{"id":"W4399781072","doi":"10.1007/978-1-0716-3890-3_2","title":"Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella","year":2024,"lang":"en","type":"article","venue":"Methods in molecular biology","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":0,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Saskatchewan; Agriculture and Agri-Food Canada","funders":"","keywords":"Salmonella; Biology; Microbiology; Epidemiology; Medicine; Genetics; Bacteria; Pathology","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":[0.002780597,0.00117517,0.001162551,0.002110734,0.0007383206,0.001367776,0.0009767249,0.00166815,0.002563513],"category_scores_gemma":[0.00801492,0.0007342338,0.001616434,0.001743262,0.001907829,0.001679809,0.001918433,0.003328193,0.002388115],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007198375,"about_ca_system_score_gemma":0.0008683024,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001769161,"about_ca_topic_score_gemma":0.002031444,"domain_scores_codex":[0.9965194,0.001810989,0.0001314169,0.0004372888,0.0009256834,0.0001752716],"domain_scores_gemma":[0.9951433,0.003000354,0.00025545,0.0007762943,0.0006573591,0.0001673096],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0005089621,0.000480274,0.005318195,0.004029671,0.0002947577,0.0005479093,0.001580932,0.009257479,0.3081008,0.1466633,0.02010911,0.5031086],"study_design_scores_gemma":[0.0002114332,0.0007955837,0.006578905,0.001140801,0.0002675756,0.003497852,0.001090055,0.03796151,0.2390783,0.3699856,0.3390258,0.0003664797],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.00649822,0.02306167,0.9624167,0.001867139,0.000578415,0.0001350635,0.000311825,0.0007040851,0.004426952],"genre_scores_gemma":[0.05710223,0.01857717,0.9132285,0.000842629,0.0003164841,0.000334274,0.0004984747,0.0003462021,0.008754108],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.002780597,"threshold_uncertainty_score":0.01470542,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1049480939182559,"score_gpt":0.4336812188802445,"score_spread":0.3287331249619886,"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."}}