{"id":"W2557972923","doi":"10.1145/2975167.2985652","title":"Prediction of Cell Type Specific Transcription Factor Binding Site Occupancy","year":2016,"lang":"en","type":"article","venue":"","topic":"Machine Learning in Bioinformatics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"","keywords":"Transcription factor; ENCODE; DNA binding site; Logistic regression; Computer science; Motif (music); Computational biology; Transcription (linguistics); Occupancy; Sequence motif; Artificial intelligence; Biology; DNA; Machine learning; Promoter; Genetics; Gene; Gene expression","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00006249396,0.00007822397,0.00006939737,0.00003837502,0.00002351215,0.000005901427,0.00007039266,0.00009179851,0.0002608861],"category_scores_gemma":[0.00001967791,0.00005268395,0.00004480333,0.00005375691,0.000026068,0.000005475156,0.00001838732,0.00003604398,0.00009283589],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008680746,"about_ca_system_score_gemma":0.00001448593,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00000231888,"about_ca_topic_score_gemma":0.000001709265,"domain_scores_codex":[0.9994913,0.00001867564,0.0001821258,0.0001122635,0.00008731233,0.000108315],"domain_scores_gemma":[0.9996532,0.000006364121,0.00007315217,0.0001823581,0.00005291683,0.00003200912],"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":[0.00003544063,0.000016283,0.01730411,0.00002077849,0.000006698578,8.155213e-8,0.00004538354,0.000002573686,0.9789357,0.00002211059,0.001771023,0.001839813],"study_design_scores_gemma":[0.0004439258,0.0002965808,0.01486825,0.00001714833,0.000005786399,0.00000240406,0.00001714127,0.00007498648,0.916766,0.000004801274,0.06741545,0.00008745733],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9738982,0.00007313299,0.01960284,0.00002865113,0.0002255907,0.00008236707,0.00008619908,0.00001965857,0.005983371],"genre_scores_gemma":[0.9938626,0.0002713406,0.002405672,0.00001831211,0.00008564453,0.000001240358,0.00009490693,0.000009858773,0.003250388],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06564443,"threshold_uncertainty_score":0.285652,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01842271547555852,"score_gpt":0.2308693664184352,"score_spread":0.2124466509428767,"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."}}