{"id":"W4416711410","doi":"10.1101/2025.11.25.690604","title":"A Globally Representative Immunopeptidomics Approach to Identify Population-Wide Vaccine Candidates","year":2025,"lang":"","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"vaccines and immunoinformatics approaches","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"","keywords":"Human leukocyte antigen; Proteome; Major histocompatibility complex; Epitope; Antigen; Population; Reverse vaccinology; MHC class I","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001376835,0.000720975,0.0008654675,0.001256364,0.0003249417,0.000733491,0.0005492208,0.0004660142,0.001912866],"category_scores_gemma":[0.001394307,0.0002719933,0.0007190203,0.0008461298,0.0001850344,0.0003712722,0.000827063,0.0005555591,0.0007185729],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003603284,"about_ca_system_score_gemma":0.0005104566,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006625831,"about_ca_topic_score_gemma":0.001065445,"domain_scores_codex":[0.999544,0.0001304066,0.00002197788,0.0001878735,0.00008409798,0.00003173732],"domain_scores_gemma":[0.999496,0.0001645475,0.00009500943,0.00007814964,0.0001208292,0.00004555508],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.001854675,0.0007343047,0.130169,0.0009014804,0.001560659,0.001231528,0.0003767805,0.1217371,0.5389395,0.005297744,0.01192951,0.1852677],"study_design_scores_gemma":[0.0003075266,0.001683778,0.1110397,0.00009522653,0.0009291355,0.001466002,0.0005407023,0.71124,0.1238552,0.01301013,0.03568674,0.0001458006],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6440086,0.001082384,0.3340879,0.0004719787,0.0001024176,0.0004845473,0.01157307,0.00328141,0.004907649],"genre_scores_gemma":[0.7901021,0.0004139617,0.193102,0.0004107768,0.00005593367,0.0004714831,0.0138507,0.0003363117,0.001256685],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001912866,"threshold_uncertainty_score":0.007281482,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01080982220513681,"score_gpt":0.25192925850033,"score_spread":0.2411194362951932,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}