{"id":"W2141462396","doi":"10.1093/bioinformatics/btm629","title":"A hybrid model for robust detection of transcription factor binding sites","year":2008,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":15,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"University of Toronto; Ontario Genomics Institute; Genome Canada","keywords":"Transcription factor; Computer science; Factor (programming language); DNA binding site; Binding site; Computational biology; Biology; Genetics; Promoter; Gene; Programming language; 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":[0.00005366648,0.0001016574,0.0001100404,0.00004648481,0.00008835526,0.000008663454,0.00009054081,0.00007972265,0.000001667088],"category_scores_gemma":[0.00002357607,0.00009988222,0.0001029859,0.0000313173,0.00003525268,0.000008245096,0.00001935424,0.00003271012,0.000002163987],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001572344,"about_ca_system_score_gemma":0.00004307049,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001668847,"about_ca_topic_score_gemma":0.000007730948,"domain_scores_codex":[0.9994192,0.000004166977,0.00027966,0.00008263718,0.00007403797,0.0001403678],"domain_scores_gemma":[0.9995942,0.000005144436,0.0001338767,0.0001550046,0.00007484869,0.00003698304],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00003601187,0.00002908402,0.0001198311,0.0001370442,0.00002768068,1.120615e-7,0.0003861629,0.01138945,0.9860337,0.00001873308,0.0001410983,0.001681036],"study_design_scores_gemma":[0.0003260172,0.0001278407,0.00009991142,0.000005698933,0.00001062729,0.00001462598,0.00005617043,0.7441391,0.2548908,0.00002489714,0.0002007608,0.0001035752],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6200826,0.00003095847,0.3795035,0.000004229523,0.00004379357,0.0001304725,0.0001407414,0.000006812608,0.00005686083],"genre_scores_gemma":[0.9549153,0.000141671,0.04445127,0.00002482676,0.00003677012,0.00001161923,0.0002465952,0.00001359288,0.0001582991],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7327496,"threshold_uncertainty_score":0.4073079,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02511979486837297,"score_gpt":0.2165823897692456,"score_spread":0.1914625949008726,"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."}}