{"id":"W3003389116","doi":"10.3390/microorganisms8020196","title":"Evaluation of A Phylogenetic Pipeline to Examine Transmission Networks in A Canadian HIV Cohort","year":2020,"lang":"en","type":"article","venue":"Microorganisms","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"Alberta Health Services; Alberta Children's Hospital; University of Calgary","funders":"Natural Sciences and Engineering Research Council of Canada; Cumming School of Medicine, University of Calgary; Alberta Children's Hospital Research Institute; Canada Foundation for Innovation","keywords":"Transmission (telecommunications); Sanger sequencing; Inference; Confidence interval; Population; Phylogenetic tree; Biology; Pipeline (software); Medicine; Data mining; Genetics; Computer science; Computational biology; Artificial intelligence; DNA sequencing; Internal medicine; Gene","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0005624471,0.0001156729,0.0002048378,0.0001196334,0.00004622927,0.000005062543,0.0001410887,0.0001229453,0.001824572],"category_scores_gemma":[0.00007982806,0.0001044283,0.00003213077,0.0003001914,0.00003874043,0.00001526921,0.00002314771,0.0001328904,0.0006724977],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001662983,"about_ca_system_score_gemma":0.0004160126,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.02087532,"about_ca_topic_score_gemma":0.03822146,"domain_scores_codex":[0.9987944,0.0002547061,0.0002243014,0.000251928,0.00007802884,0.0003966076],"domain_scores_gemma":[0.999526,0.00002452313,0.00002654247,0.0001379822,0.0001261656,0.0001587993],"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":[0.00006825821,0.00008365091,0.01878232,0.000007547128,0.00006629082,0.00001224224,0.0008542461,0.0007868626,0.9436191,0.000004323949,0.004170003,0.03154515],"study_design_scores_gemma":[0.005626017,0.0007196667,0.1769318,0.00005199474,0.0002105324,0.00002353618,0.000144664,0.001523082,0.7693539,0.00002364379,0.04508367,0.00030756],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9889061,0.003683843,0.002789569,0.0028162,0.00005690132,0.001004147,0.00009835242,0.00001724932,0.0006276572],"genre_scores_gemma":[0.9988087,0.0000382249,0.0001920012,0.0003844087,0.00001682118,0.00003411544,0.0003174499,0.00001446798,0.0001938509],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1742652,"threshold_uncertainty_score":0.9990879,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02171902782923727,"score_gpt":0.2591051584789282,"score_spread":0.2373861306496909,"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."}}