{"id":"W4412168729","doi":"10.1101/2025.07.09.663893","title":"Rehabilitating the benefits of gene tree correction in the presence of incomplete lineage sorting","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Sherbrooke","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Sorting; Lineage (genetic); Tree (set theory); Coalescent theory; Gene; Computational biology; Biology; Evolutionary biology; Computer science; Genetics; Mathematics; Phylogenetic tree; Algorithm; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.01274136,0.001129683,0.001047016,0.001485171,0.001457128,0.001987936,0.003050067,0.002442378,0.001798284],"category_scores_gemma":[0.06890169,0.0005645321,0.000673816,0.001630973,0.002263475,0.002914616,0.002994514,0.003320931,0.00143321],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008497508,"about_ca_system_score_gemma":0.002189097,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002838462,"about_ca_topic_score_gemma":0.003728626,"domain_scores_codex":[0.9950648,0.002484643,0.0002266019,0.0007644764,0.001139382,0.000320214],"domain_scores_gemma":[0.9551308,0.02664299,0.00321156,0.009050846,0.004730048,0.001233864],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"theoretical_or_conceptual","study_design_scores_codex":[0.001191685,0.0003027905,0.05376556,0.0008974758,0.0005380632,0.002063113,0.002053312,0.3333469,0.1017056,0.08238766,0.01927189,0.402476],"study_design_scores_gemma":[0.00005077153,0.0001116945,0.003559015,0.0001089031,0.00007668876,0.0008172711,0.0002509892,0.8679632,0.03498505,0.07975227,0.01223556,0.00008862391],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.09750285,0.0008177921,0.8921331,0.002436277,0.0005630625,0.00003861339,0.0002783963,0.004606025,0.001623957],"genre_scores_gemma":[0.5391307,0.000401946,0.4541653,0.0008566257,0.0003037375,0.00007348051,0.0006219862,0.002532029,0.001914127],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01274136,"threshold_uncertainty_score":0.06738353,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01424218820815978,"score_gpt":0.2293989268371836,"score_spread":0.2151567386290238,"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."}}