{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00008699215,0.0001041146,0.0002118256,0.0001479025,0.00007736041,0.000002396547,0.00007676849,0.0001385876,0.0001503249],"category_scores_gemma":[0.00004926159,0.00009450912,0.00002699809,0.0000834181,0.0001252575,0.00002925009,0.00006183142,0.0001402769,0.00008607419],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002805484,"about_ca_system_score_gemma":0.00005942002,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009706923,"about_ca_topic_score_gemma":0.00004596603,"domain_scores_codex":[0.9990467,0.0002258368,0.0002545399,0.0002159803,0.00002992539,0.0002270587],"domain_scores_gemma":[0.9993956,0.0003620941,0.00007882598,0.00007664737,0.00006566455,0.00002114755],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00009471225,0.0002420644,0.9775823,0.00001591958,0.0001435505,0.00001357249,0.0002305196,0.005418896,0.01299343,0.001339492,0.00003270581,0.001892835],"study_design_scores_gemma":[0.002077309,0.0003296892,0.9924828,0.00002567999,0.00001190387,0.00008684971,0.0000251402,0.002332929,0.001098457,0.001337037,0.00008056785,0.0001116652],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9911009,0.001480196,0.006833814,0.00009269403,0.00006149828,0.0001913024,0.00009364505,0.00001564136,0.0001302821],"genre_scores_gemma":[0.9981452,0.0002349297,0.0004433526,0.00003699557,0.00001562367,0.00002525712,0.001055261,0.000006429995,0.0000369458],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01490047,"threshold_uncertainty_score":0.385397,"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."}}