{"id":"https://openalex.org/W4321749402","doi":"https://doi.org/10.1093/bioinformatics/btad103","title":"On the effectiveness of compact biomedical transformers","display_name":"On the effectiveness of compact biomedical transformers","publication_year":2023,"publication_date":"2023-02-24","ids":{"openalex":"https://openalex.org/W4321749402","doi":"https://doi.org/10.1093/bioinformatics/btad103","pmid":"https://pubmed.ncbi.nlm.nih.gov/36825820"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad103","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad103","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad103/49571998/btad103.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad103/49571998/btad103.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059154016","display_name":"Omid Rohanian","orcid":"https://orcid.org/0000-0002-8771-8386"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Omid Rohanian","raw_affiliation_strings":["Department of Engineering Science, University of Oxford , Oxford, UK","NLPie Research , Oxford, UK"],"raw_orcid":"https://orcid.org/0000-0002-8771-8386","affiliations":[{"raw_affiliation_string":"Department of Engineering Science, University of Oxford , Oxford, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"NLPie Research , Oxford, UK","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088008419","display_name":"Mohammadmahdi Nouriborji","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Mohammadmahdi Nouriborji","raw_affiliation_strings":["NLPie Research , Oxford, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NLPie Research , Oxford, UK","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008431949","display_name":"Samaneh Kouchaki","orcid":"https://orcid.org/0000-0002-5870-4030"},"institutions":[{"id":"https://openalex.org/I28290843","display_name":"University of Surrey","ror":"https://ror.org/00ks66431","country_code":"GB","type":"education","lineage":["https://openalex.org/I28290843"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Samaneh Kouchaki","raw_affiliation_strings":["Department of Electrical and Electronic Engineering, University of Surrey , Guildford, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Electronic Engineering, University of Surrey , Guildford, UK","institution_ids":["https://openalex.org/I28290843"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040302008","display_name":"David A. Clifton","orcid":"https://orcid.org/0000-0002-9848-8555"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210125878","display_name":"Suzhou Research Institute","ror":"https://ror.org/03ebk0c60","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210125878"]}],"countries":["CN","GB"],"is_corresponding":false,"raw_author_name":"David A Clifton","raw_affiliation_strings":["Department of Engineering Science, University of Oxford , Oxford, UK","Oxford-Suzhou Centre for Advanced Research , Suzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Engineering Science, University of Oxford , Oxford, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Oxford-Suzhou Centre for Advanced Research , Suzhou, China","institution_ids":["https://openalex.org/I4210125878"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5059154016","https://openalex.org/A5088008419"],"corresponding_institution_ids":["https://openalex.org/I40120149"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.1975,"has_fulltext":true,"cited_by_count":41,"citation_normalized_percentile":{"value":0.83210513,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"39","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11636","display_name":"Artificial Intelligence in Healthcare and Education","score":0.33480000495910645,"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"}},"topics":[{"id":"https://openalex.org/T11636","display_name":"Artificial Intelligence in Healthcare and Education","score":0.33480000495910645,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.32910001277923584,"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/T10028","display_name":"Topic Modeling","score":0.08169999718666077,"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":0.7931951284408569},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.6216593384742737},{"id":"https://openalex.org/keywords/security-token","display_name":"Security token","score":0.5779758095741272},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5510981678962708},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5421752333641052},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5269287824630737},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5057649612426758},{"id":"https://openalex.org/keywords/distillation","display_name":"Distillation","score":0.4747222661972046},{"id":"https://openalex.org/keywords/pruning","display_name":"Pruning","score":0.46748656034469604}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7931951284408569},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.6216593384742737},{"id":"https://openalex.org/C48145219","wikidata":"https://www.wikidata.org/wiki/Q1335365","display_name":"Security token","level":2,"score":0.5779758095741272},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5510981678962708},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5421752333641052},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5269287824630737},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5057649612426758},{"id":"https://openalex.org/C204030448","wikidata":"https://www.wikidata.org/wiki/Q101017","display_name":"Distillation","level":2,"score":0.4747222661972046},{"id":"https://openalex.org/C108010975","wikidata":"https://www.wikidata.org/wiki/Q500094","display_name":"Pruning","level":2,"score":0.46748656034469604},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C6557445","wikidata":"https://www.wikidata.org/wiki/Q173113","display_name":"Agronomy","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/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D007802","descriptor_name":"Language","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":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad103","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad103","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad103/49571998/btad103.