{"id":"W3089847646","doi":"10.1016/j.cll.2020.08.003","title":"Clinical Pathogen Genomics","year":2020,"lang":"en","type":"review","venue":"Clinics in Laboratory Medicine","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":19,"is_retracted":false,"has_abstract":false,"ca_institutions":"Memorial University of Newfoundland","funders":"Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine; Medical Center, University of Rochester","keywords":"Metagenomics; Genomics; Whole genome sequencing; DNA sequencing; Computational biology; Infectious disease (medical specialty); Biology; Genome; Medicine; Disease; Genetics; Gene; Pathology","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":[0.001739955,0.0005503515,0.002444393,0.00009566177,0.00005239599,0.000009153511,0.0006544816,0.0008910822,0.00002084163],"category_scores_gemma":[0.001343732,0.0004525371,0.000390711,0.0003678131,0.0004047558,4.951798e-7,0.0004160956,0.0007250166,0.00006296978],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005146243,"about_ca_system_score_gemma":0.001152173,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001658083,"about_ca_topic_score_gemma":0.00001260955,"domain_scores_codex":[0.9959398,0.0005556999,0.001969609,0.001009516,0.0001655045,0.0003598521],"domain_scores_gemma":[0.9978372,0.0002496186,0.0006370416,0.0008756222,0.000147171,0.0002533542],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00002884767,0.00009172079,0.0006302307,0.002043518,0.0004030873,0.00009076626,0.00005377948,0.00000114047,0.00010616,0.0001079228,0.008808275,0.9876345],"study_design_scores_gemma":[0.0005955676,0.0005356502,0.0000604926,0.001113793,0.0003762058,0.000006828666,0.00004049856,0.000002012749,0.000001430716,0.00005577555,0.9967963,0.0004154987],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.0003498741,0.996023,0.0000203636,0.00009789101,0.002028995,0.0005887778,0.0003349532,0.000007078905,0.0005490503],"genre_scores_gemma":[0.00003693437,0.9935517,0.0004816942,0.0009319348,0.004392175,0.00006626735,0.0003367908,0.0001117,0.00009085508],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.987988,"threshold_uncertainty_score":0.9997926,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06960159214589208,"score_gpt":0.4049854087978636,"score_spread":0.3353838166519715,"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."}}