{"id":"https://openalex.org/W4406271212","doi":"https://doi.org/10.1109/bibm62325.2024.10822077","title":"DeepTAPE: Enhancing Systemic Lupus Erythematosus Diagnosis with Deep Learning Based on TCR\u03b2 CDR3 Sequences","display_name":"DeepTAPE: Enhancing Systemic Lupus Erythematosus Diagnosis with Deep Learning Based on TCR\u03b2 CDR3 Sequences","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406271212","doi":"https://doi.org/10.1109/bibm62325.2024.10822077"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822077","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822077","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/A5046146934","display_name":"Tongfei Shen","orcid":"https://orcid.org/0009-0008-7621-8125"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Tongfei Shen","raw_affiliation_strings":["City University of Hong Kong,Department of Computer Science,Kowloon,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"City University of Hong Kong,Department of Computer Science,Kowloon,China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067964641","display_name":"Miaozhe Huo","orcid":"https://orcid.org/0000-0002-3891-3812"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Miaozhe Huo","raw_affiliation_strings":["City University of Hong Kong,Department of Computer Science,Kowloon,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"City University of Hong Kong,Department of Computer Science,Kowloon,China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078522162","display_name":"Wan Nie","orcid":"https://orcid.org/0000-0002-0590-6608"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Wan Nie","raw_affiliation_strings":["City University of Hong Kong,Department of Computer Science,Kowloon,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"City University of Hong Kong,Department of Computer Science,Kowloon,China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078425505","display_name":"K.K. Li","orcid":"https://orcid.org/0000-0001-5467-763X"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Kaiqi Li","raw_affiliation_strings":["City University of Hong Kong,Department of Computer Science,Kowloon,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"City University of Hong Kong,Department of Computer Science,Kowloon,China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101964409","display_name":"Ziwei Ma","orcid":"https://orcid.org/0000-0001-9833-8568"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Ziwei Ma","raw_affiliation_strings":["City University of Hong Kong,Department of Computer Science,Kowloon,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"City University of Hong Kong,Department of Computer Science,Kowloon,China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100599551","display_name":"Xikang Feng","orcid":"https://orcid.org/0000-0003-4029-3795"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xikang Feng","raw_affiliation_strings":["Northwestern Polytechnical University,School of Software,Xi&#x2019; an,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northwestern Polytechnical University,School of Software,Xi&#x2019; an,China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083428910","display_name":"Shuai Cheng Li","orcid":"https://orcid.org/0000-0001-6246-6349"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Shuai Cheng Li","raw_affiliation_strings":["City University of Hong Kong,Department of Computer Science,Kowloon,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"City University of Hong Kong,Department of Computer Science,Kowloon,China","institution_ids":["https://openalex.org/I168719708"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5046146934"],"corresponding_institution_ids":["https://openalex.org/I168719708"],"apc_list":null,"apc_paid":null,"fwci":1.2769,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.82297115,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"1149","last_page":"1154"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10308","display_name":"Systemic Lupus Erythematosus Research","score":0.9714000225067139,"subfield":{"id":"https://openalex.org/subfields/2745","display_name":"Rheumatology"},"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/T10308","display_name":"Systemic Lupus Erythematosus Research","score":0.9714000225067139,"subfield":{"id":"https://openalex.org/subfields/2745","display_name":"Rheumatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/t-cell-receptor","display_name":"T-cell