{"id":"W4362660287","doi":"10.1101/2023.04.05.535762","title":"Fast genome-based species delimitation: Enterobacterales and beyond","year":2023,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Wilfrid Laurier University","funders":"","keywords":"Biology; Genus; Citrobacter; Shigella; Similarity (geometry); Genome; Enterobacter; Proteus; Zoology; Evolutionary biology; Genetics; Salmonella; Escherichia coli; Bacteria","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":[0.002508103,0.001270681,0.001010978,0.001877609,0.0004978715,0.001694943,0.0006557195,0.0006991369,0.001985515],"category_scores_gemma":[0.007336535,0.0004311537,0.0009587511,0.001821167,0.0003461635,0.001680383,0.001343444,0.0009634069,0.001201809],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004427088,"about_ca_system_score_gemma":0.0005170356,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001699551,"about_ca_topic_score_gemma":0.001365998,"domain_scores_codex":[0.9988527,0.0002784852,0.0000967392,0.0003922641,0.0002847934,0.00009499556],"domain_scores_gemma":[0.996235,0.001543007,0.0008754756,0.0003652962,0.0007405715,0.0002406468],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.004374919,0.0004101301,0.1284355,0.003292708,0.0005948233,0.0003739539,0.001718648,0.01836948,0.3345463,0.005244158,0.008668175,0.4939713],"study_design_scores_gemma":[0.0002431681,0.002288934,0.2952129,0.0007912607,0.0004353182,0.001982962,0.001256143,0.3664648,0.2483209,0.01639983,0.06607161,0.0005322273],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7629423,0.006794763,0.1993793,0.0004238946,0.0001761737,0.000285342,0.009380564,0.01549795,0.005119754],"genre_scores_gemma":[0.6442629,0.001209193,0.3368051,0.0001758439,0.00005670036,0.0002922558,0.0142769,0.0009040336,0.002017161],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002508103,"threshold_uncertainty_score":0.0132643,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01882628265276401,"score_gpt":0.2100649630792544,"score_spread":0.1912386804264904,"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."}}