{"id":"W2528483098","doi":"10.1093/molbev/msw217","title":"Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison","year":2016,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":70,"is_retracted":false,"has_abstract":true,"ca_institutions":"Western University; AIDS Vancouver; University of British Columbia","funders":"Engineering and Physical Sciences Research Council; National Institute of Allergy and Infectious Diseases; Medical Research Council; Directorate for Biological Sciences; National Institutes of Health; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; National Institute of General Medical Sciences; National Institute for Health and Care Research; Michael Smith Health Research BC; Providence Health Care; Western Canada Research Grid; Canadian Institutes of Health Research; National Science Foundation; Compute Canada; Imperial College London; Wellcome Trust; Biotechnology and Biological Sciences Research Council; Bill and Melinda Gates Foundation","keywords":"Phylogenetic tree; Biology; Coalescent theory; Phylogenetics; Human immunodeficiency virus (HIV); Transmission (telecommunications); Viral phylodynamics; Psychological intervention; Demography; Evolutionary biology; Incidence (geometry); Virology; Genetics; Medicine; Computer science; Mathematics","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":[0.0004924618,0.0001621005,0.0002757412,0.00004255633,0.0002737496,0.00001198318,0.0001675037,0.0003016748,0.0001136182],"category_scores_gemma":[0.0004989196,0.00008727426,0.0001041909,0.00005308535,0.0003820099,0.00003571726,0.00008270506,0.000114556,0.0003007389],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005318246,"about_ca_system_score_gemma":0.00003463875,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00008512537,"about_ca_topic_score_gemma":0.00002187723,"domain_scores_codex":[0.9980961,0.0008840069,0.0002289162,0.0003622116,0.00001728475,0.0004114975],"domain_scores_gemma":[0.9985146,0.001084397,0.00006565711,0.0002545342,0.00004815841,0.00003266552],"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":[0.0002402281,0.00004024234,0.05927931,0.000003267451,0.0002885876,9.384689e-7,0.00005914061,0.000001251411,0.8967885,0.00334879,0.005312649,0.03463712],"study_design_scores_gemma":[0.009171955,0.0009051489,0.219431,0.00006093831,0.0003991354,0.00003585924,0.0001382207,0.00009574432,0.5668821,0.0335829,0.1687655,0.0005315623],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6124869,0.01821884,0.3652689,0.002796827,0.000184272,0.000410722,0.0005625664,0.00002978467,0.0000412014],"genre_scores_gemma":[0.9897291,0.0003048098,0.008171818,0.0002475087,0.00004239797,0.0001936386,0.000923728,0.00001198792,0.0003750126],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3772422,"threshold_uncertainty_score":0.3865491,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03715155121480297,"score_gpt":0.355940747861949,"score_spread":0.3187891966471461,"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."}}