{"id":"https://openalex.org/W4385456320","doi":"https://doi.org/10.1145/3611651","title":"Pre-trained Language Models in Biomedical Domain: A Systematic Survey","display_name":"Pre-trained Language Models in Biomedical Domain: A Systematic Survey","publication_year":2023,"publication_date":"2023-08-01","ids":{"openalex":"https://openalex.org/W4385456320","doi":"https://doi.org/10.1145/3611651"},"language":"en","primary_location":{"id":"doi:10.1145/3611651","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3611651","pdf_url":null,"source":{"id":"https://openalex.org/S157921468","display_name":"ACM Computing Surveys","issn_l":"0360-0300","issn":["0360-0300","1557-7341"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Computing Surveys","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057282504","display_name":"Benyou Wang","orcid":"https://orcid.org/0000-0002-1501-9914"},"institutions":[{"id":"https://openalex.org/I4210099586","display_name":"Shenzhen Research Institute of Big Data","ror":"https://ror.org/00z1gwf89","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210099586"]},{"id":"https://openalex.org/I4210116924","display_name":"Chinese University of Hong Kong, Shenzhen","ror":"https://ror.org/02d5ks197","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633","https://openalex.org/I180726961","https://openalex.org/I4210116924"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Benyou Wang","raw_affiliation_strings":["SRIBD &amp; SDS, The Chinese University of Hong Kong, Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0002-1501-9914","affiliations":[{"raw_affiliation_string":"SRIBD &amp; SDS, The Chinese University of Hong Kong, Shenzhen, China","institution_ids":["https://openalex.org/I4210099586","https://openalex.org/I4210116924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101868563","display_name":"Qianqian Xie","orcid":"https://orcid.org/0000-0002-9588-7454"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Qianqian Xie","raw_affiliation_strings":["Department of Computer Science, University of Manchester, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-9588-7454","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Manchester, United Kingdom","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061075100","display_name":"Jiahuan Pei","orcid":"https://orcid.org/0000-0001-6951-8340"},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Jiahuan Pei","raw_affiliation_strings":["University of Amsterdam, Netherlands"],"raw_orcid":"https://orcid.org/0000-0001-6951-8340","affiliations":[{"raw_affiliation_string":"University of Amsterdam, Netherlands","institution_ids":["https://openalex.org/I887064364"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100430139","display_name":"Zhihong Chen","orcid":"https://orcid.org/0000-0003-4064-7987"},"institutions":[{"id":"https://openalex.org/I4210099586","display_name":"Shenzhen Research Institute of Big Data","ror":"https://ror.org/00z1gwf89","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210099586"]},{"id":"https://openalex.org/I4210116924","display_name":"Chinese University of Hong Kong, Shenzhen","ror":"https://ror.org/02d5ks197","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633","https://openalex.org/I180726961","https://openalex.org/I4210116924"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhihong Chen","raw_affiliation_strings":["SRIBD &amp; SSE, The Chinese University of Hong Kong, Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0003-4064-7987","affiliations":[{"raw_affiliation_string":"SRIBD &amp; SSE, The Chinese University of Hong Kong, Shenzhen, China","institution_ids":["https://openalex.org/I4210099586","https://openalex.org/I4210116924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082046789","display_name":"Prayag Tiwari","orcid":"https://orcid.org/0000-0002-2851-4260"},"institutions":[{"id":"https://openalex.org/I746986","display_name":"Halmstad University","ror":"https://ror.org/03h0qfp10","country_code":"SE","type":"education","lineage":["https://openalex.org/I746986"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Prayag Tiwari","raw_affiliation_strings":["School of Information Technology, Halmstad University, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-2851-4260","affiliations":[{"raw_affiliation_string":"School of Information Technology, Halmstad University, Sweden","institution_ids":["https://openalex.org/I746986"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100730695","display_name":"Zhao