{"id":"W7132959953","doi":"","title":"Organizing Principles of Regulatory Elements and TF Binding Models","year":2023,"lang":"","type":"dissertation","venue":"TSpace","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Amgen (Canada)","funders":"","keywords":"Transcription factor; Regulatory sequence; ENCODE; Element (criminal law); Cis-regulatory module; Transcription (linguistics); Genome; Genomics; Sequence (biology)","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":[0.001869941,0.0006095428,0.0007086414,0.001250327,0.0009056281,0.002143922,0.002571805,0.002268282,0.005686877],"category_scores_gemma":[0.002798509,0.0005931389,0.001177859,0.0007962965,0.002589539,0.002350832,0.000857285,0.001605269,0.001447361],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001600151,"about_ca_system_score_gemma":0.0008234418,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002373379,"about_ca_topic_score_gemma":0.001106359,"domain_scores_codex":[0.9989927,0.0003001965,0.00003914977,0.0002504008,0.0002444051,0.000173137],"domain_scores_gemma":[0.9986778,0.0008093413,0.0001301806,0.0001606958,0.0001093798,0.0001126606],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"theoretical_or_conceptual","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0000297392,0.00003883209,0.0008758779,0.0001000065,0.0000228387,0.00006515549,0.0003414587,0.09161137,0.002948558,0.8938349,0.001234973,0.008896464],"study_design_scores_gemma":[0.00003368649,0.00004050255,0.0005712034,0.00002018449,0.00001730335,0.00009129262,0.0001288265,0.2472495,0.0008493165,0.745952,0.005013821,0.00003233567],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.145955,0.00262118,0.7743987,0.002977057,0.0001860196,0.0002185353,0.000540314,0.0008387999,0.07226434],"genre_scores_gemma":[0.8979247,0.001852314,0.0843699,0.0005021195,0.000227312,0.0006905164,0.0004783237,0.0001829655,0.01377174],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.005686877,"threshold_uncertainty_score":0.01902449,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02238532737288232,"score_gpt":0.2884751547025265,"score_spread":0.2660898273296442,"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."}}