{"id":"https://openalex.org/W4412454114","doi":"https://doi.org/10.1093/bioinformatics/btaf224","title":"Iterative attack-and-defend framework for improving TCR-epitope binding prediction models","display_name":"Iterative attack-and-defend framework for improving TCR-epitope binding prediction models","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4412454114","doi":"https://doi.org/10.1093/bioinformatics/btaf224","pmid":"https://pubmed.ncbi.nlm.nih.gov/40662786"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf224","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf224","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i429/63745339/btaf224.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/article-pdf/41/Supplement_1/i429/63745339/btaf224.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100426076","display_name":"Pengfei Zhang","orcid":"https://orcid.org/0000-0001-6395-5750"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Pengfei Zhang","raw_affiliation_strings":["Biodesign Institute, Arizona State University , Tempe, AZ 85281,","School of Computing and Augmented Intelligence, Arizona State University , Tempe, AZ 85281,"],"affiliations":[{"raw_affiliation_string":"Biodesign Institute, Arizona State University , Tempe, AZ 85281,","institution_ids":["https://openalex.org/I55732556"]},{"raw_affiliation_string":"School of Computing and Augmented Intelligence, Arizona State University , Tempe, AZ 85281,","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101245158","display_name":"Hao Mei","orcid":"https://orcid.org/0000-0002-4287-6794"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hao Mei","raw_affiliation_strings":["Biodesign Institute, Arizona State University , Tempe, AZ 85281,","School of Computing and Augmented Intelligence, Arizona State University , Tempe, AZ 85281,"],"affiliations":[{"raw_affiliation_string":"Biodesign Institute, Arizona State University , Tempe, AZ 85281,","institution_ids":["https://openalex.org/I55732556"]},{"raw_affiliation_string":"School of Computing and Augmented Intelligence, Arizona State University , Tempe, AZ 85281,","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007286575","display_name":"Seojin Bang","orcid":"https://orcid.org/0000-0003-2521-5051"},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Seojin Bang","raw_affiliation_strings":["Google DeepMind , Mountain View, CA 94043,"],"affiliations":[{"raw_affiliation_string":"Google DeepMind , Mountain View, CA 94043,","institution_ids":["https://openalex.org/I1291425158"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017723224","display_name":"Heewook Lee","orcid":"https://orcid.org/0000-0002-3528-6833"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Heewook Lee","raw_affiliation_strings":["Biodesign Institute, Arizona State University , Tempe, AZ 85281,","School of Computing and Augmented Intelligence, Arizona State University , Tempe, AZ 85281,"],"affiliations":[{"raw_affiliation_string":"Biodesign Institute, Arizona State University , Tempe, AZ 85281,","institution_ids":["https://openalex.org/I55732556"]},{"raw_affiliation_string":"School of Computing and Augmented Intelligence, Arizona State University , Tempe, AZ 85281,","institution_ids":["https://openalex.org/I55732556"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100426076"],"corresponding_institution_ids":["https://openalex.org/I55732556"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1581564,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"Supplement_1","first_page":"i429","last_page":"i438"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9979000091552734,"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":0.9979000091552734,"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/T11491","display_name":"CAR-T cell therapy research","score":0.9621000289916992,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11515","display_name":"Bacillus and Francisella bacterial research","score":0.9537000060081482,"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/computer-science","display_name":"Computer science","score":0.7603466510772705},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.738318920135498},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.6962018013000488},{"id":"https://openalex.org/keywords/shuffling","display_name":"Shuffling","score":0.5725885629653931},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5374562740325928},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5223842263221741},{"id":"https://openalex.org/keywords/adversarial-system","display_name":"Adversarial system","score":0.4844255745410919},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.45574402809143066},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.41769081354141235},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38798990845680237}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7603466510772705},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.738318920135498},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.6962018013000488},{"id":"https://openalex.org/C167927819","wikidata":"https://www.wikidata.org/wiki/Q1930567","display_name":"Shuffling","level":2,"score":0.5725885629653931},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5374562740325928},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5223842263221741},{"id":"https://openalex.org/C37736160","wikidata":"https://www.wikidata.org/wiki/Q1801315","display_name":"Adversarial system","level":2,"score":0.4844255745410919},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.45574402809143066},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.41769081354141235},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38798990845680237},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"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":"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":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf224","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf224","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i429/63745339/btaf224.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40662786","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40662786","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12261473","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12261473","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf224","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf224","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i429/63745339/btaf224.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7603313493","display_name":null,"funder_award_id":"R35GM155417","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4412454114.pdf"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1987971958","https://openalex.org/W2028671215","https://openalex.org/W2141312574","https://openalex.org/W2143210482","https://openalex.org/W2143247312","https://openalex.org/W2613978126","https://openalex.org/W2671261300","https://openalex.org/W2752126733","https://openalex.org/W2797967938","https://openalex.org/W2898389621","https://openalex.org/W3113525558","https://openalex.org/W3134285993","https://openalex.org/W3160420762","https://openalex.org/W3163602801","https://openalex.org/W3196626346","https://openalex.org/W4226278401","https://openalex.org/W4254055122","https://openalex.org/W4286631898","https://openalex.org/W4287674181","https://openalex.org/W4309674289","https://openalex.org/W4310949661","https://openalex.org/W4319455163","https://openalex.org/W4319461881","https://openalex.org/W4320013936","https://openalex.org/W4321392130","https://openalex.org/W4323320132","https://openalex.org/W4366091687","https://openalex.org/W4387378658","https://openalex.org/W4401983458","https://openalex.org/W6739585900","https://openalex.org/W6782465632","https://openalex.org/W6810738896"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W4213239787","https://openalex.org/W2619091065","https://openalex.org/W2045745654","https://openalex.org/W2114337652","https://openalex.org/W4377131110","https://openalex.org/W4388857216","https://openalex.org/W2059640416","https://openalex.org/W1490753184"],"abstract_inverted_index":{"The":[0],"curated":[1],"dataset":[2],"and":[3],"code":[4],"are":[5],"available":[6],"at":[7],"a":[8],"public":[9],"repository":[10],"(https://github.com/Lee-CBG/BAP_Attack_n_Defend).":[11]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