receptor","score":0.558247983455658},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.423144668340683},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.415167897939682},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.40987253189086914},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3942795395851135},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3302342891693115},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16450399160385132},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.15953809022903442},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.14338365197181702}],"concepts":[{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.558247983455658},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.423144668340683},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.415167897939682},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.40987253189086914},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3942795395851135},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3302342891693115},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16450399160385132},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.15953809022903442},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.14338365197181702}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822077","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822077","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":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W968228412","https://openalex.org/W1887232166","https://openalex.org/W2064675550","https://openalex.org/W2079763590","https://openalex.org/W2112796928","https://openalex.org/W2123249056","https://openalex.org/W2173411263","https://openalex.org/W2326758788","https://openalex.org/W2331514369","https://openalex.org/W2571045045","https://openalex.org/W2901509748","https://openalex.org/W2946830989","https://openalex.org/W3005836320","https://openalex.org/W3028149335","https://openalex.org/W3063526921","https://openalex.org/W3120717168","https://openalex.org/W3200585592","https://openalex.org/W3213449307","https://openalex.org/W4200374506","https://openalex.org/W4220721882","https://openalex.org/W4223441615","https://openalex.org/W4225693858","https://openalex.org/W4387569385","https://openalex.org/W4391774086","https://openalex.org/W4391790710"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W3031052312","https://openalex.org/W4389568370","https://openalex.org/W3032375762","https://openalex.org/W1995515455","https://openalex.org/W2080531066","https://openalex.org/W3108674512","https://openalex.org/W1506200166","https://openalex.org/W1489783725"],"abstract_inverted_index":{"Systemic":[0],"Lupus":[1],"Erythematosus":[2],"(SLE)":[3],"is":[4,93,159],"a":[5,68,96,147],"common":[6],"and":[7,56,127,169],"severe":[8],"autoimmune":[9,74],"disease":[10,164],"driven":[11],"by":[12,83],"abnormal":[13],"T":[14,42],"cell":[15,43],"responses,":[16],"which":[17,158],"are":[18],"critical":[19],"for":[20,72,108],"understanding":[21,59,184],"the":[22,27,31,38,53,57,84,132,152,154],"disease\u2019s":[23],"immune":[24],"pathology.":[25],"Given":[26],"central":[28],"role":[29],"of":[30,37,60,87,122,125,129,135,185],"Complementarity":[32],"Determining":[33],"Region":[34],"3":[35],"(CDR3)":[36],"TCR\u03b2":[39],"chain":[40],"in":[41,137,166,171],"specificity,":[44],"focused":[45],"investigation":[46],"into":[47],"CDR3":[48,79,136],"may":[49],"potentially":[50],"enhance":[51],"both":[52],"diagnostic":[54,106,133],"accuracy":[55,124],"mechanistic":[58],"SLE.":[61,186],"In":[62],"this":[63],"study,":[64],"we":[65,145],"developed":[66],"DeepTAPE,":[67],"deep":[69,140],"learning-based":[70],"engine":[71],"predicting":[73],"diseases.":[75],"It":[76,116],"primarily":[77],"uses":[78],"sequence":[80],"features,":[81],"supplemented":[82],"frequency":[85],"distribution":[86],"TCR\u03b2\u2019s":[88],"V":[89],"genes.":[90],"This":[91],"model":[92],"based":[94,150],"on":[95,143,151],"multi-layer":[97],"CNN-LSTM":[98],"architecture":[99],"with":[100,162],"residual":[101],"connections.":[102],"DeepTAPE":[103,174],"exhibits":[104],"superior":[105],"performance":[107],"SLE":[109,138,167],"when":[110],"compared":[111],"to":[112],"existing":[113],"gene-focused":[114],"studies.":[115],"achieves":[117],"an":[118],"impressive":[119],"average":[120],"AUC":[121],"97.99%,":[123],"93.97%,":[126],"recall":[128],"94.36%,":[130],"reaffirming":[131],"utility":[134],"through":[139],"learning.":[141],"Building":[142],"this,":[144],"introduced":[146],"quantitative":[148],"indicator":[149],"model,":[153],"Autoimmune":[155],"Risk":[156],"Score,":[157],"positively":[160],"correlated":[161],"clinical":[163],"activity":[165],"patients":[168],"assists":[170],"prognosis.":[172],"Overall,":[173],"not":[175],"only":[176],"offers":[177],"accurate":[178],"diagnosis":[179],"but":[180],"also":[181],"enhances":[182],"our":[183]},"counts_by_year":[{"year":2025,"cited_by_count":3}],"updated_date":"2026-05-04T08:30:34.212998","created_date":"2025-10-10T00:00:00"}
