{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0007703229,0.000511736,0.0003954653,0.001357593,0.0001842308,0.0007360945,0.0002079739,0.0004331923,0.0006360275],"category_scores_gemma":[0.001905681,0.0001580106,0.0004026555,0.001035153,0.0002660387,0.0003674272,0.0004647078,0.0003183751,0.0007115707],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001255274,"about_ca_system_score_gemma":0.0002263631,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009747382,"about_ca_topic_score_gemma":0.00145815,"domain_scores_codex":[0.9992803,0.0001997555,0.00006917878,0.0001783709,0.0002116987,0.00006074295],"domain_scores_gemma":[0.9992397,0.0002486093,0.0001934637,0.0001263333,0.0001435686,0.00004835432],"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":[0.0002831396,0.0001049245,0.07137018,0.0001910478,0.00009396616,0.0003274898,0.0002564526,0.0005470457,0.8780188,0.0001989876,0.0005303411,0.0480777],"study_design_scores_gemma":[0.00001552419,0.0005862483,0.4407922,0.0001319417,0.0002337323,0.004167784,0.0008220397,0.01251587,0.5267317,0.001061374,0.01289568,0.00004599496],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9158972,0.002129218,0.06986108,0.0002963134,0.0000705692,0.0001941585,0.007392712,0.0004145676,0.003744217],"genre_scores_gemma":[0.9079079,0.001762214,0.078847,0.0002849432,0.00003728459,0.0001083031,0.009016619,0.0001086503,0.001927192],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001357593,"threshold_uncertainty_score":0.004073858,"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."}}