{"id":"W2798356948","doi":"10.1073/pnas.1812548116","title":"HIV peptidome-wide association study reveals patient-specific epitope repertoires associated with HIV control","year":2019,"lang":"en","type":"article","venue":"Proceedings of the National Academy of Sciences","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":28,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Manitoba; Public Health Agency of Canada","funders":"National Institutes of Health; National Cancer Institute; Frederick National Laboratory for Cancer Research","keywords":"Human leukocyte antigen; Epitope; Biology; Genetic variation; Antigen; Proteome; Human immunodeficiency virus (HIV); Computational biology; Antigenic variation; Viral load; Genotype; Immunology; Virology; Genetics; Gene","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":[0.0004282744,0.0001868763,0.0003903796,0.0005453762,0.0002688271,0.0006852748,0.0001801894,0.000402229,0.001180208],"category_scores_gemma":[0.001250604,0.0001144079,0.0002347819,0.0007899398,0.0001961456,0.0002628842,0.0003608182,0.0005016749,0.0001523696],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009748617,"about_ca_system_score_gemma":0.00008479697,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004615093,"about_ca_topic_score_gemma":0.0005060671,"domain_scores_codex":[0.9995905,0.0001247366,0.00003182676,0.0001574018,0.00004378521,0.00005186459],"domain_scores_gemma":[0.9994249,0.0002343088,0.0001486238,0.00006755329,0.00004431314,0.00008032962],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0008380833,0.00006370498,0.9744629,0.00002170342,0.0002744553,0.0005193225,0.0001400734,0.0003515164,0.01376081,0.0001200321,0.000261301,0.009186204],"study_design_scores_gemma":[0.00001102135,0.0001045985,0.995858,0.000004100655,0.00006329774,0.001169926,0.0001326956,0.001226567,0.0009076218,0.0001332717,0.0003817129,0.000007175997],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9991649,0.0001607981,0.0002398932,0.00003049074,0.000002854965,0.00000274923,0.0001823336,0.000004569345,0.0002114211],"genre_scores_gemma":[0.9995933,0.00004256397,0.0001109538,0.00002178617,0.000003761956,0.000001910516,0.0001669285,0.000002413355,0.00005631104],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001180208,"threshold_uncertainty_score":0.003948152,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01851556894123681,"score_gpt":0.2616672796794308,"score_spread":0.2431517107381939,"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."}}