{"id":"W3139286063","doi":"10.1371/journal.pcbi.1008815","title":"Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper","year":2021,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Children's Hospital; University of British Columbia","funders":"","keywords":"Reference genome; Computer science; Population; Genotyping; Computational biology; Genome; Data mining; Contig; Biology; Genetics; Gene","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":[0.00008766892,0.0001020148,0.0001365586,0.00001257193,0.0001045338,0.000007248451,0.0001080553,0.00007076519,0.00001549418],"category_scores_gemma":[0.00005443704,0.00007151718,0.00004088032,0.00008168543,0.000319851,7.405895e-7,0.0001007144,0.00006115389,0.000001243292],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000003990722,"about_ca_system_score_gemma":0.0001977366,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009049309,"about_ca_topic_score_gemma":0.00002663128,"domain_scores_codex":[0.9992855,0.0000809937,0.0001807618,0.0002474996,0.00006795849,0.0001373255],"domain_scores_gemma":[0.9994112,0.00006839162,0.00005627989,0.0001731371,0.0002665491,0.0000244118],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00008380185,0.000088457,0.1455402,0.00001794637,0.0003579948,0.000003885566,0.0001590186,0.002118735,0.8431111,0.003996056,0.000136779,0.004386048],"study_design_scores_gemma":[0.0007059402,0.0007881045,0.3267238,0.00004290134,0.00009476413,0.0001116188,0.001156429,0.005159867,0.6531568,0.00603106,0.005449572,0.0005791966],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.993917,0.0008877903,0.002042817,0.00027798,0.00005077624,0.00009092294,0.0000566829,0.00000394551,0.002672096],"genre_scores_gemma":[0.9938293,0.00005067347,0.005462146,0.0003349118,0.00005852432,0.00001692599,0.0001921035,0.000007314517,0.00004810019],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1899543,"threshold_uncertainty_score":0.2916386,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03876625856620038,"score_gpt":0.2746321942831141,"score_spread":0.2358659357169137,"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."}}