{"id":"W4417017349","doi":"10.5376/cmb.2025.15.0020","title":"Standardizing Bioinformatics Pipelines for Clinical Genomics","year":2025,"lang":"","type":"article","venue":"Computational Molecular Biology","topic":"Genomics and Rare Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"","keywords":"Standardization; Workflow; Comparability; Genomics; Process (computing); Consistency (knowledge bases); Precision medicine; Quality (philosophy)","routes":{"ca_aff":false,"ca_fund":false,"ca_venue":true,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0006189542,0.0004427493,0.0005891573,0.0001945407,0.000309162,0.00009948073,0.000520109,0.0006627193,0.00001124988],"category_scores_gemma":[0.0006496215,0.000471248,0.0007346462,0.0001922801,0.0004690847,0.000005387764,0.0004456438,0.0001869506,0.00001403508],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007102925,"about_ca_system_score_gemma":0.001753832,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000002812,"about_ca_topic_score_gemma":0.000002646993,"domain_scores_codex":[0.996985,0.0002087194,0.001336212,0.0008011375,0.0001081075,0.0005608094],"domain_scores_gemma":[0.9978556,0.0002372303,0.0003811004,0.0004887723,0.0008467877,0.0001905302],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"theoretical_or_conceptual","study_design_gemma":"not_applicable","study_design_scores_codex":[0.004083184,0.00205009,0.01249986,0.001814737,0.008112878,0.00006213,0.0001946871,0.08840273,0.0610009,0.4068423,0.05834414,0.3565923],"study_design_scores_gemma":[0.007735706,0.00172586,0.001552777,0.0001669107,0.0008226814,0.00005345884,0.0002837936,0.09203613,0.004153346,0.2622327,0.6275849,0.001651771],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.0655226,0.01480749,0.9131176,0.001084478,0.002043122,0.0009153537,0.00123411,0.00001928754,0.001255972],"genre_scores_gemma":[0.9016479,0.00131053,0.0874544,0.00457643,0.0005577313,0.00007022642,0.004059462,0.00005326572,0.0002700069],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.8361254,"threshold_uncertainty_score":0.9997739,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02152590597403535,"score_gpt":0.3836228400215117,"score_spread":0.3620969340474763,"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."}}