{"id":"https://openalex.org/W4401940777","doi":"https://doi.org/10.1093/database/baae079","title":"Integrating deep learning architectures for enhanced biomedical relation extraction: a pipeline approach","display_name":"Integrating deep learning architectures for enhanced biomedical relation extraction: a pipeline approach","publication_year":2024,"publication_date":"2024-01-01","ids":{"openalex":"https://openalex.org/W4401940777","doi":"https://doi.org/10.1093/database/baae079","pmid":"https://pubmed.ncbi.nlm.nih.gov/39197056"},"language":"en","primary_location":{"id":"doi:10.1093/database/baae079","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baae079","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/database/baae079","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047546994","display_name":"M. Janina Sarol","orcid":"https://orcid.org/0000-0002-0991-4429"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"M Janina Sarol","raw_affiliation_strings":["Informatics Programs, University of Illinois Urbana-Champaign , 614 E Daniel Street, Champaign, IL 61820, United States"],"affiliations":[{"raw_affiliation_string":"Informatics Programs, University of Illinois Urbana-Champaign , 614 E Daniel Street, Champaign, IL 61820, United States","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058682631","display_name":"Gibong Hong","orcid":null},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gibong Hong","raw_affiliation_strings":["School of Information Sciences, University of Illinois Urbana-Champaign , 501 E Daniel Street, Champaign, IL 61820, United States"],"affiliations":[{"raw_affiliation_string":"School of Information Sciences, University of Illinois Urbana-Champaign , 501 E Daniel Street, Champaign, IL 61820, United States","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113352493","display_name":"Evan Guerra","orcid":null},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Evan Guerra","raw_affiliation_strings":["School of Information Sciences, University of Illinois Urbana-Champaign , 501 E Daniel Street, Champaign, IL 61820, United States"],"affiliations":[{"raw_affiliation_string":"School of Information Sciences, University of Illinois Urbana-Champaign , 501 E Daniel Street, Champaign, IL 61820, United States","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016571803","display_name":"Halil Kilicoglu","orcid":"https://orcid.org/0000-0003-3987-9393"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Halil Kilicoglu","raw_affiliation_strings":["School of Information Sciences, University of Illinois Urbana-Champaign , 501 E Daniel Street, Champaign, IL 61820, United States"],"affiliations":[{"raw_affiliation_string":"School of Information Sciences, University of Illinois Urbana-Champaign , 501 E Daniel Street, Champaign, IL 61820, United States","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5047546994"],"corresponding_institution_ids":["https://openalex.org/I157725225"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":1.1852,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.78370465,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"2024","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9969000220298767,"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":0.9765999913215637,"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":0.8785800933837891},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.7628389000892639},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7550427317619324},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.7175033092498779},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.7064438462257385},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6580675840377808},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6225173473358154},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5959597229957581},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.569089949131012},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5511606335639954},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.5132851600646973},{"id":"https://openalex.org/keywords/sentence","display_name":"Sentence","score":0.49478501081466675},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.4930069148540497},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4734741449356079},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4721914529800415},{"id":"https://openalex.org/keywords/novelty","display_name":"Novelty","score":0.4221005141735077},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2364855706691742},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.17959237098693848},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