{"id":"W4312189262","doi":"10.2196/42243","title":"Mutational Patterns Observed in SARS-CoV-2 Genomes Sampled From Successive Epochs Delimited by Major Public Health Events in Ontario, Canada: Genomic Surveillance Study","year":2022,"lang":"en","type":"article","venue":"JMIR Bioinformatics and Biotechnology","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Waterloo; University of Prince Edward Island; Western University","funders":"Compute Canada","keywords":"Genome; Whole genome sequencing; Biology; Public health; Genetics; Genomics; Public health surveillance; Copy-number variation; Evolutionary biology; Computational biology; Medicine; Gene","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":true,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005302896,0.0002392794,0.0005740318,0.0006074915,0.0001683363,0.00002771501,0.0003636071,0.0001705882,0.00002810003],"category_scores_gemma":[0.00006485306,0.0002274065,0.00004017501,0.0006430938,0.0000670831,0.00009464927,0.0004398617,0.0008370362,0.000002771766],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001964912,"about_ca_system_score_gemma":0.002624658,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.9032546,"about_ca_topic_score_gemma":0.9871725,"domain_scores_codex":[0.9975525,0.000124099,0.000851654,0.0003514859,0.0004849759,0.0006352616],"domain_scores_gemma":[0.999112,0.0001378076,0.0002774575,0.0003619526,0.00006042237,0.00005032703],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0001513323,0.000463433,0.9896781,0.00006115489,0.00008741189,0.0000816578,0.001549143,0.000001183013,0.003014805,0.00001872847,0.0002609618,0.004632094],"study_design_scores_gemma":[0.006263074,0.0008582763,0.9672762,0.00002303557,0.000006708127,0.00004163856,0.005902763,0.003861236,0.001053338,0.00008796153,0.01431129,0.0003144645],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9929618,0.0003250438,0.00006990257,0.004485962,0.00008262706,0.001566664,0.0004480504,0.0000431159,0.00001687331],"genre_scores_gemma":[0.9861188,0.00001265696,0.0001888805,0.01289898,0.000009312102,0.0002975201,0.000450698,0.00001813888,0.000005022683],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.083918,"threshold_uncertainty_score":0.9273369,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05172404523421847,"score_gpt":0.3076566426740631,"score_spread":0.2559325974398446,"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."}}