{"id":"W2969312328","doi":"10.1101/733642","title":"Genomic variant identification methods alter <i>Mycobacterium tuberculosis</i> transmission inference","year":2019,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Mycobacterium research and diagnosis","field":"Medicine","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"National Institutes of Health","keywords":"Inference; Transmission (telecommunications); Identification (biology); Biology; Phylogenetic tree; Outbreak; Computational biology; Genome; Mycobacterium tuberculosis; Genomics; Genetics; Variation (astronomy); Tuberculosis; Evolutionary biology; Computer science; Artificial intelligence; Virology; Gene; Medicine","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":[0.008893919,0.0006972758,0.000661408,0.001376338,0.0007504577,0.002282059,0.001092128,0.001028638,0.001310776],"category_scores_gemma":[0.0321662,0.0003299979,0.001057283,0.001219636,0.0008766171,0.001011045,0.001029158,0.002121858,0.0004608998],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007871538,"about_ca_system_score_gemma":0.0009014708,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002908628,"about_ca_topic_score_gemma":0.003055332,"domain_scores_codex":[0.994789,0.002771978,0.0003032635,0.00121975,0.0007175141,0.0001985636],"domain_scores_gemma":[0.9767074,0.01713454,0.001811711,0.002620224,0.001463017,0.0002631141],"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":[0.001608321,0.0004030447,0.2484306,0.0008687702,0.002319511,0.0006379207,0.0009676898,0.1666781,0.1734811,0.02494054,0.00561027,0.3740541],"study_design_scores_gemma":[0.00009749262,0.0002779537,0.06909258,0.0001929388,0.0006450419,0.0009083251,0.0003411694,0.7654868,0.1119993,0.04397565,0.006826633,0.000156107],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.3698644,0.001260544,0.6215978,0.0007323237,0.0002015375,0.0001055212,0.001116754,0.002454983,0.002666114],"genre_scores_gemma":[0.7559818,0.0002206593,0.2411133,0.0003592906,0.00008120204,0.00005600753,0.00122128,0.0004504537,0.0005159501],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.008893919,"threshold_uncertainty_score":0.04703611,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02244057670927318,"score_gpt":0.301367457780427,"score_spread":0.2789268810711538,"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."}}