Li","orcid":"https://orcid.org/0000-0002-6154-9879"},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhao Li","raw_affiliation_strings":["The University of Texas Health Science Center at Houston, USA"],"raw_orcid":"https://orcid.org/0000-0002-6154-9879","affiliations":[{"raw_affiliation_string":"The University of Texas Health Science Center at Houston, USA","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101713885","display_name":"Jie Fu","orcid":"https://orcid.org/0000-0002-4494-843X"},"institutions":[{"id":"https://openalex.org/I4210164802","display_name":"Mila - Quebec Artificial Intelligence Institute","ror":"https://ror.org/05c22rx21","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210164802"]},{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jie Fu","raw_affiliation_strings":["Mila, University of Montreal, Canada"],"raw_orcid":"https://orcid.org/0000-0002-4494-843X","affiliations":[{"raw_affiliation_string":"Mila, University of Montreal, Canada","institution_ids":["https://openalex.org/I4210164802","https://openalex.org/I70931966"]}]}],"institutions":[],"countries_distinct_count":6,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":21.4908,"has_fulltext":false,"cited_by_count":167,"citation_normalized_percentile":{"value":0.99649415,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"56","issue":"3","first_page":"1","last_page":"52"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9986000061035156,"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":0.9986000061035156,"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/T11636","display_name":"Artificial Intelligence in Healthcare and Education","score":0.9847000241279602,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9793000221252441,"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/computer-science","display_name":"Computer science","score":0.7968034148216248},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.7337824106216431},{"id":"https://openalex.org/keywords/terminology","display_name":"Terminology","score":0.6826774477958679},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5841889381408691},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5385623574256897},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4442167580127716},{"id":"https://openalex.org/keywords/taxonomy","display_name":"Taxonomy (biology)","score":0.42608022689819336},{"id":"https://openalex.org/keywords/health-informatics","display_name":"Health informatics","score":0.41990649700164795},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.2750048041343689},{"id":"https://openalex.org/keywords/health-care","display_name":"Health care","score":0.1651679277420044},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.114564448595047}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7968034148216248},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.7337824106216431},{"id":"https://openalex.org/C547195049","wikidata":"https://www.wikidata.org/wiki/Q1725664","display_name":"Terminology","level":2,"score":0.6826774477958679},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5841889381408691},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5385623574256897},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4442167580127716},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.42608022689819336},{"id":"https://openalex.org/C145642194","wikidata":"https://www.wikidata.org/wiki/Q870895","display_name":"Health informatics","level":3,"score":0.41990649700164795},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.2750048041343689},{"id":"https://openalex.org/C160735492","wikidata":"https://www.wikidata.org/wiki/Q31207","display_name":"Health care","level":2,"score":0.1651679277420044},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.114564448595047},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C50522688","wikidata":"https://www.wikidata.org/wiki/Q189833","display_name":"Economic growth","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","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}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3611651","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3611651","pdf_url":null,"source":{"id":"https://openalex.org/S157921468","display_name":"ACM Computing Surveys","issn_l":"0360-0300","issn":["0360-0300","1557-7341"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Computing Surveys","raw_type":"journal-article"},{"id":"pmh:oai:dare.uva.nl:publications/95a59436-65b1-4f7b-b301-1f3accd53140","is_oa":false,"landing_page_url":"https://handle.uba.uva.nl/personal/pure/en/publications/pretrained-language-models-in-biomedical-domain(95a59436-65b1-4f7b-b301-1f3accd53140).