{"id":"W2521080901","doi":"10.1002/tax.596015","title":"The application of cophylogenic tools to gene sets","year":2010,"lang":"en","type":"article","venue":"Taxon","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Carleton University; University of Ottawa; Agriculture and Agri-Food Canada","funders":"University of Ottawa","keywords":"Phylogenetic tree; Pairwise comparison; Inference; Phylogenetic network; Set (abstract data type); Tree (set theory); Biology; Gene; Computational biology; Phylogenetics; Evolutionary biology; Computer science; Genetics; Mathematics; Artificial intelligence; Combinatorics","routes":{"ca_aff":true,"ca_fund":true,"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":[0.0001109943,0.00006171133,0.00006145932,0.000008444263,0.0000727154,0.000008753046,0.0001620931,0.00005062228,0.00000193499],"category_scores_gemma":[0.00004671991,0.00004595534,0.00003873524,0.0000393654,0.00004380817,1.637127e-7,0.00008657965,0.00003706214,0.00001321992],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000001800633,"about_ca_system_score_gemma":0.00001883629,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001583506,"about_ca_topic_score_gemma":0.0001429208,"domain_scores_codex":[0.9995852,0.000009735752,0.0001079721,0.0001371344,0.00005135945,0.0001086754],"domain_scores_gemma":[0.9995152,0.00001380403,0.00004699866,0.0003313074,0.00005943403,0.00003326673],"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":[0.00001762399,0.000008735276,0.001293374,0.000001691532,0.00001681135,4.849925e-8,0.00001179743,0.00001464847,0.9697453,0.0002493342,0.0004666806,0.028174],"study_design_scores_gemma":[0.00009369212,0.00008943307,0.027108,4.48698e-7,0.000006157968,0.000002105389,0.00001168561,0.00001226561,0.7429267,0.0001434018,0.2295422,0.00006391366],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.997589,0.0003705469,0.0006974894,0.0001642881,0.0001474776,0.0002055688,0.00002205691,0.000001422035,0.0008021662],"genre_scores_gemma":[0.9980151,0.00009633229,0.001471262,0.000108757,0.0001200799,0.00005489104,0.00001117642,0.000007082827,0.0001153206],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2290755,"threshold_uncertainty_score":0.1874004,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01015554128469277,"score_gpt":0.2448023973801033,"score_spread":0.2346468560954106,"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."}}