{"id":"https://openalex.org/W7134964388","doi":"https://doi.org/10.1093/jamia/ocag032","title":"MedRep: medical concept representations for general electronic health record foundation models","display_name":"MedRep: medical concept representations for general electronic health record foundation models","publication_year":2026,"publication_date":"2026-02-25","ids":{"openalex":"https://openalex.org/W7134964388","doi":"https://doi.org/10.1093/jamia/ocag032","pmid":"https://pubmed.ncbi.nlm.nih.gov/41806382"},"language":"en","primary_location":{"id":"doi:10.1093/jamia/ocag032","is_oa":false,"landing_page_url":"https://doi.org/10.1093/jamia/ocag032","pdf_url":null,"source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13197182/","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082494394","display_name":"Junmo Kim","orcid":"https://orcid.org/0000-0002-3908-0488"},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]},{"id":"https://openalex.org/I2802457231","display_name":"New Generation University College","ror":"https://ror.org/015aem925","country_code":"ET","type":"education","lineage":["https://openalex.org/I2802457231"]}],"countries":["ET","KR"],"is_corresponding":false,"raw_author_name":"Junmo Kim","raw_affiliation_strings":["Interdisciplinary Program in Bioengineering, Seoul National University , Seoul 08826,","Interdisciplinary Program of Medical Informatics, Seoul National University , Seoul 03080,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interdisciplinary Program in Bioengineering, Seoul National University , Seoul 08826,","institution_ids":["https://openalex.org/I139264467"]},{"raw_affiliation_string":"Interdisciplinary Program of Medical Informatics, Seoul National University , Seoul 03080,","institution_ids":["https://openalex.org/I139264467","https://openalex.org/I2802457231"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085288448","display_name":"Namkyeong Lee","orcid":"https://orcid.org/0000-0003-3995-1148"},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Namkyeong Lee","raw_affiliation_strings":["Department of Industrial and Systems Engineering, KAIST , Daejeon 34141,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Industrial and Systems Engineering, KAIST , Daejeon 34141,","institution_ids":["https://openalex.org/I157485424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128690900","display_name":"Jiwon Kim","orcid":null},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]},{"id":"https://openalex.org/I2802457231","display_name":"New Generation University College","ror":"https://ror.org/015aem925","country_code":"ET","type":"education","lineage":["https://openalex.org/I2802457231"]}],"countries":["ET","KR"],"is_corresponding":false,"raw_author_name":"Jiwon Kim","raw_affiliation_strings":["Interdisciplinary Program in Bioengineering, Seoul National University , Seoul 08826,","Interdisciplinary Program of Medical Informatics, Seoul National University , Seoul 03080,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interdisciplinary Program in Bioengineering, Seoul National University , Seoul 08826,","institution_ids":["https://openalex.org/I139264467"]},{"raw_affiliation_string":"Interdisciplinary Program of Medical Informatics, Seoul National University , Seoul 03080,","institution_ids":["https://openalex.org/I139264467","https://openalex.org/I2802457231"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5128758023","display_name":"Kwangsoo Kim","orcid":null},"institutions":[{"id":"https://openalex.org/I2802457231","display_name":"New Generation University College","ror":"https://ror.org/015aem925","country_code":"ET","type":"education","lineage":["https://openalex.org/I2802457231"]},{"id":"https://openalex.org/I2802835388","display_name":"Seoul National University Hospital","ror":"https://ror.org/01z4nnt86","country_code":"KR","type":"healthcare","lineage":["https://openalex.org/I139264467","https://openalex.org/I2802835388"]}],"countries":["ET","KR"],"is_corresponding":false,"raw_author_name":"Kwangsoo Kim","raw_affiliation_strings":["Center for Data Science, Healthcare AI Research Institute, Seoul National University Hospital , Seoul 03080,","Department of Medicine, Seoul National University College of Medicine , Seoul 03080,","Department of Transdisciplinary Medicine, Seoul National University Hospital , Seoul 03080,"],"raw_orcid":"https://orcid.org/0000-0002-4586-5062","affiliations":[{"raw_affiliation_string":"Center for Data Science, Healthcare AI Research Institute, Seoul National University Hospital , Seoul 03080,","institution_ids":["https://openalex.org/I2802835388"]},{"raw_affiliation_string":"Department of Medicine, Seoul National University College of Medicine , Seoul 03080,","institution_ids":["https://openalex.org/I2802457231"]},{"raw_affiliation_string":"Department of Transdisciplinary Medicine, Seoul National University Hospital , Seoul 