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400088","display_name":"UvA-DARE (University of Amsterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887064364","host_organization_name":"University of Amsterdam","host_organization_lineage":["https://openalex.org/I887064364"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Wang, B, Xie, Q, Pei, J, Chen, Z, Tiwari, P, Li, Z & Fu, J 2023, 'Pre-trained Language Models in Biomedical Domain : A Systematic Survey', ACM Computing Surveys, vol. 56, no. 3, 55. https://doi.org/10.1145/3611651","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Quality Education","score":0.7400000095367432,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322942","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":284,"referenced_works":["https://openalex.org/W139989439","https://openalex.org/W580573057","https://openalex.org/W1614298861","https://openalex.org/W1679133234","https://openalex.org/W1975975525","https://openalex.org/W2012639032","https://openalex.org/W2017285544","https://openalex.org/W2034269086","https://openalex.org/W2036448803","https://openalex.org/W2045777307","https://openalex.org/W2064675550","https://openalex.org/W2076581021","https://openalex.org/W2099201756","https://openalex.org/W2101727078","https://openalex.org/W2112796928","https://openalex.org/W2119852447","https://openalex.org/W2136437513","https://openalex.org/W2152772232","https://openalex.org/W2153579005","https://openalex.org/W2154142897","https://openalex.org/W2159583324","https://openalex.org/W2162233306","https://openalex.org/W2168041406","https://openalex.org/W2168905447","https://openalex.org/W2169099542","https://openalex.org/W2170189740","https://openalex.org/W2171283231","https://openalex.org/W2293419569","https://openalex.org/W2346452181","https://openalex.org/W2396881363","https://openalex.org/W2594685110","https://openalex.org/W2600463316","https://openalex.org/W2618530766","https://openalex.org/W2735784619","https://openalex.org/W2738347542","https://openalex.org/W2741179140","https://openalex.org/W2749701213","https://openalex.org/W2768488789","https://openalex.org/W2799054028","https://openalex.org/W2896457183","https://openalex.org/W2897980926","https://openalex.org/W2899663614","https://openalex.org/W2901770990","https://openalex.org/W2909727437","https://openalex.org/W2911489562","https://openalex.org/W2912213068","https://openalex.org/W2922674004","https://openalex.org/W2923014074","https://openalex.org/W2937766897","https://openalex.org/W2947037928","https://openalex.org/W2950888501","https://openalex.org/W2951433247","https://openalex.org/W2955018588","https://openalex.org/W2955483668","https://openalex.org/W2962707339","https://openalex.org/W2962787423","https://openalex.org/W2963716420","https://openalex.org/W2963748441","https://openalex.org/W2965373594","https://openalex.org/W2965570621","https://openalex.org/W2968124245","https://openalex.org/W2970395847","https://openalex.org/W2970601365","https://openalex.org/W2970771982","https://openalex.org/W2970986790","https://openalex.org/W2971258845","https://openalex.org/W2971769670","https://openalex.org/W2972118438","https://openalex.org/W2972483465","https://openalex.org/W2973767881","https://openalex.org/W2975059944","https://openalex.org/W2979250794","https://openalex.org/W2979826702","https://openalex.org/W2980708516","https://openalex.org/W2982399380","https://openalex.org/W2982424689","https://openalex.org/W2989472987","https://openalex.org/W2993873509","https://openalex.org/W2995225687","https://openalex.org/W2995514860","https://openalex.org/W2995971510","https://openalex.org/W2996428491","https://openalex.org/W2997204042","https://openalex.org/W2997419538","https://openalex.org/W2997712488","https://openalex.org/W2998704965","https://openalex.org/W3000238064","https://openalex.org/W3002832564","https://openalex.org/W3008088841","https://openalex.org/W3008110149","https://openalex.org/W3011574394","https://openalex.org/W3014611590","https://openalex.org/W3015347994","https://openalex.org/W3015468748","https://openalex.org/W3016996576","https://openalex.org/W3017637887","https://openalex.org/W3020931369","https://openalex.org/W3021524072","https://openalex.org/W3021654819","https://openalex.org/W3022717752","https://openalex.org/W3023360076","https://openalex.org/W3024922541","https