{"id":"W2343353467","doi":"10.1101/042853","title":"Discovery of Primary, Cofactor, and Novel Transcription Factor Binding Site Motifs by Recursive, Thresholded Entropy Minimization","year":2016,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"Cytodiagnostics (Canada); Western University","funders":"Natural Sciences and Engineering Research Council of Canada; Canada Research Chairs","keywords":"Binding site; Transcription factor; Entropy (arrow of time); Minification; Computational biology; Computer science; Mathematics; Chemistry; Biology; Biochemistry; Physics; Mathematical optimization","routes":{"ca_aff":true,"ca_fund":true,"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":[0.00209151,0.0004975847,0.0005951463,0.001316242,0.0002847367,0.0005863562,0.0007819288,0.0004483643,0.0005520149],"category_scores_gemma":[0.004798625,0.0003939442,0.001004973,0.0006846779,0.0006550183,0.0006611969,0.0006952368,0.0006109172,0.0001768102],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007645644,"about_ca_system_score_gemma":0.000896071,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001934591,"about_ca_topic_score_gemma":0.003277553,"domain_scores_codex":[0.999253,0.000296334,0.00005409216,0.0001673571,0.0001600671,0.00006918131],"domain_scores_gemma":[0.9981728,0.001168397,0.0002314482,0.000217259,0.0001408486,0.00006921422],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.000679809,0.0002034941,0.02567138,0.0002431317,0.0004751747,0.0002949868,0.0001726204,0.776629,0.1093482,0.0150035,0.0008825088,0.07039618],"study_design_scores_gemma":[0.000009398143,0.00002157799,0.001545291,0.00000308616,0.00001274581,0.00002183542,0.000006209311,0.9901748,0.005317459,0.002771809,0.0001076765,0.000008164765],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.30283,0.0001311941,0.6957214,0.00006744153,0.000007303661,0.0000494918,0.0003482038,0.0004771407,0.0003677243],"genre_scores_gemma":[0.7993222,0.00005051478,0.1990378,0.00004565363,0.00000931106,0.0001023831,0.001010058,0.0001171281,0.0003049351],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.00209151,"threshold_uncertainty_score":0.01106113,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.008896743226972016,"score_gpt":0.1944719893785477,"score_spread":0.1855752461515757,"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."}}