{"id":"W4384829400","doi":"10.21203/rs.3.rs-3111932/v1","title":"The ENCODE Uniform Analysis Pipelines","year":2023,"lang":"en","type":"preprint","venue":"Research Square","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":39,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of British Columbia","funders":"National Human Genome Research Institute; National Institutes of Health","keywords":"ENCODE; Pipeline transport; Computer science; Petroleum engineering; Geology; Engineering; Biology; Genetics; Gene; Mechanical engineering","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":[0.002497562,0.002350457,0.001185348,0.002242314,0.001039525,0.003625072,0.002491664,0.001194179,0.03634146],"category_scores_gemma":[0.01257108,0.001930169,0.002566857,0.003027134,0.0008723347,0.00309446,0.002975192,0.002775627,0.03518261],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001415803,"about_ca_system_score_gemma":0.002800931,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005225088,"about_ca_topic_score_gemma":0.005984541,"domain_scores_codex":[0.9978054,0.0003913495,0.0002024816,0.0009223685,0.0004414556,0.0002370222],"domain_scores_gemma":[0.9948497,0.00146065,0.0001769073,0.002594303,0.0007183583,0.0002000252],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.002405437,0.0001488037,0.003315942,0.001086204,0.0003768787,0.0002661477,0.0003974674,0.008082483,0.02864471,0.07222715,0.6300843,0.2529643],"study_design_scores_gemma":[0.0006212993,0.0001317335,0.003099049,0.0002225397,0.000331443,0.0005058065,0.0001763697,0.07382318,0.1036449,0.1898523,0.627319,0.0002723601],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.005420168,0.0007612155,0.518294,0.001054791,0.0004635206,0.0002435196,0.08990818,0.3707412,0.01311345],"genre_scores_gemma":[0.07679513,0.001296296,0.5260938,0.001679173,0.0003129239,0.001257241,0.2744603,0.09292911,0.02517594],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.03634146,"threshold_uncertainty_score":0.1215743,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04701576701690689,"score_gpt":0.3785573238730042,"score_spread":0.3315415568560973,"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."}}