03080,","institution_ids":["https://openalex.org/I2802835388"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3967,"currency":"USD","value_usd":3967},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.32333617,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"33","issue":"6","first_page":"1089","last_page":"1099"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13702","display_name":"Machine Learning in Healthcare","score":0.9466999769210815,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.9466999769210815,"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":0.01940000057220459,"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/T10350","display_name":"Electronic Health Records Systems","score":0.012400000356137753,"subfield":{"id":"https://openalex.org/subfields/3605","display_name":"Health Information Management"},"field":{"id":"https://openalex.org/fields/36","display_name":"Health Professions"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/foundation","display_name":"Foundation (evidence)","score":0.8744999766349792},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.65420001745224},{"id":"https://openalex.org/keywords/electronic-health-record","display_name":"Electronic health record","score":0.637499988079071},{"id":"https://openalex.org/keywords/medical-record","display_name":"Medical record","score":0.4945000112056732},{"id":"https://openalex.org/keywords/baseline","display_name":"Baseline (sea)","score":0.45489999651908875},{"id":"https://openalex.org/keywords/health-records","display_name":"Health records","score":0.44679999351501465},{"id":"https://openalex.org/keywords/meaningful-use","display_name":"Meaningful use","score":0.36489999294281006},{"id":"https://openalex.org/keywords/electronic-medical-record","display_name":"Electronic medical record","score":0.36059999465942383}],"concepts":[{"id":"https://openalex.org/C2780966255","wikidata":"https://www.wikidata.org/wiki/Q5474306","display_name":"Foundation (evidence)","level":2,"score":0.8744999766349792},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.65420001745224},{"id":"https://openalex.org/C3020144179","wikidata":"https://www.wikidata.org/wiki/Q10871684","display_name":"Electronic health record","level":3,"score":0.637499988079071},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5530999898910522},{"id":"https://openalex.org/C195910791","wikidata":"https://www.wikidata.org/wiki/Q1324077","display_name":"Medical record","level":2,"score":0.4945000112056732},{"id":"https://openalex.org/C12725497","wikidata":"https://www.wikidata.org/wiki/Q810247","display_name":"Baseline (sea)","level":2,"score":0.45489999651908875},{"id":"https://openalex.org/C3019952477","wikidata":"https://www.wikidata.org/wiki/Q1324077","display_name":"Health records","level":3,"score":0.44679999351501465},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3905999958515167},{"id":"https://openalex.org/C3019659195","wikidata":"https://www.wikidata.org/wiki/Q5690566","display_name":"Meaningful use","level":3,"score":0.36489999294281006},{"id":"https://openalex.org/C3018060332","wikidata":"https://www.wikidata.org/wiki/Q10871684","display_name":"Electronic medical record","level":2,"score":0.36059999465942383},{"id":"https://openalex.org/C56739046","wikidata":"https://www.wikidata.org/wiki/Q192060","display_name":"Knowledge management","level":1,"score":0.352400004863739},{"id":"https://openalex.org/C55587333","wikidata":"https://www.wikidata.org/wiki/Q1133029","display_name":"Engineering ethics","level":1,"score":0.33820000290870667},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3174000084400177},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3131999969482422},{"id":"https://openalex.org/C3017977704","wikidata":"https://www.wikidata.org/wiki/Q18745135","display_name":"Health data","level":3,"score":0.3100000023841858},{"id":"https://openalex.org/C2779473830","wikidata":"https://www.wikidata.org/wiki/Q1540899","display_name":"MEDLINE","level":2,"score":0.3010999858379364},{"id":"https://openalex.org/C77618280","wikidata":"https://www.wikidata.org/wiki/Q1155772","display_name":"Scheme (mathematics)","level":2,"score":0.29440000653266907},{"id":"https://openalex.org/C161301231","wikidata":"https://www.wikidata.org/wiki/Q3478658","display_name":"Knowledge representation and reasoning","level":2,"score":0.28439998626708984},{"id":"https://openalex.org/C2776034101","wikidata":"https://www.wikidata.org/wiki/Q1509347","display_name":"Commission","level":2,"score":0.2759000062942505},{"id":"https://openalex.org/C2776354556","wikidata":"https://www.wikidata.org/wiki/Q10910281","display_name":"Health information technology","level":3,"score":0.25920000672340393},{"id":"https://openalex.org/C2993731853","wikidata":"https://www.wikidata.org/wiki/Q1324077","display_name":"Patient record","level":2,"score":0.25699999928474426},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.2551000118255615},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.25459998846054077}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/jamia/ocag032","is_oa":false,"landing_page_url":"https://doi.org/10.1093/jamia/ocag032","pdf_url":null,"source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},{"id":"pmid:41806382","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41806382","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":"Journal