{"id":"W2767405109","doi":"10.7717/peerj.4218","title":"Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory","year":2018,"lang":"en","type":"article","venue":"PeerJ","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":57,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Centre for Disease Control; University of British Columbia","funders":"Canada Research Chairs; Genome British Columbia","keywords":"Workflow; Evidence-based design; Computer science; Data science; Test (biology); Genomics; Domain (mathematical analysis); Visualization; Medicine; Medical physics; Data mining; Genome; Pathology","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":["metaresearch"],"consensus_categories":[],"category_scores_codex":[0.01469459,0.00006814131,0.0002755543,0.00004673001,0.00007171102,0.000004399243,0.00008072802,0.000116545,0.00005818443],"category_scores_gemma":[0.01757535,0.00004221928,0.00004788707,0.00009431856,0.000442626,0.00003792785,0.00002711593,0.0001417661,0.00001236023],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000743011,"about_ca_system_score_gemma":0.001009189,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005956864,"about_ca_topic_score_gemma":0.00002505028,"domain_scores_codex":[0.998232,0.0007520731,0.0004156733,0.0002550785,0.0001430646,0.0002020743],"domain_scores_gemma":[0.9949708,0.00304723,0.0001553146,0.0003477342,0.00139715,0.00008175106],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0009013431,0.00004574095,0.03094123,0.00008551519,0.0001298844,0.0000104801,0.0001132184,0.00009131485,0.9510219,0.00005212923,0.007259871,0.009347434],"study_design_scores_gemma":[0.006855588,0.009573742,0.675099,0.0007195373,0.001477455,0.0004924745,0.0003743093,0.146626,0.04173888,0.001303935,0.1153231,0.0004159326],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9600827,0.003818718,0.02179552,0.01288709,0.0001234056,0.001172441,0.00002541547,0.00001751276,0.00007717461],"genre_scores_gemma":[0.9906272,0.0001729165,0.007363165,0.001346597,0.0002650223,0.00009777064,0.00004661859,0.000007637832,0.00007309404],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.909283,"threshold_uncertainty_score":0.9907,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.4541183850274857,"score_gpt":0.4925940901119986,"score_spread":0.03847570508451292,"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."}}