{"id":"W4320731536","doi":"10.1016/j.ygeno.2023.110580","title":"Identification of bacterial and fungal pathogens directly from clinical blood cultures using whole genome sequencing","year":2023,"lang":"en","type":"article","venue":"Genomics","topic":"Bacterial Identification and Susceptibility Testing","field":"Biochemistry, Genetics and Molecular Biology","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"Health Sciences Centre; Manitoba Health; Public Health Agency of Canada","funders":"","keywords":"Biology; Multilocus sequence typing; Whole genome sequencing; Blood culture; Typing; Antimicrobial; Microbiology; Genome; Pathogen; Genotype; Gene; Genetics; Antibiotics","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":[0.0005308842,0.0001014462,0.0001624072,0.00003455619,0.00009262585,0.0000602648,0.0001233502,0.00014838,0.00001162413],"category_scores_gemma":[0.0002644511,0.0001098975,0.00007302215,0.00008498805,0.000079293,0.000006729603,0.0001279306,0.00005996116,0.00001057711],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001608629,"about_ca_system_score_gemma":0.00008358411,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004368,"about_ca_topic_score_gemma":0.00003771291,"domain_scores_codex":[0.9988031,0.0001058388,0.0005080946,0.0003726205,0.00006507502,0.0001453001],"domain_scores_gemma":[0.9992985,0.00002606754,0.0002118824,0.000310735,0.00009021202,0.00006259823],"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":[0.00002548408,0.00001886733,0.004677808,0.00001160858,0.00004269719,0.000001320035,0.0002153849,0.0000431784,0.9943773,0.00000560208,0.00002479596,0.000555978],"study_design_scores_gemma":[0.0007570497,0.00008832208,0.1358686,0.00001415578,0.0001483135,0.0000135542,0.0005872622,0.00133338,0.8572962,0.0001776708,0.003385088,0.0003303592],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9986565,0.0001340508,0.0002021942,0.00002198418,0.0004002694,0.0001264471,0.000418512,0.00002444854,0.0000155685],"genre_scores_gemma":[0.9967883,0.0001558851,0.001367738,0.00002357993,0.0005729898,0.000003356581,0.0009600294,0.0000187732,0.0001093259],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.137081,"threshold_uncertainty_score":0.4481491,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04119061093126097,"score_gpt":0.305284747210407,"score_spread":0.2640941362791461,"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."}}