{"id":"https://openalex.org/W7117699139","doi":"https://doi.org/10.1145/3761712.3761763","title":"Comparing Large Language Models for Food-Microbiome Relation Extraction from Research Papers","display_name":"Comparing Large Language Models for Food-Microbiome Relation Extraction from Research Papers","publication_year":2025,"publication_date":"2025-05-16","ids":{"openalex":"https://openalex.org/W7117699139","doi":"https://doi.org/10.1145/3761712.3761763"},"language":null,"primary_location":{"id":"doi:10.1145/3761712.3761763","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3761712.3761763","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2025 9th International Conference on Medical and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1145/3761712.3761763","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040499657","display_name":"Research Dawadi","orcid":"https://orcid.org/0000-0002-3524-1459"},"institutions":[{"id":"https://openalex.org/I4210086383","display_name":"National Institute of Biomedical Innovation, Health and Nutrition","ror":"https://ror.org/001rkbe13","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210086383"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Research Dawadi","raw_affiliation_strings":["Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan"],"raw_orcid":"https://orcid.org/0000-0002-3524-1459","affiliations":[{"raw_affiliation_string":"Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan","institution_ids":["https://openalex.org/I4210086383"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121684987","display_name":"Jie Ting Tay","orcid":null},"institutions":[{"id":"https://openalex.org/I4210086383","display_name":"National Institute of Biomedical Innovation, Health and Nutrition","ror":"https://ror.org/001rkbe13","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210086383"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Jie Ting Tay","raw_affiliation_strings":["Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan"],"raw_orcid":"https://orcid.org/0009-0008-8385-8649","affiliations":[{"raw_affiliation_string":"Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan","institution_ids":["https://openalex.org/I4210086383"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121650488","display_name":"Agustin Martin-Morales","orcid":null},"institutions":[{"id":"https://openalex.org/I4210086383","display_name":"National Institute of Biomedical Innovation, Health and Nutrition","ror":"https://ror.org/001rkbe13","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210086383"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Agustin Martin-Morales","raw_affiliation_strings":["Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan"],"raw_orcid":"https://orcid.org/0000-0002-3564-4776","affiliations":[{"raw_affiliation_string":"Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan","institution_ids":["https://openalex.org/I4210086383"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Thien Vu","orcid":"https://orcid.org/0000-0002-6956-0191"},"institutions":[{"id":"https://openalex.org/I4210086383","display_name":"National Institute of Biomedical Innovation, Health and Nutrition","ror":"https://ror.org/001rkbe13","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210086383"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Thien Vu","raw_affiliation_strings":["Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan"],"raw_orcid":"https://orcid.org/0000-0002-6956-0191","affiliations":[{"raw_affiliation_string":"Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan","institution_ids":["https://openalex.org/I4210086383"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036111738","display_name":"Phap Tran Ngoc Hoang","orcid":"https://orcid.org/0000-0002-4314-8393"},"institutions":[{"id":"https://openalex.org/I4210086383","display_name":"National Institute of Biomedical Innovation, Health and Nutrition","ror":"https://ror.org/001rkbe13","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210086383"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Phap Tran Ngoc Hoang","raw_affiliation_strings":["Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan"],"raw_orcid":"https://orcid.org/0000-0002-4314-8393","affiliations":[{"raw_affiliation_string":"Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan","institution_ids":["https://openalex.org/I4210086383"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121688341","display_name":"Masaki Yamamoto","orcid":null},"institutions":[{"id":"https://openalex.org/I4210086383","display_name":"National Institute of Biomedical Innovation, Health and Nutrition","ror":"https://ror.org/001rkbe13","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210086383"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masaki Yamamoto","raw_affiliation_strings":["Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan"],"raw_orcid":"https://orcid.org/0000-0001-9179-6080","affiliations":[{"raw_affiliation_string":"Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan","institution_ids":["https://openalex.org/I4210086383"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Naoki Watanabe","orcid":"https://orcid.org/0009-0005-2703-0044"},"institutions":[{"id":"https://openalex.org/I4210086383","display_name":"National Institute of Biomedical Innovation, Health and Nutrition","ror":"https://ror.org/001rkbe13","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210086383"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Naoki Watanabe","raw_affiliation_strings":["Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan"],"raw_orcid":"https://orcid.org/0009-0005-2703-0044","affiliations":[{"raw_affiliation_string":"Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan","institution_ids":["https://openalex.org/I4210086383"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080028788","display_name":"Yuki Kuriya","orcid":"https://orcid.org/0000-0001-5118-7803"},"institutions":[{"id":"https://openalex.org/I4210086383","display_name":"National Institute of Biomedical Innovation, Health and Nutrition","ror":"https://ror.org/001rkbe13","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210086383"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuki