{"id":"https://openalex.org/W4409011676","doi":"https://doi.org/10.1371/journal.pcbi.1012153","title":"Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction","display_name":"Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction","publication_year":2025,"publication_date":"2025-03-31","ids":{"openalex":"https://openalex.org/W4409011676","doi":"https://doi.org/10.1371/journal.pcbi.1012153","pmid":"https://pubmed.ncbi.nlm.nih.gov/40163503"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012153","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012153","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012153&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012153&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018493905","display_name":"Meng Wang","orcid":"https://orcid.org/0000-0002-3453-7805"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Meng Wang","raw_affiliation_strings":["Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-3453-7805","affiliations":[{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030594124","display_name":"Jonathan Patsenker","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]},{"id":"https://openalex.org/I4210131439","display_name":"Applied Mathematics (United States)","ror":"https://ror.org/03seew607","country_code":"US","type":"company","lineage":["https://openalex.org/I4210131439"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Patsenker","raw_affiliation_strings":["Program in Applied Mathematics, Yale University, New Haven, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program in Applied Mathematics, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472","https://openalex.org/I4210131439"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005031691","display_name":"Henry Li","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]},{"id":"https://openalex.org/I4210131439","display_name":"Applied Mathematics (United States)","ror":"https://ror.org/03seew607","country_code":"US","type":"company","lineage":["https://openalex.org/I4210131439"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Henry Li","raw_affiliation_strings":["Program in Applied Mathematics, Yale University, New Haven, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program in Applied Mathematics, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472","https://openalex.org/I4210131439"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020473435","display_name":"Yuval Kluger","orcid":"https://orcid.org/0000-0002-3035-071X"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]},{"id":"https://openalex.org/I4210131439","display_name":"Applied Mathematics (United States)","ror":"https://ror.org/03seew607","country_code":"US","type":"company","lineage":["https://openalex.org/I4210131439"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuval Kluger","raw_affiliation_strings":["Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America","Program in Applied Mathematics, Yale University, New Haven, Connecticut, United States of America","Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Program in Applied Mathematics, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472","https://openalex.org/I4210131439"]},{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066562919","display_name":"Steven H. Kleinstein","orcid":"https://orcid.org/0000-0003-4957-1544"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Steven H. Kleinstein","raw_affiliation_strings":["Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America","Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America","Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-4957-1544","affiliations":[{"raw_affiliation_string":"Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5066562919"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":6.907,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.9764668,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"21","issue":"3","first_page":"e1012153","last_page":"e1012153"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9970999956130981,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9968000054359436,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"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/antibody-repertoire","display_name":"Antibody Repertoire","score":0.7175249457359314},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.5963312387466431},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5657697319984436},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.5091003775596619},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4628064036369324},{"id":"https://openalex.org/keywords/repertoire","display_name":"Repertoire","score":0.45687049627304077},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.45093145966529846},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.3650681972503662},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3586497902870178},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24029481410980225}],"concepts":[{"id":"https://openalex.org/C2910693471","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody Repertoire","level":3,"score":0.7175249457359314},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.5963312387466431},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5657697319984436},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.5091003775596619},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4628064036369324},{"id":"https://openalex.org/C2778473898","wikidata":"https://www.wikidata.org/wiki/Q2145110","display_name":"Repertoire","level":2,"score":0.45687049627304077},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.45093145966529846},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.3650681972503662},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3586497902870178},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24029481410980225},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000517","qualifier_name":"prevention & control","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000517","qualifier_name":"prevention & control","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000517","qualifier_name":"prevention & control","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086663","descriptor_name":"COVID-19 Vaccines","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086663","descriptor_name":"COVID-19 Vaccines","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086663","descriptor_name":"COVID-19 Vaccines","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000914","descriptor_name":"Antibodies, Viral","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000914","descriptor_name":"Antibodies, Viral","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000914","descriptor_name":"Antibodies, Viral","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000918","descriptor_name":"Antibody