{"id":"https://openalex.org/W4296886375","doi":"https://doi.org/10.1109/inista55318.2022.9894270","title":"Biomedical Named Entity Recognition Using Transformers with biLSTM + CRF and Graph Convolutional Neural Networks","display_name":"Biomedical Named Entity Recognition Using Transformers with biLSTM + CRF and Graph Convolutional Neural Networks","publication_year":2022,"publication_date":"2022-08-08","ids":{"openalex":"https://openalex.org/W4296886375","doi":"https://doi.org/10.1109/inista55318.2022.9894270"},"language":"en","primary_location":{"id":"doi:10.1109/inista55318.2022.9894270","is_oa":false,"landing_page_url":"https://doi.org/10.1109/inista55318.2022.9894270","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 International Conference on INnovations in Intelligent SysTems and Applications (INISTA)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85139596222&origin=inward","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089870148","display_name":"G\u00f6kberk \u00c7elikmasat","orcid":null},"institutions":[{"id":"https://openalex.org/I74897591","display_name":"Marmara University","ror":"https://ror.org/02kswqa67","country_code":"TR","type":"education","lineage":["https://openalex.org/I74897591"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Gokberk Celikmasat","raw_affiliation_strings":["Marmara University,Computer Engineering Department,Istanbul,Turkey","Computer Engineering Department, Marmara University, Istanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Marmara University,Computer Engineering Department,Istanbul,Turkey","institution_ids":["https://openalex.org/I74897591"]},{"raw_affiliation_string":"Computer Engineering Department, Marmara University, Istanbul, Turkey","institution_ids":["https://openalex.org/I74897591"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042885506","display_name":"Muhammed Enes Akturk","orcid":null},"institutions":[{"id":"https://openalex.org/I74897591","display_name":"Marmara University","ror":"https://ror.org/02kswqa67","country_code":"TR","type":"education","lineage":["https://openalex.org/I74897591"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Muhammed Enes Akturk","raw_affiliation_strings":["Marmara University,Computer Engineering Department,Istanbul,Turkey","Computer Engineering Department, Marmara University, Istanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Marmara University,Computer Engineering Department,Istanbul,Turkey","institution_ids":["https://openalex.org/I74897591"]},{"raw_affiliation_string":"Computer Engineering Department, Marmara University, Istanbul, Turkey","institution_ids":["https://openalex.org/I74897591"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081010893","display_name":"Yunus Emre Ertunc","orcid":null},"institutions":[{"id":"https://openalex.org/I74897591","display_name":"Marmara University","ror":"https://ror.org/02kswqa67","country_code":"TR","type":"education","lineage":["https://openalex.org/I74897591"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Yunus Emre Ertunc","raw_affiliation_strings":["Marmara University,Computer Engineering Department,Istanbul,Turkey","Computer Engineering Department, Marmara University, Istanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Marmara University,Computer Engineering Department,Istanbul,Turkey","institution_ids":["https://openalex.org/I74897591"]},{"raw_affiliation_string":"Computer Engineering Department, Marmara University, Istanbul, Turkey","institution_ids":["https://openalex.org/I74897591"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046908145","display_name":"Abdul Majeed Issifu","orcid":null},"institutions":[{"id":"https://openalex.org/I74897591","display_name":"Marmara University","ror":"https://ror.org/02kswqa67","country_code":"TR","type":"education","lineage":["https://openalex.org/I74897591"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Abdul Majeed Issifu","raw_affiliation_strings":["Marmara University,Computer Engineering Department,Istanbul,Turkey","Computer Engineering Department, Marmara University, Istanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Marmara University,Computer Engineering Department,Istanbul,Turkey","institution_ids":["https://openalex.org/I74897591"]},{"raw_affiliation_string":"Computer Engineering Department, Marmara University, Istanbul, Turkey","institution_ids":["https://openalex.org/I74897591"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056971742","display_name":"Murat Can