{"id":"W2340057483","doi":"10.1186/s12866-016-0680-0","title":"SuperPhy: predictive genomics for the bacterial pathogen Escherichia coli","year":2016,"lang":"en","type":"article","venue":"BMC Microbiology","topic":"Escherichia coli research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":13,"is_retracted":false,"has_abstract":true,"ca_institutions":"Public Health Agency of Canada","funders":"Public Health Agency; Public Health Agency of Canada; Oxford Nanopore Technologies","keywords":"Biology; Genomics; Genome; Whole genome sequencing; Comparative genomics; Computational biology; Genetics; Context (archaeology); Gene","routes":{"ca_aff":true,"ca_fund":true,"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":[0.000320076,0.0001906448,0.0001920945,0.00002039117,0.0001910645,0.00001526497,0.0003969842,0.0002028587,0.0000485327],"category_scores_gemma":[0.0003808033,0.0001058414,0.0001459397,0.00004773777,0.0003840766,0.000003093308,0.0003503934,0.00006477656,0.0000242213],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004051856,"about_ca_system_score_gemma":0.0002548348,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009022995,"about_ca_topic_score_gemma":0.0001680505,"domain_scores_codex":[0.9987179,0.000159291,0.0001977315,0.0004278627,0.00003252917,0.0004646914],"domain_scores_gemma":[0.9990681,0.0002473461,0.00006818715,0.0004061372,0.0001529274,0.00005731889],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.000704321,0.00003004611,0.001519506,0.00001069003,0.0001583085,3.676085e-7,0.0000393607,0.000002769611,0.9887898,0.00008557191,0.008197571,0.0004617103],"study_design_scores_gemma":[0.001649407,0.0007896975,0.003555293,0.000007666084,0.00004224252,0.00001249719,0.00009005016,0.00002106574,0.3311602,0.00009362483,0.662329,0.0002492964],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9792725,0.001044091,0.01669547,0.0005201756,0.0005125377,0.0008625288,0.0009445762,0.00001924908,0.0001288487],"genre_scores_gemma":[0.9884228,0.001101843,0.004677919,0.0005548664,0.001794854,0.0007016674,0.0003003538,0.00006563529,0.00238003],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6576296,"threshold_uncertainty_score":0.4316086,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01609826859124033,"score_gpt":0.2526561810989851,"score_spread":0.2365579125077448,"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."}}