{"id":"W2133103440","doi":"10.1186/1471-2105-13-s19-s15","title":"Gene trees and species trees: irreconcilable differences","year":2012,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":31,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; McGill University","funders":"","keywords":"Gene duplication; Biology; Tree (set theory); Gene; Inference; Phylogenetic tree; Tree rearrangement; Extant taxon; Function (biology); Phylogenomics; Phylogenetics; Evolutionary biology; Set (abstract data type); Computational biology; Genetics; Computer science; Mathematics; Combinatorics; Artificial intelligence","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.008143555,0.0004790935,0.0006099572,0.002064217,0.001389136,0.002983964,0.001662433,0.002106417,0.002830569],"category_scores_gemma":[0.04442899,0.0004316908,0.0006114327,0.002602953,0.006664125,0.007888864,0.003036901,0.003072656,0.0006178237],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001767781,"about_ca_system_score_gemma":0.0006207665,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003220046,"about_ca_topic_score_gemma":0.0004532276,"domain_scores_codex":[0.9957611,0.002372987,0.0001629371,0.0006644534,0.0009061816,0.0001322567],"domain_scores_gemma":[0.9659758,0.02615048,0.002312111,0.003775185,0.001302735,0.0004836257],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"theoretical_or_conceptual","study_design_gemma":"theoretical_or_conceptual","study_design_scores_codex":[0.0001575376,0.00001907555,0.00478057,0.0002654524,0.00006781606,0.0003592293,0.001970108,0.015268,0.001685569,0.9088235,0.001756159,0.06484701],"study_design_scores_gemma":[0.000008845739,0.00001723703,0.001477584,0.00007163379,0.00001785384,0.0005153362,0.0002475339,0.02593674,0.0009359765,0.9625786,0.008173373,0.00001926848],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":"theoretical_or_conceptual","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.1343129,0.01078561,0.827883,0.00867598,0.0003993361,0.00006746841,0.0003468235,0.0004878464,0.0170411],"genre_scores_gemma":[0.807497,0.002851864,0.1861481,0.0006831384,0.0003258153,0.0001052915,0.000403707,0.0002665046,0.001718519],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.008143555,"threshold_uncertainty_score":0.04306775,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02380593738769434,"score_gpt":0.2215970825356099,"score_spread":0.1977911451479155,"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."}}