{"id":"W3039881561","doi":"10.1101/2020.07.03.186726","title":"A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of <i>Neisseria gonorrhoeae</i> at Pathogenwatch","year":2020,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Reproductive tract infections research","field":"Immunology and Microbiology","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"Public Health Agency of Canada","funders":"Generalitat Valenciana; University of Oxford; Li Ka Shing Foundation","keywords":"Genomics; Public health; Genome; Antibiotic resistance; Whole genome sequencing; Imputation (statistics); Typing; Public health surveillance","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":[0.004433515,0.001990306,0.001354245,0.006678645,0.001125158,0.002724021,0.002601861,0.001872367,0.02448838],"category_scores_gemma":[0.01457415,0.0009619563,0.001516398,0.005448939,0.0005206343,0.002887903,0.006572834,0.001971649,0.02210194],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007794456,"about_ca_system_score_gemma":0.003674312,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.009478136,"about_ca_topic_score_gemma":0.01123781,"domain_scores_codex":[0.9974635,0.0005013478,0.0002495013,0.0009114088,0.0006286922,0.00024568],"domain_scores_gemma":[0.9925331,0.002083792,0.0008139673,0.001968992,0.001384786,0.001215382],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.002258347,0.0003705036,0.03924401,0.006028596,0.0006325342,0.001448166,0.001612738,0.007807303,0.02318085,0.006133998,0.7565461,0.1547369],"study_design_scores_gemma":[0.000777806,0.0004352065,0.06777426,0.002296343,0.0004850776,0.0009469077,0.0009762859,0.03651932,0.02212612,0.02090257,0.8461522,0.0006079196],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"dataset","genre_gemma":"software","genre_scores_codex":[0.01264044,0.001191555,0.03510596,0.001017945,0.0003823156,0.0006688461,0.8149244,0.1269824,0.007086136],"genre_scores_gemma":[0.03075859,0.0006950011,0.0786536,0.0005879921,0.0001389206,0.0007767541,0.8777018,0.008015079,0.002672332],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.02448838,"threshold_uncertainty_score":0.08192182,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03911074714914164,"score_gpt":0.2629236555276551,"score_spread":0.2238129083785134,"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."}}