{"id":"W2998862434","doi":"10.1093/cid/ciz1247","title":"Evaluation of Phylogenetic Methods for Inferring the Direction of Human Immunodeficiency Virus (HIV) Transmission: HIV Prevention Trials Network (HPTN) 052","year":2020,"lang":"en","type":"article","venue":"Clinical Infectious Diseases","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":34,"is_retracted":false,"has_abstract":true,"ca_institutions":"HIV Legal Network","funders":"National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bill and Melinda Gates Foundation","keywords":"Transmission (telecommunications); Phylogenetic tree; Human immunodeficiency virus (HIV); Biology; Genome; Virology; Sample (material); Genetics; Computational biology; Gene; Computer science","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":[0.150603,0.001538751,0.001768465,0.003067614,0.001608627,0.001776374,0.002602309,0.002255734,0.003724698],"category_scores_gemma":[0.2225579,0.0007740323,0.002086949,0.002605166,0.0009794011,0.001634964,0.002903064,0.002337374,0.0006343122],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001493976,"about_ca_system_score_gemma":0.003435555,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002899816,"about_ca_topic_score_gemma":0.003510295,"domain_scores_codex":[0.8562078,0.1333587,0.002776762,0.003334862,0.003784114,0.0005378081],"domain_scores_gemma":[0.7263894,0.2389,0.0118989,0.01057859,0.009926108,0.002306987],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.02504322,0.001241109,0.4291207,0.003873552,0.0167491,0.0008608661,0.001602198,0.1760629,0.003479741,0.009225978,0.01914037,0.3136003],"study_design_scores_gemma":[0.00484773,0.004886077,0.05637005,0.0008742936,0.0035134,0.001777423,0.0005381463,0.9034806,0.00318608,0.009775029,0.01058294,0.0001681191],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.5437167,0.008264546,0.4102366,0.005454455,0.0009017128,0.005819545,0.01527728,0.002079403,0.008249774],"genre_scores_gemma":[0.547572,0.0008225944,0.4374148,0.0008669458,0.0001658956,0.004452964,0.007424715,0.0003786857,0.0009014939],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.150603,"threshold_uncertainty_score":0.7964743,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.2192624885677261,"score_gpt":0.5068649480760551,"score_spread":0.287602459508329,"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."}}