{"id":"https://openalex.org/W4390971344","doi":"https://doi.org/10.1109/bibm58861.2023.10385479","title":"Multimodal-AIR-BERT: A Multimodal Pre-trained Model for Antigen Specificity Prediction in Adaptive Immune Receptors","display_name":"Multimodal-AIR-BERT: A Multimodal Pre-trained Model for Antigen Specificity Prediction in Adaptive Immune Receptors","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390971344","doi":"https://doi.org/10.1109/bibm58861.2023.10385479"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10385479","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10385479","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","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/A5100620334","display_name":"Yang Xiao","orcid":"https://orcid.org/0000-0002-9411-4660"},"institutions":[{"id":"https://openalex.org/I2250653659","display_name":"Tencent (China)","ror":"https://ror.org/00hhjss72","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250653659"]},{"id":"https://openalex.org/I4210114105","display_name":"Tsinghua\u2013Berkeley Shenzhen Institute","ror":"https://ror.org/02hhwwz98","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210114105","https://openalex.org/I95457486","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Xiao","raw_affiliation_strings":["Tsinghua University,Tsinghua Shenzhen International Graduate School,Shenzhen,China","AI Lab, Tencent, Shenzhen, China","Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tsinghua University,Tsinghua Shenzhen International Graduate School,Shenzhen,China","institution_ids":["https://openalex.org/I4210114105","https://openalex.org/I99065089"]},{"raw_affiliation_string":"AI Lab, Tencent, Shenzhen, China","institution_ids":["https://openalex.org/I2250653659"]},{"raw_affiliation_string":"Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China","institution_ids":["https://openalex.org/I4210114105","https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051052822","display_name":"Yueshan Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I2250653659","display_name":"Tencent (China)","ror":"https://ror.org/00hhjss72","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250653659"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yueshan Huang","raw_affiliation_strings":["Tencent,AI Lab,Shenzhen,China","AI Lab, Tencent, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tencent,AI Lab,Shenzhen,China","institution_ids":["https://openalex.org/I2250653659"]},{"raw_affiliation_string":"AI Lab, Tencent, Shenzhen, China","institution_ids":["https://openalex.org/I2250653659"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080161214","display_name":"Yu Zhao","orcid":"https://orcid.org/0000-0001-8179-4903"},"institutions":[{"id":"https://openalex.org/I2250653659","display_name":"Tencent (China)","ror":"https://ror.org/00hhjss72","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250653659"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu Zhao","raw_affiliation_strings":["Tencent,AI Lab,Shenzhen,China","AI Lab, Tencent, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tencent,AI Lab,Shenzhen,China","institution_ids":["https://openalex.org/I2250653659"]},{"raw_affiliation_string":"AI Lab, Tencent, Shenzhen, China","institution_ids":["https://openalex.org/I2250653659"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019712612","display_name":"Fan Xu","orcid":"https://orcid.org/0000-0003-2758-3114"},"institutions":[{"id":"https://openalex.org/I2250653659","display_name":"Tencent (China)","ror":"https://ror.org/00hhjss72","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250653659"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fan Xu","raw_affiliation_strings":["Tencent,AI Lab,Shenzhen,China","AI Lab, Tencent, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tencent,AI Lab,Shenzhen,China","institution_ids":["https://openalex.org/I2250653659"]},{"raw_affiliation_string":"AI Lab, Tencent, Shenzhen, China","institution_ids":["https://openalex.org/I2250653659"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100941560","display_name":"Qin Ren","orcid":null},"institutions":[{"id":"https://openalex.org/I2250653659","display_name":"Tencent (China)","ror":"https://ror.org/00hhjss72","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250653659"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qin Ren","raw_affiliation_strings":["Tencent,AI Lab,Shenzhen,China","AI Lab, Tencent, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tencent,AI Lab,Shenzhen,China","institution_ids":["https://openalex.org/I2250653659"]},{"raw_affiliation_string":"AI Lab, Tencent, Shenzhen, China","institution_ids":["https://openalex.org/I2250653659"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100654854","display_name":"Bing He","orcid":"https://orcid.org/0000-0003-1719-9290"},"institutions":[{"id":"https://openalex.org/I2250653659","display_name":"Tencent (China)","ror":"https://ror.org/00hhjss72","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250653659"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bing He","raw_affiliation_strings":["Tencent,AI Lab,Shenzhen,China","AI Lab, Tencent, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tencent,AI Lab,Shenzhen,China","institution_ids":["https://openalex.org/I2250653659"]},{"raw_affiliation_string":"AI Lab, Tencent, Shenzhen, China","institution_ids":["https://openalex.org/I2250653659"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100695406","display_name":"Jianhua Yao","orcid":"https://orcid.org/0000-0001-9157-9596"},"institutions":[{"id":"https://openalex.org/I2250653659","display_name":"Tencent (China)","ror":"https://ror.org/00hhjss72","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250653659"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianhua Yao","raw_affiliation_strings":["Tencent,AI Lab,Shenzhen,China","AI Lab, Tencent, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tencent,AI Lab,Shenzhen,China","institution_ids":["https://openalex.org/I2250653659"]},{"raw_affiliation_string":"AI Lab, Tencent, Shenzhen, China","institution_ids":["https://openalex.org/I2250653659"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100441124","display_name":"Xiao Liu","orcid":"https://orcid.org/0009-0009-5860-5508"},"institutions":[{"id":"https://openalex.org/I4210114105","display_name":"Tsinghua\u2013Berkeley Shenzhen Institute","ror":"https://ror.org/02hhwwz98","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210114105","https://openalex.org/I95457486","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiao Liu","raw_affiliation_strings":["Tsinghua University,Tsinghua Shenzhen