{"id":"W2980787671","doi":"10.1101/808410","title":"Accurate and Complete Genomes from Metagenomes","year":2019,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":36,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Lawrence Berkeley National Laboratory; Biological and Environmental Research; Office of Science; National Institutes of Health; Innovative Genomics Institute; Genome Canada; University of California Berkeley; U.S. Department of Energy","keywords":"Genome; Metagenomics; Bacterial genome size; Biology; Computational biology; Genomics; Shotgun sequencing; Genetics; Gene","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0002251302,0.0005719393,0.0006091309,0.00008763785,0.0001366005,0.0001610302,0.0004880965,0.0004451778,0.00002085617],"category_scores_gemma":[0.00005222913,0.0005925822,0.0001645569,0.00008260034,0.0001470906,0.000001917851,0.001413322,0.0002907368,0.0000428957],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000336236,"about_ca_system_score_gemma":0.0002271244,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00007175386,"about_ca_topic_score_gemma":0.000005963885,"domain_scores_codex":[0.9977109,0.00009527869,0.0003927945,0.001185253,0.0001684602,0.0004472576],"domain_scores_gemma":[0.9980226,0.00003414239,0.0003028643,0.001246865,0.0002158877,0.000177676],"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":[0.00002745745,0.00002907204,0.01126558,0.00008996444,0.0006516893,0.000006211344,0.000009366622,0.0001428505,0.9874782,0.00006124251,0.0002348783,0.000003487865],"study_design_scores_gemma":[0.001089153,0.0001848959,0.4885689,0.0001002174,0.0004227993,2.888537e-8,0.000012517,0.0003150246,0.3587309,0.00001649812,0.1486988,0.001860282],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.956882,0.03964092,0.0005234243,0.0001210307,0.000854842,0.0005223633,0.001406343,0.00002434531,0.00002470149],"genre_scores_gemma":[0.9880227,0.007040417,0.003765127,0.0003214109,0.0006361913,0.00007977471,0.000003455746,0.0001117323,0.00001918009],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6287473,"threshold_uncertainty_score":0.9996526,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01886500729238868,"score_gpt":0.2179875918905235,"score_spread":0.1991225845981348,"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."}}