{"id":"W3010317290","doi":"10.1101/2020.03.02.973750","title":"Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper","year":2020,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Children's Hospital; University of British Columbia","funders":"","keywords":"Reference genome; Computer science; Population; Contig; Genotyping; Data mining; Genome; Computational biology; 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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0003723107,0.0004710779,0.0004561149,0.00004616818,0.0001640347,0.00008902981,0.0006409972,0.0005016102,0.0000138411],"category_scores_gemma":[0.0001216868,0.0003770201,0.0001579587,0.0002543931,0.0004828323,0.00001048163,0.0003048459,0.0006080468,0.000002926736],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003099554,"about_ca_system_score_gemma":0.0008551943,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009185376,"about_ca_topic_score_gemma":0.00001716712,"domain_scores_codex":[0.9978136,0.000135517,0.0004919086,0.0008681989,0.000301807,0.000389009],"domain_scores_gemma":[0.997996,0.00002423989,0.0002505838,0.001169825,0.0003995583,0.0001598317],"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":[0.0001636244,0.00007064352,0.02951509,0.0002071032,0.0002018845,0.00001375341,0.00002037302,0.00005694824,0.9694764,0.0001401832,0.0001205815,0.00001341018],"study_design_scores_gemma":[0.0002289923,0.0001569079,0.0316784,0.0001901474,0.00009602921,4.928399e-8,0.00001749216,0.0004390056,0.9650548,0.000001531572,0.001624517,0.0005121765],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.993154,0.0008034797,0.004498126,0.0002025204,0.0003565271,0.0005399233,0.0002081777,0.00009479713,0.0001423859],"genre_scores_gemma":[0.9952754,0.0001827452,0.003729356,0.0003460299,0.0002897742,0.00008211098,0.00000343728,0.0000853147,0.000005866231],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.004421654,"threshold_uncertainty_score":0.9998682,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03179059470450318,"score_gpt":0.2351160422038328,"score_spread":0.2033254474993296,"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."}}