International Graduate School,Shenzhen,China","Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tsinghua University,Tsinghua Shenzhen International Graduate School,Shenzhen,China","institution_ids":["https://openalex.org/I4210114105","https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China","institution_ids":["https://openalex.org/I4210114105","https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.3436,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.8403351,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"69","last_page":"75"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9997000098228455,"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"}},"topics":[{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9997000098228455,"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"}},{"id":"https://openalex.org/T11020","display_name":"Immune Cell Function and Interaction","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10580","display_name":"Immunotherapy and Immune Responses","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.6806014776229858},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6360675096511841},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5454311370849609},{"id":"https://openalex.org/keywords/acquired-immune-system","display_name":"Acquired immune system","score":0.5273619294166565},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.49175766110420227},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.472595751285553},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3635967969894409},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3250184655189514},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31262266635894775},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.142410010099411}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.6806014776229858},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6360675096511841},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5454311370849609},{"id":"https://openalex.org/C193419808","wikidata":"https://www.wikidata.org/wiki/Q1645075","display_name":"Acquired immune system","level":3,"score":0.5273619294166565},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.49175766110420227},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.472595751285553},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3635967969894409},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3250184655189514},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31262266635894775},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.142410010099411}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm58861.2023.10385479","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10385479","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.46000000834465027,"display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1984747306","https://openalex.org/W2017956110","https://openalex.org/W2064676287","https://openalex.org/W2072149435","https://openalex.org/W2154330708","https://openalex.org/W2409902605","https://openalex.org/W2671261300","https://openalex.org/W2752126733","https://openalex.org/W2896457183","https://openalex.org/W3036326371","https://openalex.org/W3048782167","https://openalex.org/W3080380488","https://openalex.org/W3111174583","https://openalex.org/W3128961456","https://openalex.org/W3135351475","https://openalex.org/W3135760102","https://openalex.org/W3151229614","https://openalex.org/W3153732845","https://openalex.org/W3160101264","https://openalex.org/W3204092016","https://openalex.org/W3217516687","https://openalex.org/W4317532687","https://openalex.org/W4319455163","https://openalex.org/W4377093052","https://openalex.org/W6755207826","https://openalex.org/W6787324736","https://openalex.org/W6805010082"],"related_works":["https://openalex.org/W2003194288","https://openalex.org/W2513589746","https://openalex.org/W2486559672","https://openalex.org/W2153919606","https://openalex.org/W2213189664","https://openalex.org/W2074002899","https://openalex.org/W2062254828","https://openalex.org/W4237480606","https://openalex.org/W2936968863","https://openalex.org/W1971792277"],"abstract_inverted_index":{"The":[0,27,66,143],"in":[1,7,39,44,64,103,159,173],"silico":[2],"prediction":[3,99,176,186],"of":[4,54,69,100,136,145,177,183],"antigen":[5,80],"specificity":[6,81,102,185],"adaptive":[8],"immune":[9,196,206],"receptors":[10,15],"(AIRs),":[11],"such":[12],"as":[13],"T-cell":[14],"(TCRs),":[16],"is":[17,31],"essential":[18],"for":[19,79,194],"understanding":[20],"immunological":[21],"processes":[22],"and":[23,59,114,122,127,132,198],"developing":[24],"targeted":[25,195],"therapies.":[26],"V(D)J":[28,130,146],"gene":[29,112,131,147],"rearrangement":[30],"a":[32,51,72,90,107,111,115],"critical":[33],"biological":[34],"process":[35],"that":[36],"generates":[37],"diversity":[38,68],"amino":[40],"acid":[41],"(AA)":[42],"sequences":[43,155],"antigen-binding":[45,101,178],"regions,":[46],"enabling":[47],"AIRs":[48,70],"to":[49,75,125,163],"recognize":[50],"wide":[52],"range":[53],"antigens":[55],"from":[56,154],"various":[57],"pathogens":[58],"\"altered":[60],"self":[61],"cells\"":[62],"observed":[63],"cancers.":[65],"huge":[67],"presents":[71],"significant":[73],"challenge":[74],"existing":[76],"computational":[77],"methods":[78],"prediction.":[82],"To":[83],"address":[84],"these":[85],"complexities,":[86],"we":[87],"introduce":[88],"Multimodal-AIR-BERT,":[89],"novel":[91],"multimodal":[92,116],"pre-trained":[93,108],"model":[94],"aimed":[95],"at":[96],"enhancing":[97],"the":[98,129,174,181,192,202,205],"TCRs.":[104],"It":[105],"comprises":[106],"sequence":[109,134],"encoder,":[110,113],"fusion":[117,124],"module":[118],"with":[119],"gating-based":[120],"attention":[121],"tensor":[123],"calibrate":[126],"integrate":[128],"AA":[133],"features":[135],"TCRs,":[137],"thereby":[138],"generating":[139],"more":[140],"informative":[141],"representations.":[142],"integration":[144],"information,":[148],"which":[149],"provides":[150,170],"insights":[151,200],"often":[152],"unobtainable":[153],"alone,":[156],"benefits":[157],"Multimodal-AIR-BERT":[158],"performance":[160],"enhancement":[161],"compared":[162],"its":[164],"sequence-modality-only":[165],"counterpart.":[166],"Collectively,":[167],"our":[168],"work":[169],"an":[171],"advancement":[172],"accurate":[175],"specificity.":[179],"As":[180],"precision":[182],"this":[184],"improves,":[187],"it":[188],"can":[189],"potentially":[190],"pave":[191],"way":[193],"therapies":[197],"deeper":[199],"into":[201],"interactions":[203],"within":[204],"system.":[207]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
