{"id":"W4214521759","doi":"10.1093/bioinformatics/btac134","title":"HAMdetector: a Bayesian regression model that integrates information to detect HLA-associated mutations","year":2022,"lang":"en","type":"article","venue":"Bioinformatics","topic":"vaccines and immunoinformatics approaches","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"AIDS Vancouver; Simon Fraser University","funders":"Canadian Institutes of Health Research; Deutsche Forschungsgemeinschaft; Michael Smith Health Research BC","keywords":"Human leukocyte antigen; Major histocompatibility complex; CTL*; Computational biology; Biology; Epitope; Bayesian probability; Bayes' theorem; Population; Bayesian inference; Computer science; Genetics; CD8; Artificial intelligence; Immune system; Antigen","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004031252,0.0002532057,0.0002040771,0.0002169166,0.0005324138,0.000135573,0.000406918,0.0001158231,0.00004178258],"category_scores_gemma":[0.0002093507,0.0002219699,0.0001378289,0.0003257357,0.00002460111,0.00008128565,0.0004567569,0.0002095589,0.00003872534],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001067351,"about_ca_system_score_gemma":0.0001585993,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001649995,"about_ca_topic_score_gemma":0.00001585839,"domain_scores_codex":[0.9984765,0.00003880843,0.0006456928,0.0001206797,0.0003603382,0.0003580042],"domain_scores_gemma":[0.9989272,0.00001492574,0.0003636624,0.0004463509,0.0001189397,0.0001288612],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001422963,0.0005940914,0.00287092,0.0007685295,0.00105639,0.000004382631,0.04671213,0.4210268,0.06477216,0.001342666,0.2075655,0.2518634],"study_design_scores_gemma":[0.001430616,0.0009378948,0.0005128019,0.00004471416,0.00005907825,0.00004490657,0.009488048,0.9113364,0.03022154,0.0003687864,0.04475311,0.0008020755],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6530185,0.0002161801,0.3343225,0.0006224955,0.0005704517,0.001711996,0.0007313528,0.0002128544,0.008593654],"genre_scores_gemma":[0.9694584,0.00003249315,0.02714255,0.001066765,0.0000257884,0.0002057522,0.001643941,0.00002502419,0.000399282],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4903096,"threshold_uncertainty_score":0.9051669,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01617440677839255,"score_gpt":0.2369433670564221,"score_spread":0.2207689602780296,"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."}}