{"id":"W4307889170","doi":"10.1101/2022.10.31.514503","title":"Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination and Drug Susceptibility Prediction","year":2022,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; Centre Hospitalier de l’Université de Montréal","funders":"Australian Government","keywords":"Minion; Tuberculosis; Sputum; Multiplex; Mycobacterium tuberculosis; Drug resistance; Biology; DNA sequencing; Typing; Computational biology; Virology; Medicine; Genetics; Nanopore sequencing; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001118641,0.0003274966,0.0003521595,0.0009987929,0.0002142437,0.0007845205,0.0002758903,0.0003440967,0.001570351],"category_scores_gemma":[0.002864171,0.0001673581,0.0002528216,0.0006183485,0.0002153681,0.0001878003,0.0004251942,0.0002445992,0.0005841436],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002450366,"about_ca_system_score_gemma":0.0004484917,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001298252,"about_ca_topic_score_gemma":0.002401499,"domain_scores_codex":[0.9989591,0.0004100464,0.0001199627,0.0002138429,0.000220357,0.00007681227],"domain_scores_gemma":[0.9981828,0.0006782837,0.0003917801,0.0001748227,0.0004329152,0.0001395795],"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":[0.001379627,0.0001138867,0.3775901,0.0006075102,0.0001513229,0.0005087967,0.000375667,0.001957019,0.5307022,0.00028357,0.001170228,0.08516007],"study_design_scores_gemma":[0.00005689538,0.001329118,0.6381577,0.000338297,0.000348574,0.004186717,0.000707997,0.0176117,0.3265854,0.0008247991,0.00980182,0.00005103717],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9616629,0.00248254,0.02870495,0.0002170951,0.00004578778,0.0001912112,0.00443402,0.0003311655,0.001930288],"genre_scores_gemma":[0.9494482,0.000800653,0.04515439,0.0002410308,0.00003098356,0.00009867878,0.003497909,0.00006519476,0.0006630144],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001570351,"threshold_uncertainty_score":0.005916059,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02490415240535777,"score_gpt":0.2773159522473851,"score_spread":0.2524117998420274,"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."}}