{"id":"W4413232635","doi":"10.1093/sysbio/syag040","title":"Modeling Site-and-Branch-Heterogeneity with GFmix","year":2025,"lang":"en","type":"preprint","venue":"Systematic Biology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"Natural Sciences and Engineering Research Council of Canada; Université Paris-Saclay; Dalhousie University; Simons Foundation","keywords":"Computer science","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.000421212,0.0004063918,0.0008403946,0.00007402612,0.0001195414,0.00003433281,0.0002984211,0.0005595975,0.000001533603],"category_scores_gemma":[0.00008747485,0.0003027834,0.0001449997,0.00003918275,0.0001191841,2.83668e-7,0.001352673,0.0002580621,0.00000329906],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001667747,"about_ca_system_score_gemma":0.0001303402,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001096144,"about_ca_topic_score_gemma":0.0002212222,"domain_scores_codex":[0.9979971,0.0003172293,0.0005195399,0.0007904702,0.00006880737,0.0003068288],"domain_scores_gemma":[0.9987385,0.00003651254,0.0002028682,0.0008100337,0.0001426115,0.00006945979],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0005842431,0.0003338152,0.1141483,0.2288872,0.01035195,0.00001645135,0.00222255,0.08441528,0.5537926,0.004427596,0.0001602197,0.0006598047],"study_design_scores_gemma":[0.02131972,0.01072799,0.01917666,0.1017668,0.01526283,0.001331745,0.005160022,0.4771745,0.2275891,0.09374414,0.002095846,0.02465059],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9647759,0.01400718,0.01923148,0.00008968047,0.0003704324,0.001046818,0.000161153,0.00001138112,0.000305936],"genre_scores_gemma":[0.9968727,0.0004290924,0.00185111,0.0001657093,0.0001424042,0.0003170035,0.0001179151,0.00002042752,0.00008363357],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3927592,"threshold_uncertainty_score":0.9999424,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01835944855441289,"score_gpt":0.2608480138736451,"score_spread":0.2424885653192322,"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."}}