{"id":"W4225604045","doi":"10.1093/bioinformatics/btac283","title":"Continuous chromatin state feature annotation of the human epigenome","year":2022,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"Natural Sciences and Engineering Research Council of Canada; Genome British Columbia; Michael Smith Health Research BC; Compute Canada; Genome Canada","keywords":"Epigenome; Chromatin; Epigenomics; Computer science; Annotation; Computational biology; Genome; Biology; Genetics; Artificial intelligence; Gene; DNA methylation; 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":[0.0001693122,0.0001001071,0.0001113958,0.00002657766,0.00025165,0.00001632533,0.0003183096,0.00004112185,0.0000210952],"category_scores_gemma":[0.00001682547,0.00008207124,0.00008597938,0.0001044203,0.00005341133,0.000003247033,0.0003045229,0.00009940741,0.000002372993],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002607694,"about_ca_system_score_gemma":0.00006466515,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000008095404,"about_ca_topic_score_gemma":0.00001072518,"domain_scores_codex":[0.9992862,0.00003519549,0.0002782942,0.00008245068,0.0001706677,0.000147182],"domain_scores_gemma":[0.9992644,0.000004696828,0.0002980485,0.0003536459,0.00005232306,0.00002686141],"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":[0.00004344728,0.0002245817,0.01003447,0.0003095815,0.0001925627,0.000001886403,0.005801931,0.009199396,0.9483413,0.001607545,0.01759735,0.006645946],"study_design_scores_gemma":[0.007212692,0.003838834,0.2072718,0.0001038507,0.0002476888,0.0002437934,0.01919707,0.05263809,0.3600552,0.005054838,0.3413547,0.00278146],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9972931,0.0001025871,0.0004051563,0.0000894363,0.0001497442,0.0002286924,0.000205877,0.000007497277,0.00151797],"genre_scores_gemma":[0.9961309,0.00001370613,0.002067467,0.0001827836,0.00002837228,0.00001724041,0.0002530781,0.0000137828,0.00129263],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5882861,"threshold_uncertainty_score":0.3346768,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.004797717254827892,"score_gpt":0.2073578379386773,"score_spread":0.2025601206838495,"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."}}