Specificity","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000918","descriptor_name":"Antibody Specificity","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000918","descriptor_name":"Antibody Specificity","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"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":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D007252","descriptor_name":"Influenza Vaccines","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D007252","descriptor_name":"Influenza Vaccines","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D007252","descriptor_name":"Influenza Vaccines","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D018448","descriptor_name":"Models, Immunological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018448","descriptor_name":"Models, Immunological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018448","descriptor_name":"Models, Immunological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019267","descriptor_name":"Hemagglutinin Glycoproteins, Influenza Virus","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D019267","descriptor_name":"Hemagglutinin Glycoproteins, Influenza Virus","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D019267","descriptor_name":"Hemagglutinin Glycoproteins, Influenza Virus","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1012153","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012153","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012153&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:40163503","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40163503","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:189a7a6eadab4c6bb1ea1653c5463dc7","is_oa":true,"landing_page_url":"https://doaj.org/article/189a7a6eadab4c6bb1ea1653c5463dc7","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 21, Iss 3, p e1012153 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12013870","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12013870","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1012153","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012153","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012153&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1040404194","display_name":null,"funder_award_id":"R01 GM131642","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G1358700859","display_name":null,"funder_award_id":"P50 CA121974","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4339945631","display_name":null,"funder_award_id":"R01-AI104739","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409011676.pdf"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1986240377","https://openalex.org/W2133564696","https://openalex.org/W2594817103","https://openalex.org/W2798812533","https://openalex.org/W2896457183","https://openalex.org/W2898389621","https://openalex.org/W2914054085","https://openalex.org/W2963026768","https://openalex.org/W2964308564","https://openalex.org/W3082694457","https://openalex.org/W3111174583","https://openalex.org/W3168867926","https://openalex.org/W3206187363","https://openalex.org/W3215525389","https://openalex.org/W4200635416","https://openalex.org/W4212843503","https://openalex.org/W4220757565","https://openalex.org/W4225086377","https://openalex.org/W4280625391","https://openalex.org/W4283836227","https://openalex.org/W4317717793","https://openalex.org/W4327550249","https://openalex.org/W4362664122","https://openalex.org/W4362678186","https://openalex.org/W4366823175","https://openalex.org/W4366998330","https://openalex.org/W4382138885","https://openalex.org/W4385245566","https://openalex.org/W4386758446","https://openalex.org/W4387378658","https://openalex.org/W4388020856","https://openalex.org/W4389924610","https://openalex.org/W4390649554","https://openalex.org/W4391738021","https://openalex.org/W4393950286","https://openalex.org/W4396721167","https://openalex.org/W4396787690","https://openalex.org/W4399870059","https://openalex.org/W4400086446","https://openalex.org/W4400974946","https://openalex.org/W4402701012","https://openalex.org/W4402827655","https://openalex.org/W4405104445","https://openalex.org/W6739901393","https://openalex.org/W6796581206","https://openalex.org/W6862943578"],"related_works":["https://openalex.org/W2581256546","https://openalex.org/W2053091829","https://openalex.org/W4323236833","https://openalex.org/W2780245662","https://openalex.org/W179764517","https://openalex.org/W3008570337","https://openalex.org/W1933308802","https://openalex.org/W2055685841","https://openalex.org/W2982183030","https://openalex.org/W2139318866"],"abstract_inverted_index":{"Antibodies":[0],"play":[1],"a":[2,16,45],"crucial":[3],"role":[4],"in":[5,62,155],"the":[6,111,124,135,163],"adaptive":[7],"immune":[8,20,31],"response,":[9],"with":[10],"their":[11,150],"specificity":[12,26,64,85,179],"to":[13,66,83,86,101,120,139,144,152,176],"antigens":[14,88],"being":[15],"fundamental":[17],"determinant":[18],"of":[19,24,47,113,127,165],"function.":[21],"Accurate":[22],"prediction":[23,65],"antibody-antigen":[25],"is":[27],"vital":[28],"for":[29,50],"understanding":[30],"responses,":[32],"guiding":[33],"vaccine":[34],"design,":[35],"and":[36,70,89,146],"developing":[37],"antibody-based":[38],"therapeutics.":[39],"In":[40],"this":[41],"study,":[42],"we":[43,109,133],"present":[44],"method":[46],"supervised":[48,75,118,136,166],"fine-tuning":[49,76,119,167],"antibody":[51,58,80,170],"language":[52,59,81,93,171],"models,":[53],"which":[54],"improves":[55],"on":[56,77,104,168],"pre-trained":[57,79,105,169],"model":[60,94,106,114],"embeddings":[61],"binding":[63],"SARS-CoV-2":[67,147],"spike":[68],"protein":[69],"influenza":[71,145],"hemagglutinin.":[72],"We":[73],"perform":[74],"four":[78],"models":[82,138,172],"predict":[84],"these":[87],"demonstrate":[90],"that":[91],"fine-tuned":[92,137],"classifiers":[95,102],"exhibit":[96],"enhanced":[97],"predictive":[98],"accuracy":[99],"compared":[100],"trained":[103],"embeddings.":[107],"Additionally,":[108],"investigate":[110],"change":[112],"attention":[115],"activations":[116],"after":[117],"gain":[121],"insights":[122],"into":[123],"molecular":[125],"basis":[126],"antigen":[128,178],"recognition":[129],"by":[130],"antibodies.":[131],"Furthermore,":[132],"apply":[134],"BCR":[140],"repertoire":[141,156],"data":[142],"related":[143],"vaccination,":[148],"demonstrating":[149],"ability":[151],"capture":[153],"changes":[154],"following":[157],"vaccination.":[158],"Overall,":[159],"our":[160],"study":[161],"highlights":[162],"effect":[164],"as":[173],"valuable":[174],"tools":[175],"improve":[177],"prediction.":[180]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":9}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
