{"id":"https://openalex.org/W4405576517","doi":"https://doi.org/10.1007/s44163-024-00197-2","title":"Large language models to process, analyze, and synthesize biomedical texts: a scoping review","display_name":"Large language models to process, analyze, and synthesize biomedical texts: a scoping review","publication_year":2024,"publication_date":"2024-12-19","ids":{"openalex":"https://openalex.org/W4405576517","doi":"https://doi.org/10.1007/s44163-024-00197-2"},"language":"en","primary_location":{"id":"doi:10.1007/s44163-024-00197-2","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s44163-024-00197-2","pdf_url":"https://link.springer.com/content/pdf/10.1007/s44163-024-00197-2.pdf","source":{"id":"https://openalex.org/S4210220416","display_name":"Discover Artificial Intelligence","issn_l":"2731-0809","issn":["2731-0809"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Nature"],"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":"Discover Artificial Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1007/s44163-024-00197-2.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5095887439","display_name":"Simona Emilova Doneva","orcid":"https://orcid.org/0009-0000-1603-7930"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Simona Emilova Doneva","raw_affiliation_strings":["Center for Reproducible Science, University of Zurich, Zurich, Switzerland","Division of Biostatistics, EBPI, University of Zurich, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Reproducible Science, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]},{"raw_affiliation_string":"Division of Biostatistics, EBPI, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Sijing Qin","orcid":null},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Sijing Qin","raw_affiliation_strings":["Center for Reproducible Science, University of Zurich, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Reproducible Science, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053625034","display_name":"Beate Sick","orcid":"https://orcid.org/0000-0002-7264-1515"},"institutions":[{"id":"https://openalex.org/I200744771","display_name":"ZHAW Zurich University of Applied Sciences","ror":null,"country_code":"CH","type":null,"lineage":["https://openalex.org/I200744771"]},{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Beate Sick","raw_affiliation_strings":["Division of Biostatistics, EBPI, University of Zurich, Zurich, Switzerland","ZHAW School of Engineering, Zurich University of Applied Science (ZHAW), Winterthur, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biostatistics, EBPI, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]},{"raw_affiliation_string":"ZHAW School of Engineering, Zurich University of Applied Science (ZHAW), Winterthur, Switzerland","institution_ids":["https://openalex.org/I200744771"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069674228","display_name":"Tilia Ellendorff","orcid":"https://orcid.org/0000-0002-8543-4902"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Tilia Ellendorff","raw_affiliation_strings":["Department of Computational Linguistics, University of Zurich, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Linguistics, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017949306","display_name":"Jean-Philippe Goldman","orcid":"https://orcid.org/0000-0003-4000-4199"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Jean-Philippe Goldman","raw_affiliation_strings":["Department of Computational Linguistics, University of Zurich, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Linguistics, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026936665","display_name":"Gerold Schneider","orcid":"https://orcid.org/0000-0002-1905-6237"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Gerold Schneider","raw_affiliation_strings":["Department of Computational Linguistics, University of Zurich, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Linguistics, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023522998","display_name":"Benjamin Victor Ineichen","orcid":"https://orcid.org/0000-0003-1362-4819"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Benjamin Victor Ineichen","raw_affiliation_strings":["Center for Reproducible Science, University of Zurich, Zurich, Switzerland","Clinical Neuroscience Center, University of Zurich, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Reproducible Science, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]},{"raw_affiliation_string":"Clinical Neuroscience