{"id":"https://openalex.org/W4377093052","doi":"https://doi.org/10.1093/bib/bbad191","title":"SC-AIR-BERT: a pre-trained single-cell model for predicting the antigen-binding specificity of the adaptive immune receptor","display_name":"SC-AIR-BERT: a pre-trained single-cell model for predicting the antigen-binding specificity of the adaptive immune receptor","publication_year":2023,"publication_date":"2023-05-18","ids":{"openalex":"https://openalex.org/W4377093052","doi":"https://doi.org/10.1093/bib/bbad191","pmid":"https://pubmed.ncbi.nlm.nih.gov/37204192"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad191","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad191","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"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/A5101947414","display_name":"Yu Zhao","orcid":"https://orcid.org/0009-0002-6504-527X"},"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":["AI Lab, Tencent, Viseen Business Park , Gaoxin 9th South Road, 518057 Shenzhen , China"],"affiliations":[{"raw_affiliation_string":"AI Lab, Tencent, Viseen Business Park , Gaoxin 9th South Road, 518057 Shenzhen , China","institution_ids":["https://openalex.org/I2250653659"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101078855","display_name":"Xiaona Su","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"]},{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaona Su","raw_affiliation_strings":["AI Lab, Tencent, Viseen Business Park , Gaoxin 9th South Road, 518057 Shenzhen , China","School of Informatics, Xiamen University , South Siming Road 422, 361005 Xiamen , China"],"affiliations":[{"raw_affiliation_string":"AI Lab, Tencent, Viseen Business Park , Gaoxin 9th South Road, 518057 Shenzhen , China","institution_ids":["https://openalex.org/I2250653659"]},{"raw_affiliation_string":"School of Informatics, Xiamen University , South Siming Road 422, 361005 Xiamen , China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049396894","display_name":"Weitong Zhang","orcid":"https://orcid.org/0000-0001-6254-161X"},"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/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Weitong Zhang","raw_affiliation_strings":["AI Lab, Tencent, Viseen Business Park , Gaoxin 9th South Road, 518057 Shenzhen , China","Department of Computer Science, City University of Hong Kong , Kowloon Tong , Hong Kong SAR"],"affiliations":[{"raw_affiliation_string":"AI Lab, Tencent, Viseen Business Park , Gaoxin 9th South Road, 518057 Shenzhen , China","institution_ids":["https://openalex.org/I2250653659"]},{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong , Kowloon Tong , Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010270301","display_name":"Sijie Mai","orcid":"https://orcid.org/0000-0001-9763-375X"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sijie Mai","raw_affiliation_strings":["School of Electronic and Information Technology, Sun Yat-sen University , Xingangxi Road 135, 510275 Guangzhou , China"],"affiliations":[{"raw_affiliation_string":"School of Electronic and Information Technology, Sun Yat-sen University , Xingangxi Road 135, 510275 Guangzhou , China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013577377","display_name":"Zhimeng Xu","orcid":"https://orcid.org/0000-0002-5131-9922"},"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":"Zhimeng Xu","raw_affiliation_strings":["AI Lab, Tencent, Viseen Business Park , Gaoxin 9th South Road, 518057 Shenzhen , China"],"affiliations":[{"raw_affiliation_string":"AI Lab, Tencent, Viseen Business Park , Gaoxin 9th South Road, 518057 Shenzhen , China","institution_ids":["https://openalex.org/I2250653659"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056461668","display_name":"Chenchen Qin","orcid":"https://orcid.org/0009-0009-8763-8616"},"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":"Chenchen Qin","raw_affiliation_strings":["AI Lab, Tencent, Viseen Business Park , Gaoxin 9th South Road, 518057 Shenzhen , China"],"affiliations":[{"raw_affiliation_string":"AI Lab, Tencent, Viseen Business Park , Gaoxin 9th South Road, 518057 Shenzhen , China","institution_ids":["https://openalex.org/I2250653659"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068270780","display_name":"Rongshan Yu","orcid":"https://orcid.org/0000-0003-2179-173X"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Rongshan Yu","raw_affiliation_strings":["School of Informatics, Xiamen University , South Siming Road 422, 361005 Xiamen , China"],"affiliations":[{"raw_affiliation_string":"School of Informatics, Xiamen University , South Siming Road 422, 361005 Xiamen , China","institution_ids":["https://openalex.org/I191208505"]}]},{"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":true,"raw_author_name":"Bing He","raw_affiliation_strings":["AI Lab, Tencent, Viseen Business Park , Gaoxin 9th South Road, 518057 Shenzhen , China"],"affiliations":[{"raw_affiliation_string":"AI Lab, Tencent, Viseen Business Park , Gaoxin 9th South Road, 518057 Shenzhen , China","institution_ids":["https://openalex.org/I2250653659"]}]},{"author_position":"last","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":true,"raw_author_name":"Jianhua Yao","raw_affiliation_strings":["AI Lab, Tencent, Viseen Business Park , Gaoxin 9th South Road, 518057 Shenzhen , China"],"affiliations":[{"raw_affiliation_string":"AI Lab, Tencent, Viseen Business Park , Gaoxin 9th South Road, 518057 Shenzhen , China","institution_ids":["https://openalex.org/I2250653659"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5068270780","https://openalex.org/A5100654854","https://openalex.org/A5100695406"],"corresponding_institution_ids":["https://openalex.org/I191208505","https://openalex.org/I2250653659"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":3.2684,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.92295144,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"24","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9998000264167786,"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":0.9998000264167786,"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/T10031","display_name":"T-cell