"doi:10.1109/embc40787.2023.10340998","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1109/embc40787.2023.10340998","pdf_url":"https://ieeexplore.ieee.org/ielx7/10339936/10339939/10340998.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 45th Annual International Conference of the IEEE Engineering in Medicine &amp; Biology Society (EMBC)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://ieeexplore.ieee.org/ielx7/10339936/10339939/10340998.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101277688","display_name":"Weizhong Tang","orcid":null},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Weizhong Tang","raw_affiliation_strings":["Lund University,Department of Computer Science,Lund,Sweden","Department of Computer Science, Lund University, Lund, Sweden"],"affiliations":[{"raw_affiliation_string":"Lund University,Department of Computer Science,Lund,Sweden","institution_ids":["https://openalex.org/I187531555"]},{"raw_affiliation_string":"Department of Computer Science, Lund University, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029371772","display_name":"Marcus Klang","orcid":null},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Marcus Klang","raw_affiliation_strings":["Lund University,Department of Computer Science,Lund,Sweden","Department of Computer Science, Lund University, Lund, Sweden"],"affiliations":[{"raw_affiliation_string":"Lund University,Department of Computer Science,Lund,Sweden","institution_ids":["https://openalex.org/I187531555"]},{"raw_affiliation_string":"Department of Computer Science, Lund University, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024675281","display_name":"Dennis Medved","orcid":"https://orcid.org/0000-0001-5980-0748"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Dennis Medved","raw_affiliation_strings":["Lund University,Medicine Faculty,Lund,Sweden","Medicine Faculty, Lund University, Lund, Sweden"],"affiliations":[{"raw_affiliation_string":"Lund University,Medicine Faculty,Lund,Sweden","institution_ids":["https://openalex.org/I187531555"]},{"raw_affiliation_string":"Medicine Faculty, Lund University, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069585870","display_name":"Pierre Nugues","orcid":"https://orcid.org/0000-0002-9563-4000"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Pierre Nugues","raw_affiliation_strings":["Lund University,Department of Computer Science,Lund,Sweden","Department of Computer Science, Lund University, Lund, Sweden"],"affiliations":[{"raw_affiliation_string":"Lund University,Department of Computer Science,Lund,Sweden","institution_ids":["https://openalex.org/I187531555"]},{"raw_affiliation_string":"Department of Computer Science, Lund University, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023694268","display_name":"Johan Nilsson","orcid":"https://orcid.org/0000-0001-6860-6090"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Johan Nilsson","raw_affiliation_strings":["Lund University and Sk&#x00E5;ne University Hospital,Thoracic Surgery and Bioinformatics,Department of Translational Medicine,Lund,Sweden"],"affiliations":[{"raw_affiliation_string":"Lund University and Sk&#x00E5;ne University Hospital,Thoracic Surgery and Bioinformatics,Department of Translational Medicine,Lund,Sweden","institution_ids":["https://openalex.org/I187531555"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5101277688"],"corresponding_institution_ids":["https://openalex.org/I187531555"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.32460081,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"2023","issue":null,"first_page":"1","last_page":"4"},"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.9965000152587891,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9959999918937683,"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":0.7223132252693176},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6444034576416016},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4863036572933197},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.35594192147254944},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3103175163269043}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7223132252693176},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6444034576416016},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4863036572933197},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.35594192147254944},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3103175163269043}],"mesh":[{"descriptor_ui":"D000043","descriptor_name":"Abstracting and Indexing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000043","descriptor_name":"Abstracting and Indexing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000043","descriptor_name":"Abstracting and Indexing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000043","descriptor_name":"Abstracting and Indexing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000043","descriptor_name":"Abstracting and Indexing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000043","descriptor_name":"Abstracting and Indexing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/embc40787.2023.10340998","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1109/embc40787.2023.10340998","pdf_url":"https://ieeexplore.ieee.org/ielx7/10339936/10339939/10340998.