://openalex.org/W3030163527","https://openalex.org/W3032388710","https://openalex.org/W3033544963","https://openalex.org/W3034199299","https://openalex.org/W3034238904","https://openalex.org/W3035060554","https://openalex.org/W3036290069","https://openalex.org/W3036559261","https://openalex.org/W3037016244","https://openalex.org/W3037310559","https://openalex.org/W3037888463","https://openalex.org/W3038495045","https://openalex.org/W3041263301","https://openalex.org/W3041304706","https://openalex.org/W3045332379","https://openalex.org/W3046375318","https://openalex.org/W3080321165","https://openalex.org/W3080464152","https://openalex.org/W3081505754","https://openalex.org/W3082457427","https://openalex.org/W3083978629","https://openalex.org/W3086353339","https://openalex.org/W3087623576","https://openalex.org/W3089168780","https://openalex.org/W3089314434","https://openalex.org/W3090449556","https://openalex.org/W3091382176","https://openalex.org/W3091546937","https://openalex.org/W3091857764","https://openalex.org/W3092142868","https://openalex.org/W3092665896","https://openalex.org/W3092733346","https://openalex.org/W3093553144","https://openalex.org/W3093814160","https://openalex.org/W3095092693","https://openalex.org/W3095609828","https://openalex.org/W3095642204","https://openalex.org/W3096403953","https://openalex.org/W3098576111","https://openalex.org/W3098605233","https://openalex.org/W3099750501","https://openalex.org/W3100452049","https://openalex.org/W3101058639","https://openalex.org/W3102999298","https://openalex.org/W3103368673","https://openalex.org/W3104330316","https://openalex.org/W3105966348","https://openalex.org/W3106298421","https://openalex.org/W3108423942","https://openalex.org/W3110414860","https://openalex.org/W3114423350","https://openalex.org/W3120094169","https://openalex.org/W3126974869","https://openalex.org/W3129160532","https://openalex.org/W3132259035","https://openalex.org/W3133650345","https://openalex.org/W3134678353","https://openalex.org/W3135158964","https://openalex.org/W3135367836","https://openalex.org/W3135593154","https://openalex.org/W3136657289","https://openalex.org/W3138819813","https://openalex.org/W3146944767","https://openalex.org/W3149407292","https://openalex.org/W3155220426","https://openalex.org/W3155731460","https://openalex.org/W3155819677","https://openalex.org/W3156000544","https://openalex.org/W3157252883","https://openalex.org/W3157876196","https://openalex.org/W3164654615","https://openalex.org/W3164972323","https://openalex.org/W3165345393","https://openalex.org/W3166396011","https://openalex.org/W3167227435","https://openalex.org/W3169066049","https://openalex.org/W3171832821","https://openalex.org/W3172099915","https://openalex.org/W3176456866","https://openalex.org/W3177828909","https://openalex.org/W3179640609","https://openalex.org/W3180397538","https://openalex.org/W3181414820","https://openalex.org/W3185093489","https://openalex.org/W3185341429","https://openalex.org/W3188437627","https://openalex.org/W3191896067","https://openalex.org/W3193589100","https://openalex.org/W3198701654","https://openalex.org/W3199799076","https://openalex.org/W3201023666","https://openalex.org/W3202738183","https://openalex.org/W3205462295","https://openalex.org/W3210120707","https://openalex.org/W4205773061","https://openalex.org/W4212774754","https://openalex.org/W4221143384","https://openalex.org/W4223492536","https://openalex.org/W4224035735","https://openalex.org/W4224233724","https://openalex.org/W4224308101","https://openalex.org/W4225917625","https://openalex.org/W4226376045","https://openalex.org/W4233069070","https://openalex.org/W4280554020","https://openalex.org/W4281485151","https://openalex.org/W4283755958","https://openalex.org/W4285291921","https://openalex.org/W4285807172","https://openalex.org/W4286233477","https://openalex.org/W4287017694","https://openalex.org/W4287083393","https://openalex.org/W4287119853","https://openalex.org/W4287209349","https://openalex.org/W4287210290","https://openalex.org/W4287278290","https://openalex.org/W4287366208","https://openalex.org/W4287636191","https://openalex.org/W4287642220","https://openalex.org/W4287645014","https://openalex.org/W4287667694","https://openalex.org/W4287704328","https://openalex.org/W4287704453","https://openalex.org/W4287724045","https://openalex.org/W4287751330","https://openalex.org/W4287756637","https://openalex.org/W4287766070","https://openalex.org/W4287774713","https://openalex.org/W4287778518","https://openalex.org/W4287