{"id":"https://openalex.org/W4414934123","doi":"https://doi.org/10.1093/bib/bbaf522","title":"GRAPE: graph-regularized protein language modeling unlocks TCR-epitope binding specificity","display_name":"GRAPE: graph-regularized protein language modeling unlocks TCR-epitope binding specificity","publication_year":2025,"publication_date":"2025-08-31","ids":{"openalex":"https://openalex.org/W4414934123","doi":"https://doi.org/10.1093/bib/bbaf522","pmid":"https://pubmed.ncbi.nlm.nih.gov/41052278"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf522","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf522","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf522/64521535/bbaf522.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf522/64521535/bbaf522.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044283271","display_name":"Xiangzheng Fu","orcid":"https://orcid.org/0000-0001-6840-2573"},"institutions":[{"id":"https://openalex.org/I119273862","display_name":"Central South University of Forestry and Technology","ror":"https://ror.org/02czw2k81","country_code":"CN","type":"education","lineage":["https://openalex.org/I119273862"]},{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]},{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Xiangzheng Fu","raw_affiliation_strings":["Institute of Artificial Intelligence Application , College of Computer and Information Engineering, Central South University of Forestry and Technology, No. 498 Shaoshan South Road, Tianxin District, Changsha, Hunan 410004,","School of Chinese Medicine , Hong Kong Baptist University, 15 Baptist University Road, Kowloon Tong, Kowloon, Hong Kong SAR 999077,","Institute of Artificial Intelligence Application, College of Computer and Information Engineering, Central South University of Forestry and Technology, No. 498 Shaoshan South Road, Tianxin District, Changsha, Hunan 410004, China","School of Chinese Medicine, Hong Kong Baptist University, 15 Baptist University Road, Kowloon Tong, Kowloon, Hong Kong SAR 999077, China"],"raw_orcid":"https://orcid.org/0000-0001-6840-2573","affiliations":[{"raw_affiliation_string":"Institute of Artificial Intelligence Application , College of Computer and Information Engineering, Central South University of Forestry and Technology, No. 498 Shaoshan South Road, Tianxin District, Changsha, Hunan 410004,","institution_ids":["https://openalex.org/I119273862"]},{"raw_affiliation_string":"School of Chinese Medicine , Hong Kong Baptist University, 15 Baptist University Road, Kowloon Tong, Kowloon, Hong Kong SAR 999077,","institution_ids":["https://openalex.org/I141568987"]},{"raw_affiliation_string":"Institute of Artificial Intelligence Application, College of Computer and Information Engineering, Central South University of Forestry and Technology, No. 498 Shaoshan South Road, Tianxin District, Changsha, Hunan 410004, China","institution_ids":["https://openalex.org/I119273862","https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Chinese Medicine, Hong Kong Baptist University, 15 Baptist University Road, Kowloon Tong, Kowloon, Hong Kong SAR 999077, China","institution_ids":["https://openalex.org/I141568987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100432712","display_name":"Peng Li","orcid":"https://orcid.org/0000-0002-5078-5091"},"institutions":[{"id":"https://openalex.org/I121296143","display_name":"Hunan University of Science and Technology","ror":"https://ror.org/02m9vrb24","country_code":"CN","type":"education","lineage":["https://openalex.org/I121296143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li Peng","raw_affiliation_strings":["College of Computer Science and Engineering , Hunan University of Science and Technology, No. 1 Taoyuan Road, Yuhu District, Xiangtan, Hunan 411201,","College of Computer Science and Engineering, Hunan University of Science and Technology, No. 1 Taoyuan Road, Yuhu District, Xiangtan, Hunan 411201, China"],"raw_orcid":"https://orcid.org/0000-0002-5078-5091","affiliations":[{"raw_affiliation_string":"College of Computer Science and Engineering , Hunan University of Science and Technology, No. 1 Taoyuan Road, Yuhu District, Xiangtan, Hunan 411201,","institution_ids":["https://openalex.org/I121296143"]},{"raw_affiliation_string":"College of Computer Science and Engineering, Hunan University of Science and Technology, No. 1 Taoyuan Road, Yuhu District, Xiangtan, Hunan 411201, China","institution_ids":["https://openalex.org/I121296143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101527359","display_name":"Haowen Chen","orcid":"https://orcid.org/0000-0002-4777-7525"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]},{"id":"https://openalex.org/I48168531","display_name":"South University","ror":"https://ror.org/01rjfjt94","country_code":"US","type":"education","lineage":["https://openalex.org/I48168531"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Haowen Chen","raw_affiliation_strings":["College of Science and Electronic Engineering , Hunan University, 2 Lushan South Road, Yuelu District, Changsha, Hunan 410082,","College of Science and Electronic Engineering, Hunan University, 2 Lushan South Road, Yuelu District, Changsha, Hunan 410082, China"],"raw_orcid":"https://orcid.org/0000-0002-4777-7525","affiliations":[{"raw_affiliation_string":"College