of the American Medical Informatics Association : JAMIA","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:13197182","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13197182/","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Am Med Inform Assoc","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:13197182","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13197182/","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Am Med Inform Assoc","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W2034626816","https://openalex.org/W2061326496","https://openalex.org/W2088263677","https://openalex.org/W2090090687","https://openalex.org/W2113839990","https://openalex.org/W2165748167","https://openalex.org/W2473930607","https://openalex.org/W2597505554","https://openalex.org/W2767766003","https://openalex.org/W2776803885","https://openalex.org/W3001279689","https://openalex.org/W3017637887","https://openalex.org/W3033039844","https://openalex.org/W3086301066","https://openalex.org/W3090402404","https://openalex.org/W3131100818","https://openalex.org/W3139842669","https://openalex.org/W3160137267","https://openalex.org/W3210129127","https://openalex.org/W4288447278","https://openalex.org/W4306914842","https://openalex.org/W4313439128","https://openalex.org/W4323359744","https://openalex.org/W4384652504","https://openalex.org/W4388052771","https://openalex.org/W4389132345","https://openalex.org/W4400098873","https://openalex.org/W4401845057","https://openalex.org/W4402645752","https://openalex.org/W4411266063","https://openalex.org/W4414687708"],"related_works":[],"abstract_inverted_index":{"OBJECTIVE:":[0],"Traditional":[1],"electronic":[2],"health":[3],"record":[4],"(EHR)":[5],"foundation":[6,37,170,185,196,236,250],"models":[7,94,150,186,197,227,251],"fail":[8],"to":[9,191,224],"process":[10],"unseen":[11],"medical":[12,27,32,71],"codes,":[13],"limiting":[14],"generalizability":[15,182],"across":[16,103,167],"institutions":[17,201,223],"with":[18,88,124],"different":[19,200],"vocabularies.":[20,72],"To":[21],"address":[22],"this":[23],"problem,":[24],"we":[25],"introduce":[26],"concept":[28,33,78],"representation":[29,247],"(MedRep),":[30],"standardized":[31],"representations":[34],"for":[35,248],"EHR":[36,169,184,195,235,249],"models,":[38,119],"enabling":[39,221],"recognition":[40],"of":[41,46,127,183],"semantically":[42],"similar":[43,189,193],"concepts":[44,68,155,190],"regardless":[45],"their":[47],"specific":[48],"IDs.":[49],"MATERIALS":[50],"AND":[51],"METHODS:":[52],"We":[53,91],"utilized":[54],"Observational":[55],"Medical":[56],"Outcomes":[57],"Partnership":[58],"(OMOP)":[59],"Common":[60],"Data":[61],"Model":[62],"(CDM)":[63],"vocabulary":[64],"covering":[65],"7.5":[66],"million":[67],"from":[69,208,226],"66":[70],"MedRep":[73,115,179,233],"integrates":[74],"large":[75],"language":[76],"model-generated":[77],"descriptions":[79],"and":[80,99,111,137,176,240],"OMOP":[81,253],"graph":[82,85],"ontology":[83],"using":[84],"contrastive":[86],"learning":[87],"knowledge":[89,207],"distillation.":[90],"evaluated":[92],"MedRep-based":[93,149],"on":[95,229],"MIMIC-IV":[96],"(internal":[97],"validation)":[98,102],"EHRSHOT":[100],"(external":[101],"9":[104],"prediction":[105],"tasks":[106],"including":[107,173],"clinical":[108],"outcomes,":[109],"phenotypes,":[110],"in-hospital":[112],"events.":[113],"RESULTS:":[114],"consistently":[116],"outperformed":[117],"baseline":[118,161,246],"particularly":[120],"in":[121,129,139],"external":[122],"validation":[123],"average":[125],"improvements":[126,164],"0.088":[128],"area":[130,140],"under":[131,141],"the":[132,142,160,181],"receiver":[133],"operating":[134],"characteristic":[135],"curve":[136],"0.208":[138],"precision-recall":[143],"curve.":[144],"Qualitative":[145],"analysis":[146],"demonstrated":[147],"that":[148],"identified":[151],"more":[152],"clinically":[153],"relevant":[154],"when":[156],"making":[157],"decisions":[158],"than":[159],"models.":[162],"Performance":[163],"remained":[165],"stable":[166],"diverse":[168],"model":[171,237],"architectures,":[172],"BEHRT,":[174],"Med-BERT,":[175],"CDM-BERT.":[177],"DISCUSSION:":[178],"improves":[180,234],"by":[187,220],"encouraging":[188],"have":[192],"representations.":[194],"developed":[198],"at":[199],"could":[202,216],"cooperate":[203],"through":[204],"MedRep,":[205],"merging":[206],"multiple":[209],"hospital":[210],"datasets.":[211,231],"In":[212],"addition,":[213],"our":[214],"approach":[215],"reduce":[217],"healthcare":[218],"disparities":[219],"smaller":[222],"benefit":[225],"trained":[228],"larger":[230],"CONCLUSION:":[232],"performance,":[238],"interpretability,":[239],"generalizability,":[241],"serving":[242],"as":[243],"a":[244],"standard":[245],"adopting":[252],"CDM.":[254]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2026-03-12T00:00:00"}