Center, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5095887439"],"corresponding_institution_ids":["https://openalex.org/I202697423"],"apc_list":{"value":1340,"currency":"USD","value_usd":1340},"apc_paid":{"value":1340,"currency":"USD","value_usd":1340},"fwci":5.5893,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.96438112,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"4","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9990000128746033,"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":0.9990000128746033,"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":0.9966999888420105,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.9945999979972839,"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":0.6114417910575867},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5819361209869385},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.36537396907806396},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3568190932273865},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16014015674591064}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6114417910575867},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5819361209869385},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.36537396907806396},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3568190932273865},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16014015674591064}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1007/s44163-024-00197-2","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s44163-024-00197-2","pdf_url":"https://link.springer.com/content/pdf/10.1007/s44163-024-00197-2.pdf","source":{"id":"https://openalex.org/S4210220416","display_name":"Discover Artificial Intelligence","issn_l":"2731-0809","issn":["2731-0809"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Nature"],"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":"Discover Artificial Intelligence","raw_type":"journal-article"},{"id":"pmh:oai:digitalcollection.zhaw.ch:11475/36882","is_oa":true,"landing_page_url":"https://hdl.handle.net/11475/36882","pdf_url":null,"source":{"id":"https://openalex.org/S4306401811","display_name":"Z\u00fcrcher Hochschule f\u00fcr Angewandte Wissenschaften digital collection (Zurich University of Applied Sciences)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I200744771","host_organization_name":"ZHAW Zurich University of Applied Sciences","host_organization_lineage":["https://openalex.org/I200744771"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:32848932dc964fe88300eda4cac1ed05","is_oa":false,"landing_page_url":"https://doaj.org/article/32848932dc964fe88300eda4cac1ed05","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Discover Artificial Intelligence, Vol 4, Iss 1, Pp 1-21 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1007/s44163-024-00197-2","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s44163-024-00197-2","pdf_url":"https://link.springer.com/content/pdf/10.1007/s44163-024-00197-2.pdf","source":{"id":"https://openalex.org/S4210220416","display_name":"Discover Artificial Intelligence","issn_l":"2731-0809","issn":["2731-0809"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Nature"],"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":"Discover Artificial Intelligence","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.7300000190734863,"id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G3904419009","display_name":"ANIMONE: An in vivo data warehouse for neuroscience - biocuration of preclinical research to inform optimization and exploitation of preclinical studies","funder_award_id":"206504","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G5011856635","display_name":null,"funder_award_id":"407940-206504","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320323874","display_name":"Universit\u00e4t Z\u00fcrich","ror":"https://ror.org/02crff812"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4405576517.pdf","grobid_xml":"https://content.openalex.org/works/W4405576517.grobid-xml"},"referenced_works_count":107,"referenced_works":["https://openalex.org/W2052217781","https://openalex.org/W2071879021","https://openalex.org/W2075322787","https://openalex.org/W2100627415","https://openalex.org/W2145870108","https://openalex.org/W2154142897","https://openalex.org/W2168041406","https://openalex.org/W2169099542","https://openalex.org/W2170189740","https://openalex.org/W2286261512","https://openalex.org/W2346452181","https://openalex.org/W2396881363","https://openalex.org/W2502073295","https://openalex.org/W2780532712","https://openalex.org/W2911489562","https://openalex.org/W2970224261","https://openalex.org/W2970283086","https://openalex.org/W2970771982","https://openalex.org/W2971258845","https://openalex.org/W2989227969","https://openalex.org/W2991479131","https://openalex.org/W2997204042","https://openalex.org/W3013183258","https://openalex.org/W3092726880","https://openalex.org/W3093419084","https://openalex.org/W3094588489","https://openalex.org/W3097301690","https://openalex.org/W3100209521","https://openalex.org/W3104080943","https://openalex.org/W3105313172","https://openalex.org/W3105623222","https://openalex.org/W3106263887","https://openalex.org/W3109234882","https://openalex.org/W3109919947","https://openalex.org/W3111278950","https://openalex.org/W3141847762","https://openalex.org/W3165248111","https://openalex.org/W3175873000","https://openalex.org/W3176273155","https://openalex.org/W3179963059","https://openalex.org/W3195865364","https://openalex.org/W3208587672","https://openalex.