{"id":"W2981906317","doi":"10.1101/818385","title":"CCSeq: Clusters of Colocalized Sequences","year":2019,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"NF-κB Signaling Pathways","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"University of Alberta; Compute Canada","keywords":"Enhancer; Computational biology; Genome; DNA binding site; Genetics; Transcription factor; Biology; Annotation; Computer science; Promoter; Gene","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"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":[0.0006381539,0.0005534315,0.000675952,0.0001598894,0.00006741514,0.00006887964,0.0008851108,0.0009395977,0.00003981908],"category_scores_gemma":[0.0002421879,0.0005936468,0.0002892222,0.0002223505,0.0002666801,0.000006545058,0.0007951853,0.0004481142,0.00004032423],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008884111,"about_ca_system_score_gemma":0.001027105,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006192522,"about_ca_topic_score_gemma":0.000003190434,"domain_scores_codex":[0.9971564,0.0001878307,0.0006397209,0.001111633,0.0003920375,0.0005123263],"domain_scores_gemma":[0.9969226,0.00003412116,0.0006415119,0.001698674,0.0005132017,0.0001899609],"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":[0.00009148088,0.00008287718,0.003251082,0.0003862278,0.0002290156,0.00001282229,0.000004996714,0.0008463532,0.9940344,0.00008683018,0.0009732493,6.627316e-7],"study_design_scores_gemma":[0.0006957612,0.0001821187,0.001911445,0.0002835425,0.0001011839,2.343192e-8,0.000003497897,0.0002702947,0.9876474,0.000001828678,0.00823356,0.0006693748],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9918749,0.001957065,0.003349595,0.0000897736,0.001416609,0.0007796737,0.000391248,0.00009647518,0.00004465796],"genre_scores_gemma":[0.9945807,0.0002735762,0.004273243,0.0002526144,0.0003745007,0.00009504792,0.00000278255,0.0001246235,0.00002289538],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.007260311,"threshold_uncertainty_score":0.9996515,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01314883179153442,"score_gpt":0.2251447523070836,"score_spread":0.2119959205155492,"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."}}