{"id":"https://openalex.org/W4406259754","doi":"https://doi.org/10.1109/bibm62325.2024.10822369","title":"BERT-Based Deep Learning for Classification of IgA Nephropathy, Diabetes, and Hypertension from Clinical Notes","display_name":"BERT-Based Deep Learning for Classification of IgA Nephropathy, Diabetes, and Hypertension from Clinical Notes","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406259754","doi":"https://doi.org/10.1109/bibm62325.2024.10822369"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822369","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822369","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-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/A5015196020","display_name":"Samuele Buosi","orcid":"https://orcid.org/0000-0001-7901-2124"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":true,"raw_author_name":"Samuele Buosi","raw_affiliation_strings":["University of Galway,Data Science Institute,Galway,Ireland"],"affiliations":[{"raw_affiliation_string":"University of Galway,Data Science Institute,Galway,Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013904947","display_name":"Mohan Timilsina","orcid":"https://orcid.org/0000-0003-3886-9898"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Mohan Timilsina","raw_affiliation_strings":["University of Galway,Data Science Institute,Galway,Ireland"],"affiliations":[{"raw_affiliation_string":"University of Galway,Data Science Institute,Galway,Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019119993","display_name":"Luke Harris","orcid":null},"institutions":[{"id":"https://openalex.org/I2802635630","display_name":"University Hospital Galway","ror":"https://ror.org/04scgfz75","country_code":"IE","type":"healthcare","lineage":["https://openalex.org/I2800263200","https://openalex.org/I2802635630","https://openalex.org/I37076085","https://openalex.org/I4210128306","https://openalex.org/I4210136517"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Luke Harris","raw_affiliation_strings":["Galway University Hospital,Nephrology Department,Galway,Ireland"],"affiliations":[{"raw_affiliation_string":"Galway University Hospital,Nephrology Department,Galway,Ireland","institution_ids":["https://openalex.org/I2802635630"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090880806","display_name":"Sarah Monahan","orcid":null},"institutions":[{"id":"https://openalex.org/I2802635630","display_name":"University Hospital Galway","ror":"https://ror.org/04scgfz75","country_code":"IE","type":"healthcare","lineage":["https://openalex.org/I2800263200","https://openalex.org/I2802635630","https://openalex.org/I37076085","https://openalex.org/I4210128306","https://openalex.org/I4210136517"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Sarah Monahan","raw_affiliation_strings":["Galway University Hospital,Acute Medical Unit,Galway,Ireland"],"affiliations":[{"raw_affiliation_string":"Galway University Hospital,Acute Medical Unit,Galway,Ireland","institution_ids":["https://openalex.org/I2802635630"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045425100","display_name":"Kieran Arthur","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kieran Arthur","raw_affiliation_strings":["HSE Inetgrated Information Services,Galway,Ireland"],"affiliations":[{"raw_affiliation_string":"HSE Inetgrated Information Services,Galway,Ireland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033341305","display_name":"Niamh Corcoran","orcid":null},"institutions":[{"id":"https://openalex.org/I2802635630","display_name":"University Hospital Galway","ror":"https://ror.org/04scgfz75","country_code":"IE","type":"healthcare","lineage":["https://openalex.org/I2800263200","https://openalex.org/I2802635630","https://openalex.org/I37076085","https://openalex.org/I4210128306","https://openalex.org/I4210136517"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Niamh Corcoran","raw_affiliation_strings":["Galway University Hospital,Acute Medical Unit,Galway,Ireland"],"affiliations":[{"raw_affiliation_string":"Galway University Hospital,Acute Medical Unit,Galway,Ireland","institution_ids":["https://openalex.org/I2802635630"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Nina Deacon","orcid":null},"institutions":[{"id":"https://openalex.org/I2802635630","display_name":"University Hospital Galway","ror":"https://ror.org/04scgfz75","country_code":"IE","type":"healthcare","lineage":["https://openalex.org/I2800263200","https://openalex.org/I2802635630","https://openalex.org/I37076085","https://openalex.org/I4210128306","https://openalex.org/I4210136517"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Nina Deacon","raw_affiliation_strings":["Galway University Hospital,Acute Medical Unit,Galway,Ireland"],"affiliations":[{"raw_affiliation_string":"Galway University Hospital,Acute Medical Unit,Galway,Ireland","institution_ids":["https://openalex.org/I2802635630"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114433200","display_name":"Michael Wrynn","orcid":null},"institutions":[{"id":"https://openalex.org/I2802635630","display_name":"University Hospital Galway","ror":"https://ror.org/04scgfz75","country_code":"IE","type":"healthcare","lineage":["https://openalex.org/I2800263200","https://openalex.org/I2802635630","https://openalex.org/I37076085","https://openalex.org/I4210128306","https://openalex.org/I4210136517"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Michael Wrynn","raw_affiliation_strings":["Galway