828392","https://openalex.org/W4287989678","https://openalex.org/W4288088047","https://openalex.org/W4292779060","https://openalex.org/W4294170691","https://openalex.org/W4295288972","https://openalex.org/W4295917908","https://openalex.org/W4295935531","https://openalex.org/W4296027312","https://openalex.org/W4297253404","https://openalex.org/W4304701343","https://openalex.org/W4304731765","https://openalex.org/W4307006119","https://openalex.org/W4308760226","https://openalex.org/W4309134651","https://openalex.org/W4309953923","https://openalex.org/W4310568840","https://openalex.org/W4311642023","https://openalex.org/W4312266387","https://openalex.org/W4313197536","https://openalex.org/W4317840265","https://openalex.org/W4318350718","https://openalex.org/W4327810118","https://openalex.org/W4367046742","https://openalex.org/W4367860620","https://openalex.org/W4377009978","https://openalex.org/W4378465250","https://openalex.org/W4378469337","https://openalex.org/W4379089507","https://openalex.org/W4382998948","https://openalex.org/W4385567129","https://openalex.org/W4385573131","https://openalex.org/W4394659038","https://openalex.org/W6605666487","https://openalex.org/W6718053083","https://openalex.org/W6741950772","https://openalex.org/W6755977528","https://openalex.org/W6761205521","https://openalex.org/W6763868836","https://openalex.org/W6765671411","https://openalex.org/W6772203101","https://openalex.org/W6774110404","https://openalex.org/W6776048684","https://openalex.org/W6780673046","https://openalex.org/W6781533629","https://openalex.org/W6781808575","https://openalex.org/W6783267081","https://openalex.org/W6794176988","https://openalex.org/W6796159650","https://openalex.org/W6802852670","https://openalex.org/W6810081322","https://openalex.org/W6851787984","https://openalex.org/W6852800892"],"related_works":["https://openalex.org/W2350593162","https://openalex.org/W2390350206","https://openalex.org/W1969477129","https://openalex.org/W2921208823","https://openalex.org/W2131808775","https://openalex.org/W2353483812","https://openalex.org/W2360756181","https://openalex.org/W2374093222","https://openalex.org/W3154008094","https://openalex.org/W2359533638"],"abstract_inverted_index":{"Pre-trained":[0],"language":[1,13,110,141],"models":[2,111],"(PLMs)":[3],"have":[4],"been":[5],"the":[6,19,52,105,113,126,131,136,184],"de":[7],"facto":[8],"paradigm":[9],"for":[10,47,183],"most":[11],"natural":[12],"processing":[14],"tasks.":[15,50,122],"This":[16,102],"also":[17,97],"benefits":[18],"biomedical":[20,35,38,49,56,91,114,121,132,150,163],"domain:":[21],"researchers":[22],"from":[23,68,155],"informatics,":[24],"medicine,":[25],"and":[26,44,74,93,100,116,134,175],"computer":[27],"science":[28],"communities":[29],"propose":[30,145],"various":[31,48,156,173],"PLMs":[32,57,92,129,151],"trained":[33],"on":[34],"datasets,":[36],"e.g.,":[37],"text,":[39],"electronic":[40],"health":[41],"records,":[42],"protein,":[43],"DNA":[45],"sequences":[46],"However,":[51],"cross-discipline":[53],"characteristics":[54],"of":[55,108,128,139,148],"hinder":[58],"their":[59,94,117,160],"spreading":[60],"among":[61],"communities;":[62],"some":[63],"existing":[64,149],"works":[65],"are":[66,166],"isolated":[67],"each":[69],"other":[70],"without":[71],"comprehensive":[72],"comparison":[73],"discussions.":[75],"It":[76],"is":[77],"nontrivial":[78],"to":[79,180],"make":[80],"a":[81,146],"survey":[82],"that":[83,152],"not":[84],"only":[85],"systematically":[86],"reviews":[87],"recent":[88,106],"advances":[89],"in":[90,112,119,130,162],"applications":[95,118,161],"but":[96],"standardizes":[98],"terminology":[99],"benchmarks.":[101],"article":[103],"summarizes":[104],"progress":[107],"pre-trained":[109,140],"domain":[115,133],"downstream":[120,164],"Particularly,":[123],"we":[124,171],"discuss":[125],"motivations":[127],"introduce":[135],"key":[137],"concepts":[138],"models.":[142],"We":[143],"then":[144],"taxonomy":[147],"categorizes":[153],"them":[154],"perspectives":[157],"systematically.":[158],"Plus,":[159],"tasks":[165],"exhaustively":[167],"discussed,":[168],"respectively.":[169],"Last,":[170],"illustrate":[172],"limitations":[174],"future":[176,185],"trends,":[177],"which":[178],"aims":[179],"provide":[181],"inspiration":[182],"research.":[186]},"counts_by_year":[{"year":2026,"cited_by_count":19},{"year":2025,"cited_by_count":67},{"year":2024,"cited_by_count":57},{"year":2023,"cited_by_count":20},{"year":2022,"cited_by_count":4}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