org/W3211384762","https://openalex.org/W4200057797","https://openalex.org/W4205621476","https://openalex.org/W4206727248","https://openalex.org/W4213304257","https://openalex.org/W4220967417","https://openalex.org/W4225269900","https://openalex.org/W4225275379","https://openalex.org/W4226102430","https://openalex.org/W4285229780","https://openalex.org/W4285744810","https://openalex.org/W4290094205","https://openalex.org/W4294878359","https://openalex.org/W4295951577","https://openalex.org/W4297253404","https://openalex.org/W4309728330","https://openalex.org/W4310238942","https://openalex.org/W4311040600","https://openalex.org/W4311587210","https://openalex.org/W4313523866","https://openalex.org/W4318694082","https://openalex.org/W4319350602","https://openalex.org/W4327946446","https://openalex.org/W4365143687","https://openalex.org/W4366824871","https://openalex.org/W4377136936","https://openalex.org/W4381587418","https://openalex.org/W4384261711","https://openalex.org/W4384561707","https://openalex.org/W4384819947","https://openalex.org/W4385227045","https://openalex.org/W4385343507","https://openalex.org/W4385456320","https://openalex.org/W4385570692","https://openalex.org/W4385571033","https://openalex.org/W4385571301","https://openalex.org/W4385571823","https://openalex.org/W4385572029","https://openalex.org/W4385572374","https://openalex.org/W4385573513","https://openalex.org/W4385573931","https://openalex.org/W4385573954","https://openalex.org/W4386120650","https://openalex.org/W4386530347","https://openalex.org/W4387090000","https://openalex.org/W4388140134","https://openalex.org/W4388464636","https://openalex.org/W4388977526","https://openalex.org/W4389001184","https://openalex.org/W4389520458","https://openalex.org/W4389524123","https://openalex.org/W4390239756","https://openalex.org/W4391940656","https://openalex.org/W4392044798","https://openalex.org/W4392643126","https://openalex.org/W4392791588","https://openalex.org/W4394009157","https://openalex.org/W4394911776","https://openalex.org/W4395703766","https://openalex.org/W6600648412","https://openalex.org/W6607733003","https://openalex.org/W6675775337","https://openalex.org/W6679436768","https://openalex.org/W6702248584","https://openalex.org/W6778883912"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"The":[0],"advent":[1],"of":[2,18,44,51,64,68,83,90,122,152,188,207],"large":[3],"language":[4],"models":[5,183,190],"(LLMs)":[6],"such":[7,221],"as":[8,222],"BERT":[9],"and,":[10],"more":[11],"recently,":[12],"GPT,":[13],"is":[14,35],"transforming":[15],"our":[16,142],"approach":[17],"analyzing":[19],"and":[20,72,93,98,138,165,177,218,226],"understanding":[21],"biomedical":[22,52,69,156,208],"texts.":[23,53],"To":[24],"stay":[25],"informed":[26],"about":[27],"the":[28,42,65,80,120,155,186,204],"latest":[29],"advancements":[30],"in":[31,46,116,124,154,215],"this":[32,55],"area,":[33],"there":[34],"a":[36,61,76,87,128,149],"need":[37],"for":[38,96,113,141],"up-to-date":[39],"summaries":[40],"on":[41,79],"role":[43,82],"LLM":[45],"Natural":[47],"Language":[48],"Processing":[49],"(NLP)":[50],"Thus,":[54],"scoping":[56],"review":[57],"aims":[58],"to":[59,104,148,202],"provide":[60],"detailed":[62],"overview":[63],"current":[66],"state":[67],"NLP":[70,114],"research":[71],"its":[73],"applications,":[74],"with":[75,224],"special":[77],"focus":[78],"evolving":[81],"LLMs.":[84],"We":[85,118,196],"conducted":[86],"systematic":[88],"search":[89],"PubMed,":[91],"EMBASE,":[92],"Google":[94],"Scholar":[95],"studies":[97,126],"conference":[99,139],"proceedings":[100,140],"published":[101],"from":[102],"2017":[103],"December":[105],"19,":[106],"2023,":[107],"that":[108],"develop":[109],"or":[110],"utilize":[111],"LLMs":[112,144,210],"tasks":[115,153,171],"biomedicine.":[117],"evaluated":[119],"risk":[121],"bias":[123],"these":[125,170],"using":[127],"3-item":[129],"checklist.":[130],"From":[131],"13,823":[132],"references,":[133],"we":[134],"selected":[135],"199":[136],"publications":[137],"review.":[143],"are":[145,172],"being":[146],"applied":[147],"wide":[150],"array":[151],"field,":[157],"including":[158],"knowledge":[159],"management,":[160],"text":[161,173],"mining,":[162],"drug":[163],"discovery,":[164],"evidence":[166,219],"synthesis.":[167],"Prominent":[168],"among":[169],"classification,":[174],"relation":[175],"extraction,":[176],"named":[178],"entity":[179],"recognition.":[180],"Although":[181],"BERT-based":[182],"remain":[184],"prevalent,":[185],"use":[187],"GPT-based":[189],"has":[191],"substantially":[192],"increased":[193],"since":[194],"2023.":[195],"conclude":[197],"that,":[198],"despite":[199],"offering":[200],"opportunities":[201],"manage":[203],"growing":[205],"volume":[206],"data,":[209],"also":[211],"present":[212],"challenges,":[213],"particularly":[214],"clinical":[216],"medicine":[217],"synthesis,":[220],"issues":[223],"transparency":[225],"privacy":[227],"concerns.":[228]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":13}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