07964387536048889}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8785800933837891},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.7628389000892639},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7550427317619324},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7175033092498779},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.7064438462257385},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6580675840377808},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6225173473358154},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5959597229957581},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.569089949131012},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5511606335639954},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.5132851600646973},{"id":"https://openalex.org/C2777530160","wikidata":"https://www.wikidata.org/wiki/Q41796","display_name":"Sentence","level":2,"score":0.49478501081466675},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.4930069148540497},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4734741449356079},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4721914529800415},{"id":"https://openalex.org/C2778738651","wikidata":"https://www.wikidata.org/wiki/Q16546687","display_name":"Novelty","level":2,"score":0.4221005141735077},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2364855706691742},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.17959237098693848},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07964387536048889},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","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/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","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/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C27206212","wikidata":"https://www.wikidata.org/wiki/Q34178","display_name":"Theology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/baae079","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baae079","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:39197056","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39197056","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11352595","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11352595","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11352595/pdf/baae079.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baae079","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baae079","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7200000286102295,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332222","display_name":"University of Illinois at Urbana-Champaign","ror":"https://ror.org/047426m28"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":81,"referenced_works":["https://openalex.org/W90362830","https://openalex.org/W1489596328","https://openalex.org/W1610821757","https://openalex.org/W1832693441","https://openalex.org/W1964670939","https://openalex.org/W1994306321","https://openalex.org/W2024862171","https://openalex.org/W2032566933","https://openalex.org/W2052250375","https://openalex.org/W2071879021","https://openalex.org/W2100627415","https://openalex.org/W2122402213","https://openalex.org/W2122732537","https://openalex.org/W2126276057","https://openalex.org/W2142016317","https://openalex.org/W2142678031","https://openalex.org/W2145870108","https://openalex.org/W2154142897","https://openalex.org/W2158743996","https://openalex.org/W2159583324","https://openalex.org/W2169099542","https://openalex.org/W2170189740","https://openalex.org/W2252174377","https://openalex.org/W2335791510","https://openalex.org/W2346452181","https://openalex.org/W2414378847","https://openalex.org/W2743028754","https://openalex.org/W2753199411","https://openalex.org/W2763990719","https://openalex.org/W2805978167","https://openalex.org/W2911489562","https://openalex.org/W2916355958","https://openalex.org/W2946690328","https://openalex.org/W2949845972","https://openalex.org/W2962859618","https://openalex.org/W2984582583","https://openalex.org/W3026298482","https://openalex.org/W3028004046","https://openalex.org/W3034229721","https://openalex.org/W3046375318","https://openalex.org/W3137481621","https://openalex.org/W3164540570","https://openalex.org/W3167136668","https://openalex.org/W3212804087","https://openalex.org/W4200427693","https://openalex.org/W4221142212","https://openalex.org/W4221153690","https://openalex.org/W4224325974","https://openalex.org/W4226265641","https://openalex.org/W4283318325","https://openalex.org/W4288104771","https://openalex.org/W4293846201","https://openalex.org/W4297458751","https://openalex.org/W4307638650","https://openalex.org/W4311903220","https://openalex.org/W4376274483","https://openalex.org/W4378711639","https://openalex.org/W4381573137","https://openalex.org/W4385571451","https://openalex.org/W4385573954","https://openalex.org/W4387934104","https://openalex.org/W4393936594","https://openalex.org/W4401500773","https://openalex.org/W6603694148","https://openalex.org/W6629533874","https://openalex.org/W6638733343","https://openalex.org/W6658704000","https://openalex.org/W6704842505","https://openalex.org/W6739868092","https://openalex.org/W6761095016","https://openalex.org/W6763297974","https://openalex.org/W6767388388","https://openalex.org/W6768058859","https://openalex.org/W6776781563","https://openalex.org/W6784131931","https://openalex.org/W6784682006","https://openalex.org/W6809711173","https://openalex.org/W6852706297","https://openalex.org/W6853663800","https://openalex.org/W6871598338","https://openalex.org/W6911226964"],"related_works":["https://openalex.org/W2334378031","https://openalex.org/W2134429551","https://openalex.org/W2064314529","https://openalex.org/W842810586","https://openalex.org/W2916255597","https://openalex.org/W2548624545","https://openalex.org/W3095980030","https://openalex.org/W3004288456","https://openalex.org/W4379379356","https://openalex.org/W2572241437"],"abstract_inverted_index":{"Biomedical":[0],"relation":[1,57],"extraction":[2,58],"from":[3],"scientific":[4],"publications":[5],"is":[6],"a":[7,123,134,142],"key":[8],"task":[9,115,220],"in":[10,42],"biomedical":[11,56],"natural":[12],"language":[13],"processing":[14],"(NLP)":[15],"and":[16,30,60,69,91,116,149,151,165,176,200,202,210,231,241,248,266,276],"can":[17],"facilitate":[18],"the":[19,43,97,103,106,130,169,203,236,239,254,260],"creation":[20],"of":[21,78,105,238],"large":[22],"knowledge":[23,28],"bases,":[24],"enable":[25,263],"more":[26,264],"efficient":[27],"discovery,":[29],"accelerate":[31],"evidence":[32],"synthesis.":[33],"In":[34],"this":[35],"paper,":[36],"building":[37],"upon":[38],"our":[39,191,218,274],"previous":[40],"effort":[41],"BioCreative":[44],"VIII":[45],"BioRED":[46,98],"Track,":[47],"we":[48,121,140,167],"propose":[49],"an":[50,153],"enhanced":[51,209],"end-to-end":[52],"pipeline":[53,76,212],"approach":[54,205],"for":[55,113,119,147,158,197,206,269],"(RE)":[59],"novelty":[61],"detection":[62],"(ND)":[63],"that":[64,101,128],"effectively":[65],"leverages":[66],"existing":[67,154],"datasets":[68],"integrates":[70],"state-of-the-art":[71],"deep":[72],"learning":[73],"methods.":[74],"Our":[75,208],"consists":[77],"four":[79],"tasks":[80,250],"performed":[81,181],"sequentially:":[82],"named":[83],"entity":[84,87,161],"recognition":[85],"(NER),":[86],"linking":[88],"(EL),":[89],"RE,":[90,199],"ND.":[92],"We":[93,109,179,189,272],"trained":[94,141],"models":[95,196,243,268,275],"using":[96,194],"benchmark":[99],"corpus":[100],"was":[102],"basis":[104],"shared":[107,219],"task.":[108],"explored":[110],"several":[111],"methods":[112],"each":[114],"combinations":[117],"thereof:":[118],"NER,":[120,198],"compared":[122,216],"BERT-based":[124,195],"sequence":[125],"labeling":[126],"model":[127,146,173,187],"uses":[129],"BIO":[131],"scheme":[132],"with":[133],"span":[135],"classification":[136],"model.":[137],"For":[138,163],"EL,":[139],"convolutional":[143],"neural":[144],"network":[145],"diseases":[148],"chemicals":[150],"used":[152],"tool,":[155],"PubTator":[156],"3.0,":[157],"mapping":[159],"other":[160],"types.":[162],"RE":[164,247],"ND,":[166,201],"adapted":[168],"BERT-based,":[170],"sentence-bound":[171],"PURE":[172],"to":[174,185,217,259],"bidirectional":[175],"document-level":[177],"extraction.":[178],"also":[180],"extensive":[182],"hyperparameter":[183],"tuning":[184],"improve":[186],"performance.":[188],"obtained":[190],"best":[192],"performance":[193],"hybrid":[204],"EL.":[207],"optimized":[211],"showed":[213],"substantial":[214],"improvement":[215],"submission,":[221],"NER:":[222],"93.53":[223],"(+3.09),":[224],"EL:":[225],"83.87":[226],"(+9.73),":[227],"RE:":[228],"46.18":[229],"(+15.67),":[230],"ND:":[232],"38.86":[233],"(+14.9).":[234],"While":[235],"performances":[237],"NER":[240],"EL":[242],"are":[244],"reasonably":[245],"high,":[246],"ND":[249],"remain":[251],"challenging":[252],"at":[253,278],"document":[255],"level.":[256],"Further":[257],"enhancements":[258],"dataset":[261],"could":[262],"accurate":[265],"useful":[267],"practical":[270],"use.":[271],"provide":[273],"code":[277],"https://github.com/janinaj/e2eBioMedRE/.":[279,282],"Database":[280],"URL:":[281]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4}],"updated_date":"2026-03-24T08:02:53.985720","created_date":"2025-10-10T00:00:00"}
