{"id":"W2295400169","doi":"10.1371/journal.pone.0148459","title":"Assessment of Overlap of Phylogenetic Transmission Clusters and Communities in Simple Sexual Contact Networks: Applications to HIV-1","year":2016,"lang":"en","type":"article","venue":"PLoS ONE","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":30,"is_retracted":false,"has_abstract":true,"ca_institutions":"Douglas Mental Health University Institute; McGill University","funders":"Fonds de recherche du Québec – Nature et technologies; Fonds de Recherche du Québec - Santé; European Commission; Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; National Science Foundation","keywords":"Phylogenetic tree; Transmission (telecommunications); Weighting; Phylogenetics; Population; Cluster (spacecraft); Biology; Contact tracing; Evolutionary biology; Demography; Geography; Computer science; Medicine; Genetics; Disease; Infectious disease (medical specialty); Coronavirus disease 2019 (COVID-19)","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":[],"consensus_categories":[],"category_scores_codex":[0.003196103,0.0003392766,0.0003678835,0.002360443,0.0007438383,0.0008518095,0.0006148744,0.0007198876,0.001041977],"category_scores_gemma":[0.0221076,0.0002148324,0.0004320191,0.001404675,0.0009864278,0.001249509,0.001254248,0.0005860754,0.00006025036],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009381442,"about_ca_system_score_gemma":0.0004452908,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003902143,"about_ca_topic_score_gemma":0.003255798,"domain_scores_codex":[0.9990762,0.0005866847,0.00003441741,0.0001557269,0.00009968148,0.00004717191],"domain_scores_gemma":[0.9765264,0.0196429,0.001996013,0.0006604023,0.0006787055,0.0004956007],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"observational","study_design_scores_codex":[0.0008277211,0.0004338789,0.3233536,0.0004902745,0.0004410676,0.0003901257,0.001897302,0.6049544,0.004837652,0.01216965,0.0009839415,0.04922024],"study_design_scores_gemma":[0.00002497434,0.0001837548,0.04938146,0.00003066557,0.00004758349,0.0001937296,0.0004332626,0.9392378,0.0008714486,0.00929175,0.0002825701,0.00002100356],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9831876,0.0002571314,0.01555732,0.0001191105,0.0000059598,0.00005911669,0.0001446179,0.0000611392,0.0006078915],"genre_scores_gemma":[0.9871883,0.0000622955,0.01248119,0.00001069071,0.000004970656,0.00003679268,0.0001275092,0.000007244673,0.00008104413],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003902143,"threshold_uncertainty_score":0.0169028,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03481245286516955,"score_gpt":0.2837689042138847,"score_spread":0.2489564513487152,"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."}}