{"id":"W2097126893","doi":"10.1371/journal.pcbi.1000225","title":"Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag","year":2008,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":133,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; AIDS Vancouver","funders":"National Institute of Allergy and Infectious Diseases; Microsoft Research","keywords":"Biology; Phylogenetic tree; Human leukocyte antigen; Genetics; Clade; Phylogenetics; Population; Evolutionary biology; HLA-B Antigens; Gene; Antigen; Demography","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":true,"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":[0.001439583,0.0005403934,0.0004516099,0.002619472,0.000536906,0.0006225316,0.0006053313,0.0007438233,0.0007668779],"category_scores_gemma":[0.009406319,0.0004160489,0.0007465691,0.001732626,0.0003561947,0.0006199214,0.000622044,0.0008223138,0.0001757667],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008907698,"about_ca_system_score_gemma":0.0007829271,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01869494,"about_ca_topic_score_gemma":0.02544426,"domain_scores_codex":[0.9993094,0.0003336136,0.00004672287,0.0001881119,0.0000604353,0.00006179824],"domain_scores_gemma":[0.9930466,0.005510241,0.0006891458,0.0003373054,0.0002202869,0.0001965309],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0003877155,0.0001956706,0.6001569,0.0001752132,0.0006380918,0.0005398821,0.0002479855,0.3491129,0.003692582,0.002330964,0.003124525,0.03939751],"study_design_scores_gemma":[0.0000220386,0.00004576989,0.07139657,0.00002055334,0.00009275968,0.0002554028,0.00009745024,0.9200002,0.000529527,0.006416158,0.001106059,0.00001752505],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9491937,0.0007690653,0.04329463,0.000464878,0.00001571626,0.0000487385,0.005311449,0.0002718778,0.0006299606],"genre_scores_gemma":[0.9789958,0.0002752475,0.01433504,0.00007090661,0.00002426713,0.00004661442,0.006019402,0.00002546571,0.0002071919],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01869494,"threshold_uncertainty_score":0.03717226,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02306839420498573,"score_gpt":0.2491205790529895,"score_spread":0.2260521848480038,"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."}}