of Science and Electronic Engineering , Hunan University, 2 Lushan South Road, Yuelu District, Changsha, Hunan 410082,","institution_ids":["https://openalex.org/I16609230","https://openalex.org/I48168531"]},{"raw_affiliation_string":"College of Science and Electronic Engineering, Hunan University, 2 Lushan South Road, Yuelu District, Changsha, Hunan 410082, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073600439","display_name":"Mingqiang Rong","orcid":"https://orcid.org/0000-0002-4865-1035"},"institutions":[{"id":"https://openalex.org/I173759888","display_name":"Hunan Normal University","ror":"https://ror.org/053w1zy07","country_code":"CN","type":"education","lineage":["https://openalex.org/I173759888"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingqiang Rong","raw_affiliation_strings":["The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development , College of Life Sciences, Hunan Normal University, 36 Lushan Road, Yuelu District, Changsha, Hunan 410081,","The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, 36 Lushan Road, Yuelu District, Changsha, Hunan 410081, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development , College of Life Sciences, Hunan Normal University, 36 Lushan Road, Yuelu District, Changsha, Hunan 410081,","institution_ids":["https://openalex.org/I173759888"]},{"raw_affiliation_string":"The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, 36 Lushan Road, Yuelu District, Changsha, Hunan 410081, China","institution_ids":["https://openalex.org/I173759888"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100405157","display_name":"Yifan Chen","orcid":"https://orcid.org/0000-0003-4880-3489"},"institutions":[{"id":"https://openalex.org/I119273862","display_name":"Central South University of Forestry and Technology","ror":"https://ror.org/02czw2k81","country_code":"CN","type":"education","lineage":["https://openalex.org/I119273862"]},{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]},{"id":"https://openalex.org/I165911609","display_name":"Changsha Medical University","ror":"https://ror.org/05dt7z971","country_code":"CN","type":"education","lineage":["https://openalex.org/I165911609"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yifan Chen","raw_affiliation_strings":["Institute of Artificial Intelligence Application , College of Computer and Information Engineering, Central South University of Forestry and Technology, No. 498 Shaoshan South Road, Tianxin District, Changsha, Hunan 410004,","School of Information Engineering , Changsha Medical University, No. 1501 Leifeng Road, Wangcheng District, Changsha, 410219,","Institute of Artificial Intelligence Application, College of Computer and Information Engineering, Central South University of Forestry and Technology, No. 498 Shaoshan South Road, Tianxin District, Changsha, Hunan 410004, China","School of Information Engineering, Changsha Medical University, No. 1501 Leifeng Road, Wangcheng District, Changsha, 410219, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Artificial Intelligence Application , College of Computer and Information Engineering, Central South University of Forestry and Technology, No. 498 Shaoshan South Road, Tianxin District, Changsha, Hunan 410004,","institution_ids":["https://openalex.org/I119273862"]},{"raw_affiliation_string":"School of Information Engineering , Changsha Medical University, No. 1501 Leifeng Road, Wangcheng District, Changsha, 410219,","institution_ids":["https://openalex.org/I165911609"]},{"raw_affiliation_string":"Institute of Artificial Intelligence Application, College of Computer and Information Engineering, Central South University of Forestry and Technology, No. 498 Shaoshan South Road, Tianxin District, Changsha, Hunan 410004, China","institution_ids":["https://openalex.org/I119273862","https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Information Engineering, Changsha Medical University, No. 1501 Leifeng Road, Wangcheng District, Changsha, 410219, China","institution_ids":["https://openalex.org/I165911609"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083809384","display_name":"Dongsheng Cao","orcid":"https://orcid.org/0000-0003-3604-3785"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dongsheng Cao","raw_affiliation_strings":["Xiangya School of Pharmaceutical Sciences , Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410003,","Xiangya School of Pharmaceutical Sciences, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410003, China"],"raw_orcid":"https://orcid.org/0000-0003-3604-3785","affiliations":[{"raw_affiliation_string":"Xiangya School of Pharmaceutical Sciences , Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410003,","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"Xiangya School of Pharmaceutical Sciences, Central South University, No. 172 Tongzipo Road, Yuelu District, Changsha, Hunan 410003, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069738626","display_name":"Sisi Yuan","orcid":null},"institutions":[{"id":"https://openalex.org/I102149020","display_name":"University of North Carolina at Charlotte","ror":"https://ror.org/04dawnj30","country_code":"US","type":"education","lineage":["https://openalex.org/I102149020"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sisi