{"id":"W4401670407","doi":"10.1101/2024.08.15.607234","title":"Conservative taxonomy and quality assessment of giant virus genomes with GVClass","year":2024,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université Laval","funders":"","keywords":"Giant Virus; Genome; Biology; Metagenomics; Phylum; Taxonomic rank; Evolutionary biology; Phylogenetics; Virus classification; Gene; Genetics; Computational biology; Ecology; Taxon","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.008319196,0.0009888224,0.001003032,0.003496278,0.001159506,0.003378001,0.001362287,0.001251383,0.001964903],"category_scores_gemma":[0.02022493,0.0004602245,0.0009734766,0.001754113,0.0009034774,0.001413002,0.002492061,0.0008477721,0.001352794],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001035782,"about_ca_system_score_gemma":0.0011556,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002397899,"about_ca_topic_score_gemma":0.003204585,"domain_scores_codex":[0.9945698,0.001035241,0.0005110175,0.001462882,0.002037033,0.0003840507],"domain_scores_gemma":[0.9860826,0.00516274,0.002481285,0.001843008,0.003845209,0.0005853284],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.004242664,0.0004514116,0.4766473,0.001695399,0.0007259166,0.0005422707,0.002586728,0.02714106,0.2040262,0.003668421,0.01847115,0.2598016],"study_design_scores_gemma":[0.0002122962,0.001228082,0.1352511,0.0003875273,0.0002565238,0.001081032,0.001762394,0.5271973,0.2856654,0.004764102,0.04192419,0.0002700078],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"methods","genre_scores_codex":[0.8275217,0.001097401,0.1387304,0.0003017655,0.0001746805,0.000341513,0.008965014,0.01951086,0.003356707],"genre_scores_gemma":[0.7947437,0.0002303569,0.1713169,0.000198696,0.00004787391,0.0002877046,0.02913005,0.002555944,0.001488899],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.008319196,"threshold_uncertainty_score":0.04399663,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03044237775226228,"score_gpt":0.2565066745676526,"score_spread":0.2260642968153903,"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."}}