{"id":"W4393057683","doi":"10.1101/gr.278343.123","title":"Robust chromatin state annotation","year":2024,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":7,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"Natural Sciences and Engineering Research Council of Canada; Mitacs; Compute Canada","keywords":"Chromatin; Annotation; Biology; Computational biology; Genome; Epigenomics; Computer science; State (computer science); Genetics; DNA methylation; Gene; Algorithm","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":[0.0007781974,0.00009449771,0.0000744708,0.0001259189,0.0001218132,0.0001607297,0.0002145994,0.00007784979,0.00007813182],"category_scores_gemma":[0.00004166579,0.00009109172,0.0000520393,0.0002551522,0.00008023827,0.000003469636,0.0001723736,0.000179454,0.000307199],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004995615,"about_ca_system_score_gemma":0.0001841546,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002162089,"about_ca_topic_score_gemma":0.00002863082,"domain_scores_codex":[0.9987794,0.00008845695,0.0001557034,0.0003489948,0.0002515455,0.0003759298],"domain_scores_gemma":[0.9994529,0.00002051092,0.00001396322,0.0002997721,0.0001282293,0.00008465215],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00001454423,0.00002464141,0.00005439663,0.0001177095,0.00004719994,0.00002996171,0.0002150449,0.001546009,0.9866697,0.000443258,0.002638166,0.008199361],"study_design_scores_gemma":[0.001078391,0.001786549,0.01647954,0.0001543434,0.00002852556,0.0002296788,0.0009847599,0.06121161,0.1238851,0.0115049,0.7813424,0.001314262],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9879228,0.003376298,0.003556775,0.0002832853,0.0001235432,0.0002085737,0.00005612833,0.00002746465,0.004445139],"genre_scores_gemma":[0.9908827,0.0007320468,0.001615293,0.00002583009,0.0002653851,0.00003594863,0.0002925393,0.00003816444,0.006112092],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8627846,"threshold_uncertainty_score":0.3948523,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04793057124054938,"score_gpt":0.3274774270682498,"score_spread":0.2795468558277004,"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."}}