and B-cell Immunology","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":0.998199999332428,"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/t-cell-receptor","display_name":"T-cell receptor","score":0.5484106540679932},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5344858169555664},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.5278130769729614},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49321407079696655},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.48794692754745483},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.48388680815696716},{"id":"https://openalex.org/keywords/acquired-immune-system","display_name":"Acquired immune system","score":0.46077579259872437},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.4555552899837494},{"id":"https://openalex.org/keywords/perceptron","display_name":"Perceptron","score":0.44327327609062195},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.42622411251068115},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3277977406978607},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.32469674944877625},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.288127601146698},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1635085642337799},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.09772077202796936}],"concepts":[{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.5484106540679932},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5344858169555664},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.5278130769729614},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49321407079696655},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.48794692754745483},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.48388680815696716},{"id":"https://openalex.org/C193419808","wikidata":"https://www.wikidata.org/wiki/Q1645075","display_name":"Acquired immune system","level":3,"score":0.46077579259872437},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.4555552899837494},{"id":"https://openalex.org/C60908668","wikidata":"https://www.wikidata.org/wiki/Q690207","display_name":"Perceptron","level":3,"score":0.44327327609062195},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.42622411251068115},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3277977406978607},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.32469674944877625},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.288127601146698},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1635085642337799},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.09772077202796936}],"mesh":[{"descriptor_ui":"D000918","descriptor_name":"Antibody Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000918","descriptor_name":"Antibody Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000918","descriptor_name":"Antibody Specificity","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":"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":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad191","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad191","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37204192","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37204192","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1984747306","https://openalex.org/W1987971789","https://openalex.org/W2078169925","https://openalex.org/W2120518061","https://openalex.org/W2612690371","https://openalex.org/W2670890989","https://openalex.org/W2671261300","https://openalex.org/W2752126733","https://openalex.org/W2811117758","https://openalex.org/W2898389621","https://openalex.org/W2988217457","https://openalex.org/W3037322279","https://openalex.org/W3043768357","https://openalex.org/W3049166744","https://openalex.org/W3080380488","https://openalex.org/W3128961456","https://openalex.org/W3135760102","https://openalex.org/W3151229614","https://openalex.org/W3152973635","https://openalex.org/W3153732845","https://openalex.org/W3160101264","https://openalex.org/W3177500196","https://openalex.org/W3198659451","https://openalex.org/W3204092016","https://openalex.org/W3217516687","https://openalex.org/W4224249600","https://openalex.org/W6739901393","https://openalex.org/W6787324736"],"related_works":["https://openalex.org/W2394822632","https://openalex.org/W2040128205","https://openalex.org/W2060075608","https://openalex.org/W2026444950","https://openalex.org/W2092033815","https://openalex.org/W2168929838","https://openalex.org/W2140205174","https://openalex.org/W2064485034","https://openalex.org/W104003022","https://openalex.org/W1971240700"],"abstract_inverted_index":{"Accurately":[0],"predicting":[1],"the":[2,27,34,64,99,110],"antigen-binding":[3],"specificity":[4,59,96,124],"of":[5,29,36,52,66,76,114],"adaptive":[6],"immune":[7,24],"receptors":[8,13,17],"(AIRs),":[9],"such":[10],"as":[11],"T-cell":[12],"(TCRs)":[14],"and":[15,122],"B-cell":[16],"(BCRs),":[18],"is":[19,86],"essential":[20],"for":[21,94,120],"discovering":[22],"new":[23],"therapies.":[25],"However,":[26],"diversity":[28],"AIR":[30,54,67,78],"chain":[31],"sequences":[32,68],"limits":[33],"accuracy":[35],"current":[37,118],"prediction":[38],"methods.":[39],"This":[40],"study":[41],"introduces":[42],"SC-AIR-BERT,":[43],"a":[44,73,90],"pre-trained":[45],"model":[46,85],"that":[47],"learns":[48,63],"comprehensive":[49],"sequence":[50,104],"representations":[51],"paired":[53,77],"chains":[55,79],"to":[56,102],"improve":[57],"binding":[58,95],"prediction.":[60,125],"SC-AIR-BERT":[61,115],"first":[62],"'language'":[65],"through":[69],"self-supervised":[70],"pre-training":[71],"on":[72],"large":[74],"cohort":[75],"from":[80],"multiple":[81],"single-cell":[82],"resources.":[83],"The":[84],"then":[87],"fine-tuned":[88],"with":[89,117],"multilayer":[91],"perceptron":[92],"head":[93],"prediction,":[97],"employing":[98],"K-mer":[100],"strategy":[101],"enhance":[103],"representation":[105],"learning.":[106],"Extensive":[107],"experiments":[108],"demonstrate":[109],"superior":[111],"AUC":[112],"performance":[113],"compared":[116],"methods":[119],"TCR-":[121],"BCR-binding":[123]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