Kuriya","raw_affiliation_strings":["Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan"],"raw_orcid":"https://orcid.org/0000-0001-5118-7803","affiliations":[{"raw_affiliation_string":"Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan","institution_ids":["https://openalex.org/I4210086383"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037239790","display_name":"Michihiro Araki","orcid":"https://orcid.org/0000-0002-6686-4018"},"institutions":[{"id":"https://openalex.org/I4210086383","display_name":"National Institute of Biomedical Innovation, Health and Nutrition","ror":"https://ror.org/001rkbe13","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210086383"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Michihiro Araki","raw_affiliation_strings":["Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan and Faculty of Medicine, Kyoto University, Kyoto, Japan"],"raw_orcid":"https://orcid.org/0000-0002-6686-4018","affiliations":[{"raw_affiliation_string":"Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan and Faculty of Medicine, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I4210086383"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.58546305,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"242","last_page":"247"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.6956999897956848,"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":0.6956999897956848,"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":0.07209999859333038,"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/T13984","display_name":"Nutrition, Genetics, and Disease","score":0.018699999898672104,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.6845999956130981},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.6708999872207642},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.6466000080108643},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4779999852180481},{"id":"https://openalex.org/keywords/section","display_name":"Section (typography)","score":0.4106999933719635},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.39399999380111694}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7361000180244446},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.6845999956130981},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.6708999872207642},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.6466000080108643},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5789999961853027},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.546500027179718},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4779999852180481},{"id":"https://openalex.org/C2780129039","wikidata":"https://www.wikidata.org/wiki/Q1931107","display_name":"Section (typography)","level":2,"score":0.4106999933719635},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.39399999380111694},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.3928000032901764},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3564999997615814},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3393000066280365},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.3041999936103821},{"id":"https://openalex.org/C44291984","wikidata":"https://www.wikidata.org/wiki/Q1074173","display_name":"Question answering","level":2,"score":0.28600001335144043},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.2825999855995178},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.2513999938964844}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3761712.3761763","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3761712.3761763","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2025 9th International Conference on Medical and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3761712.3761763","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3761712.3761763","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2025 9th International Conference on Medical and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger","score":0.4488281011581421}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W2067704478","https://openalex.org/W2097960255","https://openalex.org/W2911489562","https://openalex.org/W3163741274","https://openalex.org/W3173901112","https://openalex.org/W4382450509","https://openalex.org/W4384561707","https://openalex.org/W4385571451","https://openalex.org/W4388823522","https://openalex.org/W4390672119","https://openalex.org/W4393086569","https://openalex.org/W4398238904","https://openalex.org/W4399978597"],"related_works":[],"abstract_inverted_index":{"Relation":[0],"extraction,":[1],"in":[2,70],"biomedical":[3,15],"field,":[4],"can":[5,12,36],"lead":[6],"to":[7,53,84],"discovery":[8],"of":[9,24,61,67,72,95,111,130,139],"information":[10],"that":[11,120],"help":[13],"for":[14],"data":[16],"analysis,":[17],"and":[18,81,89,109,114,137],"drug":[19],"discoveries.":[20],"However,":[21],"an":[22,131],"understanding":[23],"the":[25,51,73,92,143],"semantic":[26],"relations":[27],"between":[28,87],"entities":[29,35],"is":[30],"required,":[31],"especially":[32],"since":[33],"these":[34],"be":[37],"diverse":[38],"such":[39,55],"as":[40,142],"foods,":[41],"diseases,":[42],"genes,":[43],"proteins,":[44],"or":[45],"drugs.":[46],"Large":[47],"language":[48,122],"models":[49],"possess":[50],"capabilities":[52],"extract":[54,85],"relationships":[56,86],"using":[57],"a":[58],"vast":[59],"amount":[60],"textual":[62],"data.":[63],"We":[64],"used":[65,76],"variety":[66],"instruction":[68,132],"prompts":[69],"three":[71],"most":[74,144],"commonly":[75],"LLMs:":[77],"ChatGPT,":[78],"Claude":[79,101],"AI":[80,102],"Google":[82],"Gemini,":[83],"food":[88],"microbiome":[90],"from":[91],"result":[93],"section":[94],"ten":[96],"research":[97],"papers.":[98],"On":[99],"average,":[100],"performed":[103],"better":[104],"with":[105,134],"higher":[106],"precision,":[107],"recall,":[108],"F1-scores":[110],"0.631,":[112],"0.519,":[113],"0.531":[115],"respectively.":[116],"Furthermore,":[117],"we":[118],"found":[119],"each":[121],"model":[123],"placed":[124],"high":[125],"importance":[126],"on":[127],"different":[128],"aspects":[129],"prompt,":[133],"sentiment,":[135],"readability,":[136],"number":[138],"words":[140],"emerging":[141],"important":[145],"ones.":[146]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-12-31T00:00:00"}