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 45th Annual International Conference of the IEEE Engineering in Medicine &amp; Biology Society (EMBC)","raw_type":"proceedings-article"},{"id":"pmid:38082894","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38082894","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":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference","raw_type":null}],"best_oa_location":{"id":"doi:10.1109/embc40787.2023.10340998","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1109/embc40787.2023.10340998","pdf_url":"https://ieeexplore.ieee.org/ielx7/10339936/10339939/10340998.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 45th Annual International Conference of the IEEE Engineering in Medicine &amp; Biology Society (EMBC)","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6462591990","display_name":null,"funder_award_id":"04533","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G8820178184","display_name":null,"funder_award_id":"Vetenskapr\u00e5det","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"}],"funders":[{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4389543231.pdf","grobid_xml":"https://content.openalex.org/works/W4389543231.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W2101234009","https://openalex.org/W2150102617","https://openalex.org/W2920882081","https://openalex.org/W2978017171","https://openalex.org/W2979826702","https://openalex.org/W3037911001","https://openalex.org/W3201658153","https://openalex.org/W4211170114","https://openalex.org/W4225127358","https://openalex.org/W4285138508","https://openalex.org/W6675354045","https://openalex.org/W6681875376","https://openalex.org/W6768851824","https://openalex.org/W6810663043"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W3204019825"],"abstract_inverted_index":{"The":[0,20],"Medical":[1],"Subject":[2],"Headings":[3],"(MeSH)":[4],"is":[5,237,267],"a":[6,24,41,65,70,115,119,126,137,157,246,259],"comprehensive":[7],"indexing":[8,230],"vocabulary":[9],"used":[10,97],"to":[11,40,87,105,211,227],"label":[12],"millions":[13],"of":[14,23,27,36,108,129,141,174,182,197],"books":[15],"and":[16,35,72,94,118,146,181,241],"articles":[17,143,236],"on":[18,51,136],"PubMed.":[19],"MeSH":[21,58,74,214],"annotation":[22],"document":[25,71],"consists":[26],"one":[28],"or":[29],"more":[30,46,232],"descriptors,":[31,75],"the":[32,77,85,90,98,133,177,185,193,200,213,229],"main":[33],"headings,":[34],"qualifiers,":[37],"subheadings":[38],"specific":[39],"descriptor.":[42],"Currently,":[43],"there":[44],"are":[45,54,190],"than":[47,192],"34":[48],"million":[49],"documents":[50,88],"PubMed,":[52],"which":[53,266],"manually":[55,154],"tagged":[56],"with":[57,89,114,132,216],"terms.":[59],"In":[60,80,256],"this":[61,109,165,257],"paper,":[62],"we":[63,83,95,169,221],"describe":[64],"machine-learning":[66,260],"procedure":[67,206],"that,":[68],"given":[69],"its":[73],"predicts":[76],"respective":[78],"qualifiers.":[79],"our":[81,130],"experiment,":[82],"restricted":[84],"dataset":[86],"Heart":[91],"Transplantation":[92],"descriptor":[93,110],"only":[96],"PubMed":[99,202],"abstracts.":[100],"We":[101,123],"trained":[102],"binary":[103],"classifiers":[104],"predict":[106],"qualifiers":[107],"using":[111],"logistic":[112,178],"regression":[113,179],"tfidf":[116],"vectorizer":[117],"fine-tuned":[120],"DistilBERT":[121,186],"model.":[122,187],"carried":[124],"out":[125],"small-scale":[127],"evaluation":[128],"models":[131],"Mortality":[134],"qualifier":[135],"test":[138,150,167],"set":[139,151],"consisting":[140],"30":[142],"(15":[144],"positives":[145],"15":[147],"negatives).":[148],"This":[149],"was":[152],"then":[153],"re-annotated":[155,166],"by":[156],"cardiac":[158],"surgeon,":[159],"expert":[160],"in":[161,249,272],"thoracic":[162],"transplantation.":[163,255],"On":[164],"set,":[168],"obtained":[170],"macroaveraged":[171,194],"F1":[172,195],"scores":[173,189],"0.81":[175],"for":[176,184,239,269],"model":[180,261],"0.85":[183],"Both":[188],"higher":[191],"score":[196],"0.76":[198],"from":[199],"initial":[201],"manual":[203,264],"annotation.":[204],"Our":[205],"would":[207,223],"be":[208],"easily":[209],"extensible":[210],"all":[212],"descriptors":[215],"sufficient":[217],"training":[218],"data":[219],"and,":[220],"believe,":[222],"enable":[224],"human":[225],"annotators":[226],"complete":[228],"work":[231],"easily.Clinical":[233],"Relevance-Selecting":[234],"relevant":[235],"important":[238],"clinicians":[240],"researchers,":[242],"but":[243],"also":[244],"often":[245],"challenge,":[247],"especially":[248],"complex":[250],"subspecialties":[251],"such":[252],"as":[253],"heart":[254],"study,":[258],"outperformed":[262],"PubMed's":[263],"annotation,":[265],"promising":[268],"improved":[270],"quality":[271],"information":[273],"retrieval.":[274]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