Ganiz","orcid":"https://orcid.org/0000-0001-8338-991X"},"institutions":[{"id":"https://openalex.org/I74897591","display_name":"Marmara University","ror":"https://ror.org/02kswqa67","country_code":"TR","type":"education","lineage":["https://openalex.org/I74897591"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Murat Can Ganiz","raw_affiliation_strings":["Marmara University,VeriUs Teknoloji,Computer Engineering Department,Istanbul,Turkey","Computer Engineering Department, VeriUs Teknoloji, Marmara University, Istanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Marmara University,VeriUs Teknoloji,Computer Engineering Department,Istanbul,Turkey","institution_ids":["https://openalex.org/I74897591"]},{"raw_affiliation_string":"Computer Engineering Department, VeriUs Teknoloji, Marmara University, Istanbul, Turkey","institution_ids":["https://openalex.org/I74897591"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I74897591"],"apc_list":null,"apc_paid":null,"fwci":1.3495,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.83472783,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9952999949455261,"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":0.98580002784729,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.8825384378433228},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8217841386795044},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6659935712814331},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6575852632522583},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.6127551198005676},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5713955163955688},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5200333595275879},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.5009171962738037},{"id":"https://openalex.org/keywords/entity-linking","display_name":"Entity linking","score":0.5006535053253174},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.49254998564720154},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.4860718548297882},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.47888273000717163},{"id":"https://openalex.org/keywords/f1-score","display_name":"F1 score","score":0.44933080673217773},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.32020196318626404},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.1937229037284851},{"id":"https://openalex.org/keywords/knowledge-base","display_name":"Knowledge base","score":0.11481896042823792}],"concepts":[{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.8825384378433228},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8217841386795044},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6659935712814331},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6575852632522583},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.6127551198005676},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5713955163955688},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5200333595275879},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.5009171962738037},{"id":"https://openalex.org/C96711827","wikidata":"https://www.wikidata.org/wiki/Q17012245","display_name":"Entity linking","level":3,"score":0.5006535053253174},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.49254998564720154},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.4860718548297882},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.47888273000717163},{"id":"https://openalex.org/C148524875","wikidata":"https://www.wikidata.org/wiki/Q6975395","display_name":"F1 score","level":2,"score":0.44933080673217773},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.32020196318626404},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.1937229037284851},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.11481896042823792},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"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/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/inista55318.2022.9894270","is_oa":false,"landing_page_url":"https://doi.org/10.1109/inista55318.2022.9894270","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 International Conference on INnovations in Intelligent SysTems and Applications (INISTA)","raw_type":"proceedings-article"},{"id":"pmh:oai:openaccess.marmara.edu.tr:11424/284181","is_oa":true,"landing_page_url":"https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85139596222&origin=inward","pdf_url":null,"source":{"id":"https://openalex.org/S7407055305","display_name":"Marmara University Open Access