{"id":"W4225258284","doi":"10.1038/s41592-022-01431-4","title":"Critical Assessment of Metagenome Interpretation: the second round of challenges","year":2022,"lang":"en","type":"article","venue":"Nature Methods","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":396,"is_retracted":false,"has_abstract":true,"ca_institutions":"National Research Council Canada; University of British Columbia","funders":"Sydney Medical School Foundation; Biological and Environmental Research; Office of Science; Higher Education Discipline Innovation Project; Novo Nordisk Fonden; Russian Science Foundation; Saint Petersburg State University; Agence Nationale de la Recherche; Deutsche Forschungsgemeinschaft; U.S. Department of Energy; European Commission; National Energy Research Scientific Computing Center; Deutsches Zentrum für Infektionsforschung; Joint Genome Institute; Science and Technology Commission of Shanghai Municipality; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; Sydney Medical School; Gordon and Betty Moore Foundation; National Science Foundation","keywords":"Metagenomics; Computational biology; Interpretation (philosophy); Biology; Computer science; Genetics; Gene","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":[],"consensus_categories":[],"category_scores_codex":[0.001059853,0.00008104539,0.0001690332,0.00002481211,0.00008007963,0.000003899988,0.0002283575,0.00007530921,0.0001020169],"category_scores_gemma":[0.0001450829,0.00006082053,0.0001041895,0.00005858553,0.00009755627,4.210698e-7,0.0002829431,0.0002201103,5.723391e-8],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008445889,"about_ca_system_score_gemma":0.00004778864,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001323259,"about_ca_topic_score_gemma":0.000004893645,"domain_scores_codex":[0.9989533,0.000475398,0.0001820196,0.0001756915,0.0001193807,0.00009417222],"domain_scores_gemma":[0.9993197,0.0001915066,0.00008365082,0.0002843655,0.0001032641,0.00001750005],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00004380273,0.00007968031,0.0002476347,0.00006986805,0.0003107794,6.455214e-7,0.000547334,0.0001233872,0.9665551,0.01328732,0.0002031873,0.01853129],"study_design_scores_gemma":[0.0005877648,0.001534249,0.05440631,0.000008203296,0.0002017642,0.00003470126,0.003608369,0.0004370683,0.4213841,0.01080697,0.506642,0.0003484054],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7120193,0.2285127,0.02478892,0.002591976,0.001767487,0.0004381102,0.0002041357,0.000004083106,0.02967323],"genre_scores_gemma":[0.9389082,0.0002725279,0.06032261,0.0001919988,0.00006409424,0.0000307989,0.000005906619,0.000008468365,0.0001954164],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.545171,"threshold_uncertainty_score":0.2480189,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02486393467598424,"score_gpt":0.4023069324838383,"score_spread":0.377442997807854,"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."}}