{"id":"W1916539208","doi":"10.1534/genetics.115.177386","title":"Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution","year":2015,"lang":"en","type":"article","venue":"Genetics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":44,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institute of Genetics; Biotechnology and Biological Sciences Research Council; Directorate for Biological Sciences","keywords":"Substitution (logic); Spurious relationship; Biology; Inference; Computational biology; Evolutionary biology; Sequence (biology); Markov model; Markov chain; Algorithm; Statistics; Computer science; Genetics; Mathematics; Artificial intelligence","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":["metaresearch"],"consensus_categories":[],"category_scores_codex":[0.03478324,0.001769614,0.001472666,0.002796389,0.0008608801,0.001102068,0.002359933,0.002009342,0.0008930218],"category_scores_gemma":[0.06618842,0.0009026672,0.001152997,0.001880746,0.001074713,0.00216917,0.001531088,0.001800866,0.0003009498],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00130893,"about_ca_system_score_gemma":0.001533737,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003348273,"about_ca_topic_score_gemma":0.002438379,"domain_scores_codex":[0.9878296,0.008239502,0.0007376052,0.001099172,0.001853977,0.0002401072],"domain_scores_gemma":[0.9220932,0.06214014,0.002666398,0.004418027,0.007847023,0.0008352969],"domain_codex":null,"domain_gemma":"methods","domain_candidate":"methods","domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001014774,0.0003644007,0.06515954,0.000489257,0.001207569,0.0002622675,0.0006640614,0.6621236,0.01563582,0.01158877,0.0008038619,0.2406861],"study_design_scores_gemma":[0.00005118593,0.0001497316,0.00340749,0.00004026103,0.00005986091,0.0001096295,0.00002993361,0.9886628,0.005606184,0.001402476,0.0004408268,0.00003961239],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.3909675,0.002282999,0.602179,0.0004778066,0.00008657436,0.0002382456,0.0002575138,0.00159122,0.001919216],"genre_scores_gemma":[0.4307655,0.000932721,0.5666509,0.0001131189,0.00003544143,0.0002918046,0.0004729244,0.0003768051,0.0003608902],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.9652168,"threshold_uncertainty_score":0.1839536,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1241727706108797,"score_gpt":0.3850958573149888,"score_spread":0.2609230867041091,"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."}}