{"id":"W2592955530","doi":"10.1093/nar/gkx145","title":"A critical assessment of topologically associating domain prediction tools","year":2017,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":149,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"","keywords":"Biology; Computational biology; Domain (mathematical analysis); Annotation; Folding (DSP implementation); Genome; Interpretation (philosophy); Key (lock); Computer science; Bioinformatics; Genetics; Gene; Mathematics; Engineering","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":[0.001491127,0.00008409988,0.0001403315,0.00003497129,0.0005290806,0.0001647479,0.0005246827,0.0002090072,0.00006398953],"category_scores_gemma":[0.00185809,0.00007808811,0.00007577499,0.00003473319,0.0003868159,0.000008659263,0.000537087,0.000251656,0.000005346379],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000543389,"about_ca_system_score_gemma":0.0001366645,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001737269,"about_ca_topic_score_gemma":0.0000120968,"domain_scores_codex":[0.9986075,0.0001542038,0.0002249062,0.0002758805,0.0003938013,0.0003437635],"domain_scores_gemma":[0.9987843,0.00007516801,0.00008914115,0.0006179585,0.0003501656,0.00008325131],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00002822961,0.0001513916,0.08773807,0.00004206052,0.00004837496,0.000006226813,0.00005710264,0.00001269489,0.8946513,0.01177806,0.001020108,0.004466395],"study_design_scores_gemma":[0.000959572,0.001522581,0.9629648,0.0000533435,0.00001336691,0.00001293062,0.0006348023,0.004056642,0.01500006,0.008831288,0.005705224,0.0002453774],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9677614,0.00003272577,0.001363307,0.0006020161,0.00009490349,0.0001466059,0.00009635004,0.000007576567,0.02989512],"genre_scores_gemma":[0.9863191,0.00006140025,0.01298476,0.00002594655,0.0001857849,0.00002043468,0.0000438302,0.00001447893,0.0003442709],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8796512,"threshold_uncertainty_score":0.4069313,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04770631516308227,"score_gpt":0.3972781377121848,"score_spread":0.3495718225491025,"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."}}