{"id":"W2953157660","doi":"10.1099/mgen.0.000146","title":"MentaLiST – A fast MLST caller for large MLST schemes","year":2018,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":63,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; BC Centre for Disease Control; Simon Fraser University","funders":"","keywords":"Multilocus sequence typing; Housekeeping gene; Genotyping; Typing; Computer science; Biology; Computational biology; Genetics; Gene; Genotype","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001346871,0.0002202198,0.0001908506,0.00002996701,0.0003214393,0.00004574472,0.0002587617,0.0001427058,0.00003486294],"category_scores_gemma":[0.00002183042,0.0002268103,0.0001480013,0.00004494802,0.0001394332,8.139452e-7,0.0002934308,0.00004790202,0.00004433715],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003258232,"about_ca_system_score_gemma":0.00009505524,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000220464,"about_ca_topic_score_gemma":0.0003639402,"domain_scores_codex":[0.9988282,0.00001638084,0.0002341532,0.0004361118,0.00004737314,0.0004378097],"domain_scores_gemma":[0.9993497,0.000006689405,0.00007869975,0.0003371932,0.0001486988,0.00007905547],"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":[0.0001228174,0.00006723198,0.0004238098,0.00001274815,0.0001269337,4.614401e-7,0.0002275959,0.000002541511,0.9793718,0.0002505347,0.01866787,0.0007256394],"study_design_scores_gemma":[0.0007929714,0.0002243884,0.0003651204,0.000003268847,0.00002348086,0.000007635416,0.0001257768,0.00002547742,0.3503699,0.00004758994,0.6477873,0.0002270803],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9933021,0.0007901289,0.002619451,0.0002184199,0.0006966353,0.0004069223,0.0007036571,0.000007205673,0.00125546],"genre_scores_gemma":[0.9891244,0.0001870239,0.005240037,0.001144139,0.001642907,0.00002476766,0.0002686482,0.00005584751,0.002312302],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6291195,"threshold_uncertainty_score":0.9249057,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01093940211471517,"score_gpt":0.2450760243677387,"score_spread":0.2341366222530235,"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."}}