{"id":"W1792091924","doi":"10.1016/j.biosystems.2015.10.002","title":"The identification of cis-regulatory elements: A review from a machine learning perspective","year":2015,"lang":"en","type":"review","venue":"Biosystems","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":65,"is_retracted":false,"has_abstract":false,"ca_institutions":"Child and Family Research Institute; University of British Columbia; National Research Council Canada","funders":"Natural Sciences and Engineering Research Council of Canada; Genome Canada","keywords":"Enhancer; Computational biology; Biology; Regulatory sequence; Promoter; Chromatin; Transcription factor; Genome; Noncoding DNA; DNA sequencing; Histone; DNA binding site; Genetics; Gene; Computer science; Gene expression","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001050278,0.0002693912,0.0007871297,0.00003077463,0.00009090816,0.00003345279,0.0004654231,0.0002137135,0.0000044098],"category_scores_gemma":[0.0001782129,0.0001844013,0.0003497467,0.0001094331,0.00005167082,0.000001602386,0.0001555689,0.0001466346,0.00002271669],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001166598,"about_ca_system_score_gemma":0.0002618289,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00008482032,"about_ca_topic_score_gemma":0.00004454906,"domain_scores_codex":[0.9978758,0.0003140492,0.001041092,0.0003917236,0.0002154323,0.0001619067],"domain_scores_gemma":[0.9975217,0.00002299704,0.001398889,0.0007246715,0.0002768835,0.0000548385],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00003651957,0.0002011105,0.00005538343,0.07570624,0.003694661,0.000004903714,0.0002194661,0.000006618261,0.00670731,0.001090078,0.01396449,0.8983132],"study_design_scores_gemma":[0.00009175541,0.00005872918,0.000001646411,0.006320535,0.0003785715,0.000008434983,0.00009000608,0.00005093564,0.00002879936,0.00001991976,0.9927601,0.0001905284],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.0001124468,0.9981353,0.0000330289,0.00001541222,0.0003051742,0.0008400742,0.0003548713,0.000008086923,0.0001955804],"genre_scores_gemma":[0.0006137207,0.9970023,0.00003332847,0.000009781538,0.0002354401,0.00009836589,0.001263508,0.00004638343,0.0006971939],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.9787956,"threshold_uncertainty_score":0.7519665,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01938759512497126,"score_gpt":0.301501111215575,"score_spread":0.2821135160906038,"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."}}