University Hospital,Acute Medical Unit,Galway,Ireland"],"affiliations":[{"raw_affiliation_string":"Galway University Hospital,Acute Medical Unit,Galway,Ireland","institution_ids":["https://openalex.org/I2802635630"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031558101","display_name":"Richard Farnan","orcid":"https://orcid.org/0000-0002-3477-4034"},"institutions":[{"id":"https://openalex.org/I2802635630","display_name":"University Hospital Galway","ror":"https://ror.org/04scgfz75","country_code":"IE","type":"healthcare","lineage":["https://openalex.org/I2800263200","https://openalex.org/I2802635630","https://openalex.org/I37076085","https://openalex.org/I4210128306","https://openalex.org/I4210136517"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Richard Farnan","raw_affiliation_strings":["Galway University Hospital,Acute Medical Unit,Galway,Ireland"],"affiliations":[{"raw_affiliation_string":"Galway University Hospital,Acute Medical Unit,Galway,Ireland","institution_ids":["https://openalex.org/I2802635630"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073169134","display_name":"David Keane","orcid":"https://orcid.org/0000-0002-4744-4106"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"David Keane","raw_affiliation_strings":["University of Galway,HRB-Clinical Research Facility Galway,Galway,Ireland"],"affiliations":[{"raw_affiliation_string":"University of Galway,HRB-Clinical Research Facility Galway,Galway,Ireland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047395038","display_name":"George Mellotte","orcid":"https://orcid.org/0000-0002-6477-1491"},"institutions":[{"id":"https://openalex.org/I2802635630","display_name":"University Hospital Galway","ror":"https://ror.org/04scgfz75","country_code":"IE","type":"healthcare","lineage":["https://openalex.org/I2800263200","https://openalex.org/I2802635630","https://openalex.org/I37076085","https://openalex.org/I4210128306","https://openalex.org/I4210136517"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"George Mellotte","raw_affiliation_strings":["Galway University Hospital,Acute Medical Unit/Nephrology Department,Galway,Ireland"],"affiliations":[{"raw_affiliation_string":"Galway University Hospital,Acute Medical Unit/Nephrology Department,Galway,Ireland","institution_ids":["https://openalex.org/I2802635630"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072436024","display_name":"Donal Reddan","orcid":"https://orcid.org/0000-0001-7429-6594"},"institutions":[{"id":"https://openalex.org/I2802635630","display_name":"University Hospital Galway","ror":"https://ror.org/04scgfz75","country_code":"IE","type":"healthcare","lineage":["https://openalex.org/I2800263200","https://openalex.org/I2802635630","https://openalex.org/I37076085","https://openalex.org/I4210128306","https://openalex.org/I4210136517"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Donal Reddan","raw_affiliation_strings":["Galway University Hospital,Nephrology Department,Galway,Ireland"],"affiliations":[{"raw_affiliation_string":"Galway University Hospital,Nephrology Department,Galway,Ireland","institution_ids":["https://openalex.org/I2802635630"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090363223","display_name":"Finn Krewer","orcid":"https://orcid.org/0009-0005-1727-4459"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Finn Krewer","raw_affiliation_strings":["HSE Inetgrated Information Services,Galway,Ireland"],"affiliations":[{"raw_affiliation_string":"HSE Inetgrated Information Services,Galway,Ireland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027850521","display_name":"Edward Curry","orcid":"https://orcid.org/0000-0001-8236-6433"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Edward Curry","raw_affiliation_strings":["University of Galway,Data Science Institute,Galway,Ireland"],"affiliations":[{"raw_affiliation_string":"University of Galway,Data Science Institute,Galway,Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042032394","display_name":"Conor Judge","orcid":"https://orcid.org/0000-0001-9473-2920"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Conor Judge","raw_affiliation_strings":["University of Galway,HRB-Clinical Research Facility Galway and Data Science Institute,Galway,Ireland"],"affiliations":[{"raw_affiliation_string":"University of Galway,HRB-Clinical Research Facility Galway and Data Science Institute,Galway,Ireland","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":15,"corresponding_author_ids":["https://openalex.org/A5015196020"],"corresponding_institution_ids":["https://openalex.org/I188760350"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.34809377,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"6678","last_page":"6684"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11396","display_name":"Artificial Intelligence in Healthcare","score":0.955299973487854,"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"}},"topics":[{"id":"https://openalex.org/T11396","display_name":"Artificial Intelligence in Healthcare","score":0.955299973487854,"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"}},{"id":"https://openalex.org/T13702","display_name":"Machine Learning in Healthcare","score":0.9505000114440918,"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/nephropathy","display_name":"Nephropathy","score":0.6423181295394897},{"id":"https://openalex.org/keywords/diabetes-mellitus","display_name":"Diabetes