{"id":"W2897710284","doi":"10.1099/mgen.0.000217","title":"Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission","year":2018,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":31,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Centre for Disease Control; University of British Columbia","funders":"National Institute of Allergy and Infectious Diseases; Canadian Institutes of Health Research","keywords":"Mycobacterium tuberculosis; Concordance; Transmission (telecommunications); Biology; Genetic diversity; Outbreak; Phylogenetic tree; Genetics; Tuberculosis; False positive paradox; Single-nucleotide polymorphism; Evolutionary biology; Whole genome sequencing; Genome; Computational biology; Genotype; Virology; Medicine; Computer science; Population; Gene; Artificial intelligence; Environmental health","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":[],"consensus_categories":[],"category_scores_codex":[0.0004569386,0.0001190664,0.0003636514,0.00006832527,0.0002795393,0.000005942614,0.0000977333,0.0001452897,0.0001017735],"category_scores_gemma":[0.0001850051,0.00009928569,0.00009278225,0.00007391107,0.0002345653,0.00005315954,0.0002338946,0.0001147801,0.00000824367],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004065063,"about_ca_system_score_gemma":0.00008820651,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002334302,"about_ca_topic_score_gemma":0.00008162016,"domain_scores_codex":[0.9990605,0.00006116945,0.0002731024,0.0002660142,0.00006816938,0.0002711182],"domain_scores_gemma":[0.9992782,0.0001006457,0.000071268,0.000148191,0.0002229982,0.0001787216],"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":[0.001585042,0.0001028751,0.04893874,0.0003243135,0.0001127962,0.000001251942,0.002032968,3.461008e-7,0.9421121,0.00008215775,0.001518104,0.003189248],"study_design_scores_gemma":[0.003163846,0.002228671,0.3968528,0.0001315498,0.0002802495,0.00005475723,0.000229767,0.002346421,0.5527814,0.0002954646,0.04131708,0.0003179889],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9972806,0.0002767394,0.000448003,0.001088041,0.0001284621,0.0004295546,0.0001216114,0.00001600785,0.0002109959],"genre_scores_gemma":[0.9970582,0.000390943,0.001781198,0.0004708862,0.0001715813,0.000003410451,0.0000307021,0.000009446509,0.00008365082],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3893307,"threshold_uncertainty_score":0.4048753,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04422785186587053,"score_gpt":0.3003772448659613,"score_spread":0.2561493930000908,"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."}}