{"id":"W3179854101","doi":"10.1101/2021.07.12.451567","title":"Critical Assessment of Metagenome Interpretation - the second round of challenges","year":2021,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":45,"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; Russian Science Foundation; Saint Petersburg State University; Agence Nationale de la Recherche; Deutsche Forschungsgemeinschaft; U.S. Department of Energy; European Commission; Deutsches Zentrum für Infektionsforschung; National Energy Research Scientific Computing Center; Science and Technology Commission of Shanghai Municipality; Sydney Medical School; Gordon and Betty Moore Foundation; National Science Foundation","keywords":"Metagenomics; Interpretation (philosophy); Computer science; Computational biology; Data science; Genome; Taxonomic rank; Taxon; Biology; Ecology; Genetics; Gene; Programming language","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":[0.0004786912,0.0002734051,0.0004452296,0.00005440131,0.0000578216,0.00004273058,0.0003852504,0.0002673769,0.00002680589],"category_scores_gemma":[0.0001670181,0.0002409628,0.0002030259,0.0000756576,0.0002178334,0.000001917455,0.0006567553,0.0002212801,5.129839e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002727276,"about_ca_system_score_gemma":0.0003679852,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009627254,"about_ca_topic_score_gemma":0.00001215677,"domain_scores_codex":[0.9984384,0.0001683954,0.000459377,0.0005314681,0.0001883505,0.0002140339],"domain_scores_gemma":[0.9980099,0.00006516185,0.0003023829,0.0009306577,0.0006312173,0.00006067277],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00001260427,0.00009524244,0.0009727305,0.000477756,0.0004988022,0.000002310225,0.00003041937,0.00006415876,0.9969595,0.0008649342,0.00001654027,0.000004989138],"study_design_scores_gemma":[0.0002137242,0.0001748222,0.1914763,0.0001253633,0.0001999655,2.435821e-8,0.00005939992,0.0001449464,0.8047689,0.000008690756,0.00248081,0.000347044],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9710803,0.02630671,0.001359352,0.0001771975,0.000545815,0.0002603851,0.0001967794,0.000004598212,0.00006885026],"genre_scores_gemma":[0.9933132,0.002668157,0.003669434,0.00006043932,0.0001702113,0.00007260164,6.791862e-7,0.00004086949,0.000004441682],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1921906,"threshold_uncertainty_score":0.9826179,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01850923036570177,"score_gpt":0.262162477046996,"score_spread":0.2436532466812942,"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."}}