System","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"pmh:oai:openaccess.marmara.edu.tr:11424/284181","is_oa":true,"landing_page_url":"https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85139596222&origin=inward","pdf_url":null,"source":{"id":"https://openalex.org/S7407055305","display_name":"Marmara University Open Access System","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/conferenceObject"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.6600000262260437}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1934019294","https://openalex.org/W1940872118","https://openalex.org/W2047782770","https://openalex.org/W2071879021","https://openalex.org/W2103747062","https://openalex.org/W2114361266","https://openalex.org/W2147880316","https://openalex.org/W2154142897","https://openalex.org/W2160987310","https://openalex.org/W2169099542","https://openalex.org/W2293342966","https://openalex.org/W2296283641","https://openalex.org/W2346452181","https://openalex.org/W2588050043","https://openalex.org/W2600702321","https://openalex.org/W2621151902","https://openalex.org/W2624407581","https://openalex.org/W2757026815","https://openalex.org/W2757931374","https://openalex.org/W2769387903","https://openalex.org/W2802925146","https://openalex.org/W2806790568","https://openalex.org/W2857028992","https://openalex.org/W2896457183","https://openalex.org/W2911489562","https://openalex.org/W2919115771","https://openalex.org/W2944400536","https://openalex.org/W2952638691","https://openalex.org/W2964015378","https://openalex.org/W2970771982","https://openalex.org/W2997522493","https://openalex.org/W3011594683","https://openalex.org/W3090602117","https://openalex.org/W3142507075","https://openalex.org/W3166508187","https://openalex.org/W3166593409","https://openalex.org/W3168090480","https://openalex.org/W3206563239","https://openalex.org/W3212322867","https://openalex.org/W4200381505","https://openalex.org/W4299579390","https://openalex.org/W6640267182","https://openalex.org/W6640362995","https://openalex.org/W6675699994","https://openalex.org/W6682082992","https://openalex.org/W6726873649","https://openalex.org/W6744307560","https://openalex.org/W6744957266","https://openalex.org/W6751729766","https://openalex.org/W6752909555","https://openalex.org/W6755207826","https://openalex.org/W6792217397","https://openalex.org/W6796537594","https://openalex.org/W6803968652"],"related_works":["https://openalex.org/W2186562580","https://openalex.org/W4379379356","https://openalex.org/W3094868181","https://openalex.org/W4286980122","https://openalex.org/W2901060953","https://openalex.org/W4387606006","https://openalex.org/W2757016069","https://openalex.org/W2899463504","https://openalex.org/W2997394673","https://openalex.org/W3216421539"],"abstract_inverted_index":{"One":[0],"of":[1,4,100,102],"the":[2,30,34,84],"applications":[3],"Natural":[5],"Language":[6],"Processing":[7],"(NLP)":[8],"is":[9,41,129],"to":[10,122],"process":[11],"free":[12,35],"text":[13],"data":[14],"for":[15,28],"extracting":[16,43],"information.":[17],"Information":[18],"extraction":[19,39],"has":[20],"various":[21],"forms":[22],"like":[23,46,76,144],"Named":[24],"Entity":[25],"Recognition":[26],"(NER)":[27],"detecting":[29],"named":[31,44],"entities":[32,45],"in":[33,53,64,83],"text.":[36],"Biomedical":[37],"named-entity":[38],"task":[40],"about":[42],"drugs,":[47],"diseases,":[48],"organs,":[49],"etc.":[50],"from":[51],"texts":[52],"medical":[54],"domain.":[55],"In":[56],"our":[57],"study,":[58],"we":[59],"improve":[60],"commonly":[61],"used":[62],"models":[63,75,103,134],"this":[65],"domain,":[66],"such":[67,106,135],"as":[68,107,136],"biLSTM+CRF":[69,127],"model,":[70],"using":[71,97],"transformer":[72],"based":[73],"language":[74,133],"BERT":[77,137],"and":[78,104,111,138],"its":[79],"domain-specific":[80],"variant":[81],"BioBERT":[82,145],"embedding":[85],"layer.":[86],"We":[87],"conduct":[88],"several":[89,92,147],"experiments":[90],"on":[91,146],"different":[93],"benchmark":[94],"biomedical":[95],"datasets":[96],"a":[98,118],"variety":[99],"combination":[101],"embeddings":[105],"BioBERT+biLSTM+CRF,":[108],"BERT+biLSTM+CRF,":[109],"Fasttext+biLSTM+CRF,":[110],"Graph":[112],"Convolutional":[113],"Networks.":[114],"Our":[115],"results":[116],"show":[117],"quite":[119],"visible,":[120],"4%":[121],"13%,":[123],"improvements":[124],"when":[125],"baseline":[126],"model":[128],"initialized":[130],"with":[131,140],"pretrained":[132],"especially":[139],"domain":[141],"specific":[142],"one":[143],"datasets.":[148]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2022-09-24T00:00:00"}
