{"id":"W4306722626","doi":"10.1186/s12864-022-08936-4","title":"Cov2clusters: genomic clustering of SARS-CoV-2 sequences","year":2022,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; BC Centre for Disease Control; Public Health Agency of Canada; Simon Fraser University","funders":"British Columbia Centre for Disease Control; Michael Smith Health Research BC; Government of Canada; Australian Government","keywords":"Phylogenetic tree; Biology; Cluster analysis; Whole genome sequencing; Computational biology; Sequence (biology); Genetics; Genome; Pandemic; Genomics; Evolutionary biology; Coronavirus disease 2019 (COVID-19); Gene; Computer science; Infectious disease (medical specialty); Disease; Artificial intelligence","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001673624,0.001445847,0.00080797,0.00351553,0.001470045,0.001612308,0.001232255,0.000844572,0.003320452],"category_scores_gemma":[0.005142382,0.0006536785,0.001442045,0.002499552,0.0005813462,0.0007464443,0.001634232,0.0009797586,0.00239536],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001356921,"about_ca_system_score_gemma":0.001856266,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01189169,"about_ca_topic_score_gemma":0.02330979,"domain_scores_codex":[0.998499,0.0002576832,0.0001075668,0.0006890785,0.0003157558,0.0001308575],"domain_scores_gemma":[0.9985421,0.000316666,0.0002581927,0.0003062391,0.000447318,0.0001294806],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.002698208,0.0006148771,0.09605727,0.001981609,0.001423281,0.001401932,0.003618261,0.05428643,0.3192233,0.008827509,0.06502739,0.4448399],"study_design_scores_gemma":[0.0004524617,0.0007835877,0.1066573,0.0002972981,0.0005175323,0.001989694,0.002135317,0.5928168,0.1704449,0.01607544,0.1074934,0.0003362993],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.3738127,0.001190527,0.5556189,0.000766429,0.0003942978,0.001178861,0.0279909,0.032532,0.00651532],"genre_scores_gemma":[0.274781,0.0003435661,0.6674349,0.0002006505,0.00007956573,0.0005286267,0.05037752,0.003451079,0.002803059],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01189169,"threshold_uncertainty_score":0.02364492,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03962123514753096,"score_gpt":0.2669750735588122,"score_spread":0.2273538384112813,"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."}}