{"id":"W4410463661","doi":"10.1093/gbe/evaf092","title":"ParallelEvolCCM: Quantifying Coevolutionary Patterns Among Genomic Features","year":2025,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"Natural Sciences and Engineering Research Council of Canada; Research Nova Scotia; Genome Atlantic; Genome Canada; Alliance de recherche numérique du Canada; Dalhousie University","keywords":"Biology; Evolutionary biology; Computational biology","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":[0.0002035671,0.0001723509,0.0001631122,0.00007021482,0.0002617221,0.00001881355,0.0001513412,0.0003600579,0.0000145293],"category_scores_gemma":[0.00001644871,0.0001640473,0.00006956831,0.00007654598,0.0001896816,0.000006409959,0.0001917198,0.0001435189,0.000009174059],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003991919,"about_ca_system_score_gemma":0.00006305529,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00007600763,"about_ca_topic_score_gemma":0.0001675152,"domain_scores_codex":[0.9990247,0.00005820179,0.0002422905,0.000325856,0.0000331165,0.0003157624],"domain_scores_gemma":[0.9995539,0.00001217428,0.00008409147,0.0002463772,0.00004398762,0.00005950952],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0001576673,0.00004181229,0.86142,0.00006160393,0.00020587,0.000001133799,0.00006945361,0.0002946678,0.116711,0.01548562,0.002866616,0.002684599],"study_design_scores_gemma":[0.0004187369,0.0001078321,0.9855418,0.00001493347,0.00002626372,0.0000144211,0.00009808096,0.000409056,0.0001622245,0.002933209,0.01006826,0.0002051873],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9499826,0.01087591,0.03701918,0.0001414494,0.0003648704,0.0002031241,0.00003803183,0.00002284417,0.00135202],"genre_scores_gemma":[0.9967641,0.0009069928,0.0004470957,0.0002312558,0.0002206439,0.0000233495,0.0004336013,0.000009129893,0.0009638101],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1241218,"threshold_uncertainty_score":0.6689655,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00802317850700139,"score_gpt":0.2457731667447272,"score_spread":0.2377499882377258,"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."}}