{"id":"https://openalex.org/W7163532534","doi":"https://doi.org/10.48550/arxiv.2606.04994","title":"New Benchmarking Shows Limited Generalization Power of TCR Antigenic Epitope Prediction Models","display_name":"New Benchmarking Shows Limited Generalization Power of TCR Antigenic Epitope Prediction Models","publication_year":2026,"publication_date":"2026-06-03","ids":{"openalex":"https://openalex.org/W7163532534","doi":"https://doi.org/10.48550/arxiv.2606.04994"},"language":"en","primary_location":{"id":"pmh:doi:10.13016/m2miqk-usil","is_oa":false,"landing_page_url":"http://hdl.handle.net/11603/43391","pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2606.04994","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5137812253","display_name":"Yiming Liao","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liao, Yiming","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137912157","display_name":"Yiheng Li","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Yiheng","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137814779","display_name":"Ning Jiang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jiang, Ning","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137855777","display_name":"Bo Li","orcid":"https://orcid.org/0000-0003-1455-9596"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Bo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5002572745","display_name":"Keke Chen","orcid":"https://orcid.org/0000-0002-9996-156X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chen, Keke","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"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":0.829200029373169,"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":0.829200029373169,"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":0.1185000017285347,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.010700000450015068,"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/benchmarking","display_name":"Benchmarking","score":0.7383000254631042},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6741999983787537},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.6205000281333923},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.4668999910354614},{"id":"https://openalex.org/keywords/predictive-modelling","display_name":"Predictive modelling","score":0.46219998598098755},{"id":"https://openalex.org/keywords/power","display_name":"Power (physics)","score":0.41100001335144043},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.3898000121116638}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7383000254631042},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6741999983787537},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.6205000281333923},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5957000255584717},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5454999804496765},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5231999754905701},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.4668999910354614},{"id":"https://openalex.org/C45804977","wikidata":"https://www.wikidata.org/wiki/Q7239673","display_name":"Predictive modelling","level":2,"score":0.46219998598098755},{"id":"https://openalex.org/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.41100001335144043},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40070000290870667},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3898000121116638},{"id":"https://openalex.org/C2778136018","wikidata":"https://www.wikidata.org/wiki/Q10350689","display_name":"Predictive power","level":2,"score":0.3864000141620636},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.3483000099658966},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34610000252723694},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.3411000072956085},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.33869999647140503},{"id":"https://openalex.org/C2779714256","wikidata":"https://www.wikidata.org/wiki/Q25305062","display_name":"Multiple Models","level":2,"score":0.3163999915122986},{"id":"https://openalex.org/C167085575","wikidata":"https://www.wikidata.org/wiki/Q6803654","display_name":"Mean squared prediction error","level":2,"score":0.2703999876976013},{"id":"https://openalex.org/C2779304628","wikidata":"https://www.wikidata.org/wiki/Q3503480","display_name":"Face (sociological concept)","level":2,"score":0.2538999915122986}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:doi:10.13016/m2miqk-usil","is_oa":false,"landing_page_url":"http://hdl.handle.net/11603/43391","pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"doi:10.48550/arxiv.2606.04994","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.04994","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2606.04994","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.04994","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[{"score":0.4013473689556122,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Accurate":[0],"computational":[1],"prediction":[2,85],"of":[3,14,40,50,61],"T":[4,15],"cell":[5,16],"receptor":[6],"(TCR)":[7],"antigen":[8],"specificity":[9,30],"would":[10],"transform":[11],"the":[12,38],"study":[13],"biology":[17],"and":[18,29,53,67,79],"enable":[19],"scalable":[20],"immune":[21],"engineering,":[22],"yet":[23],"existing":[24],"models":[25],"lack":[26],"sufficient":[27],"sensitivity":[28],"for":[31,76,82],"broad":[32],"applications.":[33],"A":[34],"major":[35],"limitation":[36],"is":[37],"absence":[39],"rigorously":[41],"defined,":[42],"unseen":[43],"benchmark":[44],"datasets":[45,62],"that":[46,63,69],"allow":[47],"unbiased":[48],"evaluation":[49],"model":[51,77],"performance":[52],"generalizability.":[54],"Here,":[55],"we":[56],"describe":[57],"two":[58],"complementary":[59],"classes":[60],"meet":[64],"this":[65],"criterion":[66],"argue":[68],"they":[70],"provide":[71],"both":[72],"a":[73,80],"robust":[74],"framework":[75],"assessment":[78],"foundation":[81],"next-generation":[83],"TCR-antigen":[84],"algorithm":[86],"development.":[87]},"counts_by_year":[],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2026-06-05T00:00:00"}