Yuan","raw_affiliation_strings":["Department of Bioinformatics and Genomics , The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223,","Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Genomics , The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223,","institution_ids":["https://openalex.org/I102149020"]},{"raw_affiliation_string":"Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States","institution_ids":["https://openalex.org/I102149020"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076594495","display_name":"Aiping L\u00fc","orcid":"https://orcid.org/0000-0002-2303-0494"},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Aiping Lu","raw_affiliation_strings":["School of Chinese Medicine , Hong Kong Baptist University, 15 Baptist University Road, Kowloon Tong, Kowloon, Hong Kong SAR 999077,","School of Chinese Medicine, Hong Kong Baptist University, 15 Baptist University Road, Kowloon Tong, Kowloon, Hong Kong SAR 999077, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Chinese Medicine , Hong Kong Baptist University, 15 Baptist University Road, Kowloon Tong, Kowloon, Hong Kong SAR 999077,","institution_ids":["https://openalex.org/I141568987"]},{"raw_affiliation_string":"School of Chinese Medicine, Hong Kong Baptist University, 15 Baptist University Road, Kowloon Tong, Kowloon, Hong Kong SAR 999077, China","institution_ids":["https://openalex.org/I141568987"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":9,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.9522,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.91792016,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"26","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9929999709129333,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9929999709129333,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9858999848365784,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9695000052452087,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.6448000073432922},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.512499988079071},{"id":"https://openalex.org/keywords/regularization","display_name":"Regularization (linguistics)","score":0.44679999351501465},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.39340001344680786},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.3758000135421753},{"id":"https://openalex.org/keywords/feature-vector","display_name":"Feature vector","score":0.37439998984336853},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.35589998960494995},{"id":"https://openalex.org/keywords/graphical-model","display_name":"Graphical model","score":0.3377000093460083}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7081999778747559},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.6448000073432922},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5491999983787537},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.512499988079071},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5008000135421753},{"id":"https://openalex.org/C2776135515","wikidata":"https://www.wikidata.org/wiki/Q17143721","display_name":"Regularization (linguistics)","level":2,"score":0.44679999351501465},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.39340001344680786},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.3758000135421753},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.37439998984336853},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.35589998960494995},{"id":"https://openalex.org/C155846161","wikidata":"https://www.wikidata.org/wiki/Q1143367","display_name":"Graphical model","level":2,"score":0.3377000093460083},{"id":"https://openalex.org/C202615002","wikidata":"https://www.wikidata.org/wiki/Q783507","display_name":"Differentiable function","level":2,"score":0.3328000009059906},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.3082999885082245},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.30090001225471497},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.30000001192092896},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.29350000619888306},{"id":"https://openalex.org/C854659","wikidata":"https://www.wikidata.org/wiki/Q1859284","display_name":"Message passing","level":2,"score":0.29269999265670776},{"id":"https://openalex.org/C162307627","wikidata":"https://www.wikidata.org/wiki/Q204833","display_name":"Enhanced Data Rates for GSM Evolution","level":2,"score":0.2896000146865845},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.2824999988079071},{"id":"https://openalex.org/C13251829","wikidata":"https://www.wikidata.org/wiki/Q3085841","display_name":"Dense graph","level":5,"score":0.28110000491142273},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2768999934196472},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.2563000023365021}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","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":"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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},{"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":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbaf522","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf522","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf522/64521535/bbaf522.