{"id":"W2125885829","doi":"10.1093/gbe/evu259","title":"Modularized Evolution in Archaeal Methanogens Phylogenetic Forest","year":2014,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"University of Hong Kong","keywords":"Biology; Archaea; Methanogen; Phylogenetic tree; Evolutionary biology; Gene; Genome; Lineage (genetic); Phylogenetics; Coevolution; Horizontal gene transfer; Genetics; Ecology; Bacteria","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":[0.0003643439,0.0001754019,0.0002044945,0.00008325846,0.0001191857,0.000006106668,0.0001168707,0.0002412571,0.000003440291],"category_scores_gemma":[0.00006977331,0.0001706094,0.00005767604,0.00009460904,0.0002037553,9.908484e-7,0.000149278,0.00008288013,0.000008353948],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003777859,"about_ca_system_score_gemma":0.00003410266,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001155731,"about_ca_topic_score_gemma":0.0004476787,"domain_scores_codex":[0.9987646,0.0001662388,0.0002238418,0.0004479547,0.00004412432,0.0003532946],"domain_scores_gemma":[0.9995666,0.00001783317,0.00006766047,0.0002339673,0.0000467948,0.00006716307],"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":[0.00006494656,0.00002287306,0.2834434,0.000008293038,0.00003136129,2.250618e-7,0.00003419185,0.0003625776,0.7115389,0.00381566,0.000006353982,0.0006712697],"study_design_scores_gemma":[0.0008073994,0.0004363807,0.9773574,0.000003689735,0.00001934901,0.00001301165,0.00003727961,0.0006415307,0.001426977,0.01495811,0.004071171,0.0002277331],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.973914,0.005089041,0.02007619,0.0001021625,0.0001724581,0.0001911099,0.00001960682,0.000005405252,0.0004299964],"genre_scores_gemma":[0.9980045,0.0003632517,0.001064767,0.0000730492,0.0002802469,0.00004062796,0.00008483217,0.0000139438,0.00007475618],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7101119,"threshold_uncertainty_score":0.6957248,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007506317090261866,"score_gpt":0.2256587188629801,"score_spread":0.2181524017727182,"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."}}