{"id":"https://openalex.org/W4415974910","doi":"https://doi.org/10.1016/j.procs.2025.09.178","title":"Benchmarking Large Language Models for Biomedical Relation Extraction","display_name":"Benchmarking Large Language Models for Biomedical Relation Extraction","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4415974910","doi":"https://doi.org/10.1016/j.procs.2025.09.178"},"language":"en","primary_location":{"id":"doi:10.1016/j.procs.2025.09.178","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.procs.2025.09.178","pdf_url":null,"source":{"id":"https://openalex.org/S120348307","display_name":"Procedia Computer Science","issn_l":"1877-0509","issn":["1877-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Procedia Computer Science","raw_type":"journal-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://doi.org/10.1016/j.procs.2025.09.178","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5114853645","display_name":"Claudiu Creang\u0103","orcid":null},"institutions":[{"id":"https://openalex.org/I4210146697","display_name":"Herrick Technology Laboratories (United States)","ror":"https://ror.org/04ganmj42","country_code":"US","type":"company","lineage":["https://openalex.org/I4210146697"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Claudiu Creang\u0103","raw_affiliation_strings":["HLT Research Center","Interdisciplinary School of Doctoral Studies"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HLT Research Center","institution_ids":["https://openalex.org/I4210146697"]},{"raw_affiliation_string":"Interdisciplinary School of Doctoral Studies","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5120285580","display_name":"Teodor Marchitan","orcid":null},"institutions":[{"id":"https://openalex.org/I141595442","display_name":"University of Bucharest","ror":"https://ror.org/02x2v6p15","country_code":"RO","type":"education","lineage":["https://openalex.org/I141595442"]},{"id":"https://openalex.org/I4210146697","display_name":"Herrick Technology Laboratories (United States)","ror":"https://ror.org/04ganmj42","country_code":"US","type":"company","lineage":["https://openalex.org/I4210146697"]}],"countries":["RO","US"],"is_corresponding":false,"raw_author_name":"Teodor Marchitan","raw_affiliation_strings":["Faculty of Mathematics and Computer Science, University of Bucharest, Romania","HLT Research Center"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Computer Science, University of Bucharest, Romania","institution_ids":["https://openalex.org/I141595442"]},{"raw_affiliation_string":"HLT Research Center","institution_ids":["https://openalex.org/I4210146697"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057738797","display_name":"Liviu P. Dinu","orcid":"https://orcid.org/0000-0002-7559-6756"},"institutions":[{"id":"https://openalex.org/I141595442","display_name":"University of Bucharest","ror":"https://ror.org/02x2v6p15","country_code":"RO","type":"education","lineage":["https://openalex.org/I141595442"]},{"id":"https://openalex.org/I4210146697","display_name":"Herrick Technology Laboratories (United States)","ror":"https://ror.org/04ganmj42","country_code":"US","type":"company","lineage":["https://openalex.org/I4210146697"]}],"countries":["RO","US"],"is_corresponding":false,"raw_author_name":"Liviu P. Dinu","raw_affiliation_strings":["Faculty of Mathematics and Computer Science, University of Bucharest, Romania","HLT Research Center"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Computer Science, University of Bucharest, Romania","institution_ids":["https://openalex.org/I141595442"]},{"raw_affiliation_string":"HLT Research Center","institution_ids":["https://openalex.org/I4210146697"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5114853645"],"corresponding_institution_ids":["https://openalex.org/I4210146697"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.26060491,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"270","issue":null,"first_page":"592","last_page":"601"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9243000149726868,"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":0.9243000149726868,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.03370000049471855,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.014600000344216824,"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/benchmarking","display_name":"Benchmarking","score":0.9013000130653381},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.6488999724388123},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.6244000196456909},{"id":"https://openalex.org/keywords/association","display_name":"Association (psychology)","score":0.5166000127792358},{"id":"https://openalex.org/keywords/expressive-power","display_name":"Expressive power","score":0.39899998903274536},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.37549999356269836}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.9013000130653381},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.824999988079071},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.6488999724388123},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.6244000196456909},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6107000112533569},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5543000102043152},{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.5166000127792358},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.478300005197525},{"id":"https://openalex.org/C195818886","wikidata":"https://www.wikidata.org/wiki/Q5421724","display_name":"Expressive power","level":2,"score":0.39899998903274536},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.37549999356269836},{"id":"https://openalex.org/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.3725999891757965},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.3555999994277954},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.3443000018596649},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.32190001010894775},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.3005000054836273},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.2890999913215637},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.28360000252723694}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1016/j.procs.2025.09.178","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.procs.2025.09.178","pdf_url":null,"source":{"id":"https://openalex.org/S120348307","display_name":"Procedia Computer Science","issn_l":"1877-0509","issn":["1877-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Procedia Computer Science","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1016/j.procs.2025.09.178","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.procs.2025.09.178","pdf_url":null,"source":{"id":"https://openalex.org/S120348307","display_name":"Procedia Computer Science","issn_l":"1877-0509","issn":["1877-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Procedia Computer Science","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320324335","display_name":"Universitatea din Bucure\u0219ti","ror":"https://ror.org/02x2v6p15"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":8,"referenced_works":["https://openalex.org/W2139644711","https://openalex.org/W2604990811","https://openalex.org/W2963625095","https://openalex.org/W3035390927","https://openalex.org/W4365150760","https://openalex.org/W4389041116","https://openalex.org/W4404801570","https://openalex.org/W4412886823"],"related_works":[],"abstract_inverted_index":{"Extracting":[0],"SNP-phenotype":[1],"associations":[2],"from":[3],"biomedical":[4],"literature":[5],"is":[6],"vital":[7],"but":[8],"challenging.":[9],"We":[10],"benchmarked":[11],"diverse":[12],"NLP":[13],"models,":[14],"including":[15],"MLMs,":[16],"hybrid":[17],"architectures,":[18],"and":[19,37,56],"state-of-the-art":[20,44],"LLMs":[21,111],"(Gemini":[22,96],"2.0,":[23],"OpenAI":[24,41],"O-series,":[25],"Qwen,":[26],"Mistral),":[27],"on":[28],"the":[29,81,107],"SNPPhenA":[30],"corpus":[31],"across":[32],"three":[33],"tasks:":[34],"sentence-level,":[35],"abstract-level,":[36],"association":[38],"strength":[39,67],"classification.":[40],"O1":[42],"achieved":[43],"(SOTA)":[45],"results":[46],"using":[47],"few-shot":[48,92],"learning":[49],"for":[50,61,112],"non-finetuned":[51],"sentence-level":[52],"classification":[53,63,68],"(F1":[54,64,78],"0.89)":[55],"established":[57],"a":[58],"new":[59],"SOTA":[60],"abstract-level":[62],"0.82).":[65],"Association":[66],"proved":[69],"difficult,":[70],"though":[71],"fine-tuned":[72,95],"Gemini":[73],"2.0":[74,97],"Pro":[75],"performed":[76],"best":[77],"0.60)":[79],"in":[80,91],"first":[82],"LLM":[83],"evaluation":[84],"of":[85,109],"this":[86],"task.":[87],"Proprietary":[88],"LLMs,":[89],"especially":[90],"(O1)":[93],"or":[94],"Pro)":[98],"settings,":[99],"significantly":[100],"outperformed":[101],"other":[102],"models.":[103],"These":[104],"findings":[105],"confrm":[106],"power":[108],"modern":[110],"genomic":[113],"knowledge":[114],"extraction.":[115]},"counts_by_year":[],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-11-06T00:00:00"}
