{"id":"W4408129732","doi":"10.1016/j.molp.2025.03.002","title":"SuperDecode: An integrated toolkit for analyzing mutations induced by genome editing","year":2025,"lang":"en","type":"article","venue":"Molecular Plant","topic":"CRISPR and Genetic Engineering","field":"Biochemistry, Genetics and Molecular Biology","cited_by":13,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Saskatchewan","funders":"National Major Science and Technology Projects of China","keywords":"Biology; Genome editing; Computational biology; Genome; Genetics; Mutation; Gene","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001221354,0.0001432091,0.0001235662,0.00007183768,0.00008769199,0.00004480167,0.0001524149,0.0001150968,0.000006286019],"category_scores_gemma":[0.00009651325,0.000151058,0.00007081556,0.0001199803,0.00001542701,0.000003422424,0.00004090365,0.00007728091,0.000001337898],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001590792,"about_ca_system_score_gemma":0.00005543709,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002246589,"about_ca_topic_score_gemma":0.00003075847,"domain_scores_codex":[0.999189,0.00002473018,0.000185438,0.0003030524,0.00006045433,0.0002373471],"domain_scores_gemma":[0.9995967,0.00001174821,0.00002661787,0.0002330096,0.00006797866,0.00006401119],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00001469952,0.00002680179,0.00008533239,0.00001874068,0.00006987993,0.000002910298,0.00003273671,0.00146816,0.996291,0.0001083981,0.0004989126,0.001382471],"study_design_scores_gemma":[0.0004967423,0.0001498079,0.0003051106,0.00002009769,0.00005629543,0.000006649527,0.0001646765,0.003572553,0.9647424,0.00005455985,0.03019885,0.0002322554],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6171833,0.0004731604,0.3816316,0.00008173669,0.0001170058,0.0001739901,0.0001806061,0.00002025055,0.0001383901],"genre_scores_gemma":[0.9924408,0.00001517995,0.003637322,0.000221145,0.00007499501,0.00006029597,0.003370836,0.00002170881,0.0001577751],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3779942,"threshold_uncertainty_score":0.6159966,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006852138082357719,"score_gpt":0.2859818688953309,"score_spread":0.2791297308129732,"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."}}