{"id":"W4380550443","doi":"10.1101/2023.06.08.23291143","title":"Rigorous software pipeline for clinical somatic mutation analyses of solid tumors","year":2023,"lang":"en","type":"preprint","venue":"medRxiv","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Cytodiagnostics (Canada)","funders":"","keywords":"Germline mutation; Mutation; Computational biology; Exome sequencing; DNA sequencing; Somatic cell; Exome; Point mutation; Genome; Biology; Genetics; Computer science; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.004732388,0.001554121,0.0008501525,0.00211107,0.0006925259,0.001993879,0.001824933,0.0009094835,0.01753123],"category_scores_gemma":[0.01142089,0.0008993556,0.001829415,0.001059991,0.0006898022,0.001150364,0.002259704,0.001928612,0.01333755],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009138449,"about_ca_system_score_gemma":0.003348143,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002439255,"about_ca_topic_score_gemma":0.002405529,"domain_scores_codex":[0.9976189,0.0004433575,0.0003490579,0.0005780493,0.0008266303,0.0001839739],"domain_scores_gemma":[0.9961252,0.001679516,0.0002286829,0.0007440413,0.001034064,0.000188579],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.002533454,0.0003241683,0.01025496,0.001645019,0.000689436,0.001002082,0.0005594484,0.03909682,0.1032888,0.03149881,0.3082249,0.5008821],"study_design_scores_gemma":[0.001050703,0.0004269758,0.01121386,0.0002718277,0.0002033392,0.001587845,0.0001266577,0.5067943,0.1777622,0.0640642,0.2361497,0.0003483861],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.007159367,0.000204214,0.7751528,0.0003255768,0.0001436048,0.0004714633,0.008481377,0.2051571,0.002904491],"genre_scores_gemma":[0.1079911,0.0003628944,0.7978359,0.0006803058,0.0001396884,0.001811786,0.04599203,0.03819944,0.00698696],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01753123,"threshold_uncertainty_score":0.05864775,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.09570722406716717,"score_gpt":0.4137798553661495,"score_spread":0.3180726312989823,"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."}}