{"id":"W3007426492","doi":"10.1099/mgen.0.000337","title":"Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes","year":2020,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":76,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal","funders":"Génome Québec; Genome Canada","keywords":"Genome-wide association study; Biology; Genetics; Locus (genetics); Population; Genetic association; Computational biology; Single-nucleotide polymorphism; Gene; Genotype","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0003259171,0.0002442528,0.0003084244,0.00003302625,0.0002248729,0.00008999239,0.0001710298,0.0001492648,0.00001995036],"category_scores_gemma":[0.0001316311,0.0002687572,0.00008132088,0.0000883522,0.00003857898,0.000001893995,0.0003940701,0.00009874232,0.000003829468],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007090211,"about_ca_system_score_gemma":0.00009325044,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004295076,"about_ca_topic_score_gemma":0.00002563008,"domain_scores_codex":[0.9986043,0.0001670065,0.0003335291,0.0005106623,0.00006649813,0.0003180339],"domain_scores_gemma":[0.9993757,0.00005100477,0.0001830564,0.0001817291,0.00009929368,0.0001092004],"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":[0.0001164006,0.00004133058,0.03992152,0.00001085484,0.0002938876,0.000001540978,0.001176487,0.002530774,0.954172,0.000001026005,0.0000695417,0.001664707],"study_design_scores_gemma":[0.008945842,0.003438313,0.1687583,0.00001789499,0.00124101,0.00001611189,0.002670754,0.005995793,0.3205396,0.0001738627,0.4848765,0.003326015],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9963825,0.001483098,0.001122316,0.0001659618,0.0003029452,0.0004283752,0.00005393916,0.000008195387,0.00005270937],"genre_scores_gemma":[0.9843673,0.0003451274,0.01337926,0.0007313634,0.001022247,0.000001892695,0.00006425488,0.00004676772,0.00004178446],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6336324,"threshold_uncertainty_score":0.9999765,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02169727471179636,"score_gpt":0.2717327752966996,"score_spread":0.2500355005849033,"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."}}