{"id":"W2056905062","doi":"10.1097/qai.0b013e3181e8c7b0","title":"Longitudinal Phylogenetic Surveillance Identifies Distinct Patterns of Cluster Dynamics","year":2010,"lang":"en","type":"article","venue":"JAIDS Journal of Acquired Immune Deficiency Syndromes","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":53,"is_retracted":false,"has_abstract":true,"ca_institutions":"Public Health Agency of Canada","funders":"","keywords":"Phylogenetic tree; Cluster (spacecraft); Biology; Population; Phylogenetics; Genotype; Molecular epidemiology; Evolutionary biology; Genetics; Demography; Gene","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001014957,0.0002386515,0.0006493095,0.0004058194,0.0001750729,0.00003703008,0.0006431396,0.0001778905,0.000414743],"category_scores_gemma":[0.0004243717,0.0001790276,0.0003332008,0.0003061399,0.0004404192,0.0001620589,0.0001595882,0.0002797156,0.0002503881],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005098,"about_ca_system_score_gemma":0.0001282467,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001414204,"about_ca_topic_score_gemma":0.0002035901,"domain_scores_codex":[0.9978755,0.0002254389,0.0009449093,0.0002329048,0.000196294,0.000525],"domain_scores_gemma":[0.9981039,0.0003861963,0.0006311618,0.0004546071,0.0003724806,0.00005161645],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0002592387,0.0005651794,0.7645046,0.0001083835,0.0004798555,0.0001387305,0.0002784908,0.00001662055,0.2274911,0.0001378216,0.0002381373,0.005781876],"study_design_scores_gemma":[0.001716723,0.0009486314,0.9758116,0.00007968579,0.00006736281,0.001991783,0.0002841091,0.00001437392,0.01860019,0.0001232971,0.0001752619,0.0001869916],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9931027,0.00406401,0.0004846175,0.0001697191,0.001683671,0.0001536065,0.0001850154,0.00001863128,0.0001379788],"genre_scores_gemma":[0.9985172,0.0002485478,0.00009696367,0.000004021991,0.00002473031,0.000005665002,0.0000699517,0.00002519188,0.001007721],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.211307,"threshold_uncertainty_score":0.7300532,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01237877262561309,"score_gpt":0.2610090829396515,"score_spread":0.2486303103140384,"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."}}