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41052278","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41052278","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},{"id":"pmh:oai:europepmc.org:11307937","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12499766","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12499766","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12499766/","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf522","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf522","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf522/64521535/bbaf522.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1208914126","display_name":null,"funder_award_id":"62402533","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4469130931","display_name":null,"funder_award_id":"62472165","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5501021228","display_name":"\u53ef\u89e3\u91ca\u591a\u6a21\u6001\u9a71\u52a8\u7684PROTAC\u5206\u5b50\u667a\u80fd\u8bbe\u8ba1\u4e0e\u4f18\u5316\u7814\u7a76","funder_award_id":"2025JJ60400","funder_id":"https://openalex.org/F4320322843","funder_display_name":"Natural Science Foundation of\u00a0Hunan Province"},{"id":"https://openalex.org/G552737822","display_name":null,"funder_award_id":"62372158","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8051027533","display_name":null,"funder_award_id":"62572178","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322843","display_name":"Natural Science Foundation of\u00a0Hunan Province","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414934123.pdf","grobid_xml":"https://content.openalex.org/works/W4414934123.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1992208280","https://openalex.org/W2117115931","https://openalex.org/W2121626779","https://openalex.org/W2156737316","https://openalex.org/W2165160727","https://openalex.org/W2560367415","https://openalex.org/W2613978126","https://openalex.org/W2670890989","https://openalex.org/W2671261300","https://openalex.org/W2738888953","https://openalex.org/W2752126733","https://openalex.org/W2894849296","https://openalex.org/W2898389621","https://openalex.org/W2899327929","https://openalex.org/W2911644242","https://openalex.org/W2912192115","https://openalex.org/W2968803773","https://openalex.org/W2968849363","https://openalex.org/W2990308980","https://openalex.org/W3040528450","https://openalex.org/W3138156743","https://openalex.org/W3198942356","https://openalex.org/W4309908854","https://openalex.org/W4319461881","https://openalex.org/W4321851522","https://openalex.org/W4323974789","https://openalex.org/W4360999048","https://openalex.org/W4380882762","https://openalex.org/W4400655183","https://openalex.org/W4408153170","https://openalex.org/W4411544972"],"related_works":[],"abstract_inverted_index":{"T-cell":[0],"receptor":[1],"(TCR)-epitope":[2],"binding":[3,32],"prediction":[4],"is":[5],"critical":[6],"for":[7,29,135,161],"immunotherapies":[8],"but":[9],"remains":[10],"challenged":[11],"by":[12],"sparse":[13,45,107],"interaction":[14,87],"networks":[15],"and":[16,48,69,171],"severe":[17],"class":[18],"imbalance":[19,136],"in":[20,44,106,150,168],"training":[21],"data.":[22],"Current":[23],"graph":[24,67,95,120],"neural":[25],"network":[26],"(GNN)":[27],"approaches":[28],"predicting":[30],"TCR-epitope":[31,46,117,163],"(TEB)":[33],"fail":[34],"to":[35,79,102],"address":[36],"two":[37],"key":[38],"limitations:":[39],"over-smoothing":[40],"during":[41,119],"message":[42],"propagation":[43],"graphs":[47],"biased":[49],"predictions":[50],"toward":[51],"dominant":[52],"epitope-TCR":[53],"pairs.":[54],"Here,":[55],"we":[56,92],"present":[57],"GRAPE":[58,72,145,156],"(Graph-Regularized":[59],"Attentive":[60],"Protein":[61],"Embeddings),":[62],"a":[63,85,110,124,158],"framework":[64,160],"unifying":[65],"spectral":[66,94],"regularization":[68],"imbalance-aware":[70],"learning.":[71],"first":[73],"leverages":[74],"protein":[75],"language":[76],"models":[77],"(ESM-2)":[78],"generate":[80],"evolutionary-informed":[81],"TCR/epitope":[82],"embeddings,":[83],"constructing":[84],"topology-aware":[86],"graph.":[88],"To":[89],"mitigate":[90],"over-smoothing,":[91],"introduce":[93],"regularization,":[96],"explicitly":[97],"constraining":[98],"node":[99],"feature":[100],"smoothness":[101],"preserve":[103],"discriminative":[104],"patterns":[105],"neighborhoods.":[108],"Simultaneously,":[109],"dynamic":[111],"edge":[112],"reweighting":[113],"module":[114],"prioritizes":[115],"unobserved":[116],"edges":[118],"propagation,":[121],"coupled":[122],"with":[123,165],"differentiable":[125],"area":[126],"under":[127],"the":[128],"ROC":[129],"curve-maximization":[130],"objective":[131],"that":[132,144],"directly":[133],"optimizes":[134],"resilience.":[137],"Extensive":[138],"benchmarking":[139],"on":[140],"public":[141],"datasets":[142],"demonstrates":[143],"significantly":[146],"outperforms":[147],"state-of-the-art":[148],"methods":[149],"TEB":[151],"prediction.":[152],"This":[153],"work":[154],"establishes":[155],"as":[157],"robust":[159],"elucidating":[162],"interactions,":[164],"broad":[166],"applications":[167],"immunology":[169],"research":[170],"therapeutic":[172],"design.":[173]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":3}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}