{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":["metaresearch"],"consensus_categories":[],"category_scores_codex":[0.2057544,0.001561929,0.001501945,0.002850728,0.001503509,0.002717454,0.001973712,0.002497404,0.004958988],"category_scores_gemma":[0.4061285,0.0006776926,0.003390858,0.001707321,0.003608743,0.004164227,0.0059443,0.004497669,0.0003539859],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001805776,"about_ca_system_score_gemma":0.002635193,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003321883,"about_ca_topic_score_gemma":0.002731963,"domain_scores_codex":[0.7721803,0.2148278,0.002417534,0.005186719,0.00457499,0.0008125891],"domain_scores_gemma":[0.4822365,0.4858204,0.006371305,0.01594408,0.008239607,0.00138814],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.01124326,0.001116214,0.1081894,0.005227111,0.01380396,0.0005655352,0.01092736,0.2091283,0.002649514,0.1997473,0.00806133,0.4293407],"study_design_scores_gemma":[0.001531158,0.006872018,0.0580144,0.002976475,0.00279925,0.0009926953,0.002888852,0.6401857,0.003216858,0.2518636,0.02830551,0.0003534673],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.3795643,0.01848882,0.578006,0.006619164,0.0005776777,0.001469217,0.001039584,0.0008668781,0.01336835],"genre_scores_gemma":[0.7572394,0.002484904,0.2346078,0.00144822,0.0002013104,0.001458848,0.0007565626,0.0005963264,0.001206598],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.2057544,"threshold_uncertainty_score":0.9794462,"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."}}