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36825820","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36825820","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10027428","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10027428","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10027428/pdf/btad103.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad103","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad103","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad103/49571998/btad103.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320319990","display_name":"National Institute for Health and Care Research","ror":"https://ror.org/0187kwz08"},{"id":"https://openalex.org/F4320320290","display_name":"University of Oxford","ror":"https://ror.org/052gg0110"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4321749402.pdf"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1981208470","https://openalex.org/W2071879021","https://openalex.org/W2100627415","https://openalex.org/W2136437513","https://openalex.org/W2145870108","https://openalex.org/W2149369282","https://openalex.org/W2154142897","https://openalex.org/W2169099542","https://openalex.org/W2346452181","https://openalex.org/W2788388592","https://openalex.org/W2911489562","https://openalex.org/W3008374555","https://openalex.org/W3024922541","https://openalex.org/W3141847762","https://openalex.org/W4292779060","https://openalex.org/W4385245566","https://openalex.org/W6739901393","https://openalex.org/W6773815586","https://openalex.org/W6778883912"],"related_works":["https://openalex.org/W4388335561","https://openalex.org/W2970530566","https://openalex.org/W4288261899","https://openalex.org/W4307309205","https://openalex.org/W2967478618","https://openalex.org/W4385009901","https://openalex.org/W4385572700","https://openalex.org/W2997152889","https://openalex.org/W2081900870","https://openalex.org/W4387768015"],"abstract_inverted_index":{"MOTIVATION:":[0],"Language":[1],"models":[2,57,69,125,141,155,195,202,239,272],"pre-trained":[3,21,207],"on":[4,15,23,116,126,144,184,187,208],"biomedical":[5,17,111,128,190,199],"corpora,":[6],"such":[7,35,60],"as":[8,36,61],"BioBERT,":[9],"have":[10,204],"recently":[11],"shown":[12],"promising":[13],"results":[14],"downstream":[16],"tasks.":[18],"Many":[19],"existing":[20],"models,":[22,93],"the":[24,83,117,137,159,168,209,220,223,257,260],"other":[25],"hand,":[26],"are":[27,71,103,244,267],"resource-intensive":[28],"and":[29,41,64,75,100,130,167,201,217,246,254],"computationally":[30],"heavy":[31],"owing":[32],"to":[33,54,78,135,215,252],"factors":[34],"embedding":[37],"size,":[38],"hidden":[39],"dimension":[40],"number":[42],"of":[43,123,177,219,222,256,259],"layers.":[44],"The":[45],"natural":[46],"language":[47],"processing":[48],"community":[49],"has":[50],"developed":[51],"numerous":[52],"strategies":[53],"compress":[55],"these":[56],"utilizing":[58],"techniques":[59],"pruning,":[62],"quantization":[63],"knowledge":[65,107],"distillation,":[66],"resulting":[67],"in":[68,80,86,156,165],"that":[70,142,194,203],"considerably":[72],"faster,":[73],"smaller":[74],"subsequently":[76],"easier":[77],"use":[79],"practice.":[81],"By":[82],"same":[84],"token,":[85],"this":[87],"article,":[88],"we":[89,192],"introduce":[90],"six":[91,153],"lightweight":[92,140],"namely,":[94],"BioDistilBERT,":[95],"BioTinyBERT,":[96],"BioMobileBERT,":[97,235],"DistilBioBERT,":[98],"TinyBioBERT":[99],"CompactBioBERT":[101],"which":[102,248],"obtained":[104],"either":[105],"by":[106],"distillation":[108],"from":[109,197],"a":[110,173,198],"teacher":[112,200],"or":[113],"continual":[114],"learning":[115],"Pubmed":[118],"dataset.":[119],"We":[120,151],"evaluate":[121],"all":[122],"our":[124,185,227,237],"three":[127,188],"tasks":[129],"compare":[131],"them":[132],"with":[133,146,158,180],"BioBERT-v1.1":[134],"create":[136],"best":[138,228,238],"efficient":[139],"perform":[143],"par":[145],"their":[147],"larger":[148],"counterparts.":[149],"RESULTS:":[150],"trained":[152],"different":[154,189],"total,":[157],"largest":[160],"model":[161,229],"having":[162,170],"65":[163],"million":[164],"parameters":[166,178,233,243],"smallest":[169],"15":[171],"million;":[172],"far":[174],"lower":[175],"range":[176],"compared":[179],"BioBERT's":[181],"110M.":[182],"Based":[183],"experiments":[186],"tasks,":[191],"found":[193],"distilled":[196],"been":[205],"additionally":[206],"PubMed":[210],"dataset":[211],"can":[212,249,273],"retain":[213],"up":[214,251],"98.8%":[216,255],"98.6%":[218],"performance":[221,258],"BioBERT-v1.1,":[224,261],"respectively.":[225,262],"Overall,":[226],"below":[230],"30":[231,241],"M":[232,242],"is":[234],"while":[236],"over":[240],"DistilBioBERT":[245],"CompactBioBERT,":[247],"keep":[250],"98.2%":[253],"AVAILABILITY":[263],"AND":[264],"IMPLEMENTATION:":[265],"Codes":[266],"available":[268],"at:":[269,276],"https://github.com/nlpie-research/Compact-Biomedical-Transformers.":[270],"Trained":[271],"be":[274],"accessed":[275],"https://huggingface.co/nlpie.":[277]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":7}],"updated_date":"2026-07-18T07:39:51.176621","created_date":"2025-10-10T00:00:00"}