mellitus","score":0.6022738218307495},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5760692358016968},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5671470761299133},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5554090738296509},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.4407113790512085},{"id":"https://openalex.org/keywords/diabetic-nephropathy","display_name":"Diabetic nephropathy","score":0.42066097259521484},{"id":"https://openalex.org/keywords/endocrinology","display_name":"Endocrinology","score":0.1430392861366272}],"concepts":[{"id":"https://openalex.org/C2781184683","wikidata":"https://www.wikidata.org/wiki/Q1054718","display_name":"Nephropathy","level":3,"score":0.6423181295394897},{"id":"https://openalex.org/C555293320","wikidata":"https://www.wikidata.org/wiki/Q12206","display_name":"Diabetes mellitus","level":2,"score":0.6022738218307495},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5760692358016968},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5671470761299133},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5554090738296509},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.4407113790512085},{"id":"https://openalex.org/C2779922275","wikidata":"https://www.wikidata.org/wiki/Q1129105","display_name":"Diabetic nephropathy","level":3,"score":0.42066097259521484},{"id":"https://openalex.org/C134018914","wikidata":"https://www.wikidata.org/wiki/Q162606","display_name":"Endocrinology","level":1,"score":0.1430392861366272}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822369","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822369","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320847","display_name":"Science Foundation Ireland","ror":"https://ror.org/0271asj38"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W2886250128","https://openalex.org/W2976476443","https://openalex.org/W2977682063","https://openalex.org/W3185951817","https://openalex.org/W4220734654","https://openalex.org/W4308627565","https://openalex.org/W4309433278","https://openalex.org/W4313312391","https://openalex.org/W4382986932","https://openalex.org/W4385336656","https://openalex.org/W4396998375","https://openalex.org/W6768851824"],"related_works":["https://openalex.org/W2731899572","https://openalex.org/W3215138031","https://openalex.org/W3009238340","https://openalex.org/W4360585206","https://openalex.org/W4321369474","https://openalex.org/W4285208911","https://openalex.org/W3082895349","https://openalex.org/W4213079790","https://openalex.org/W2248239756","https://openalex.org/W3086377361"],"abstract_inverted_index":{"Chronic":[0],"kidney":[1],"disease":[2,28,43],"affects":[3],"over":[4],"800":[5],"million":[6],"people":[7],"globally":[8],"and":[9,16,30,54,98,109,124,141,152,183,191,194,199,218,232,239],"has":[10,38,90],"many":[11],"etiologies,":[12],"including":[13],"hypertension,":[14],"diabetes,":[15],"IgA":[17,95,117],"nephropathy.":[18],"Effective":[19],"management":[20],"relies":[21],"on":[22,208],"precise":[23],"medical":[24],"documentation":[25],"to":[26,80,235],"monitor":[27],"progression":[29],"treatment":[31],"efficacy.":[32],"Artificial":[33],"intelligence,":[34],"specifically":[35],"BERT-based":[36],"models,":[37],"shown":[39],"promise":[40],"in":[41,59,213],"enhancing":[42],"classification":[44,211],"from":[45,52,77],"clinical":[46,50,75,166,237],"notes.":[47],"In":[48],"Ireland,":[49],"notes":[51,76,84],"hemodialysis":[53],"nephrology":[55],"outpatients":[56],"are":[57],"stored":[58],"the":[60,78,88,113,116,159,205,209,215,227],"Kidney":[61],"Disease":[62],"Clinical":[63],"Patient":[64],"Management":[65],"System":[66],"(KDCPMS).":[67],"This":[68],"study":[69],"uses":[70],"DistilBERT":[71],"with":[72,131],"2,947":[73],"unstructured":[74],"KDCPMS":[79],"classify":[81],"individual":[82],"patient":[83,89],"as":[85],"stating":[86],"that":[87],"or":[91],"does":[92],"not":[93],"have":[94],"Nephropathy,":[96],"Diabetes,":[97],"Hypertension.":[99],"The":[100,134,145,156,180,202,224],"training":[101],"pipeline":[102],"involved":[103],"data":[104],"extraction,":[105],"anonymization,":[106],"pre-processing,":[107],"annotation,":[108],"model":[110],"training.":[111],"On":[112],"test":[114,216],"set":[115,217],"Nephropathy":[118],"classifier":[119,136,147],"achieved":[120],"high":[121,149],"precision":[122,138,150,187],"(99%)":[123],"recall":[125,142,154,195],"(100%),":[126],"effectively":[127],"identifying":[128],"positive":[129],"cases":[130],"minimal":[132],"errors.":[133],"Diabetes":[135,182],"had":[137,148,186],"of":[139,143,158,169,188,196,229],"76%":[140],"90%.":[144],"Hypertension":[146,184],"(91%)":[151],"medium":[153],"(72%).":[155],"performance":[157,207],"classifiers":[160,185],"was":[161],"further":[162],"evaluated":[163],"against":[164],"a":[165,174,219],"validation":[167],"dataset":[168],"112":[170],"patients":[171],"created":[172],"through":[173],"full":[175],"chart":[176],"review":[177],"by":[178],"clinicians.":[179],"IgA,":[181],"83%,":[189,197],"61%":[190],"73%":[192,198],"respectively":[193],"83%":[200],"respectively.":[201],"results":[203,225],"highlight":[204],"models'":[206],"different":[210],"problems":[212],"both":[214],"more":[220],"clinically":[221],"focused":[222],"dataset.":[223],"emphasize":[226],"importance":[228],"ongoing":[230],"refinement":[231],"expert":[233],"collaboration":[234],"enhance":[236],"relevance":[238],"applicability.":[240]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
