{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":["metaresearch"],"consensus_categories":[],"category_scores_codex":[0.0714173,0.002199247,0.001210472,0.007754378,0.002628506,0.009259772,0.002492696,0.002298303,0.002546198],"category_scores_gemma":[0.2612979,0.0008996174,0.001527649,0.004424543,0.001523526,0.005798237,0.004372594,0.002579507,0.001627159],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001286263,"about_ca_system_score_gemma":0.002146765,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001129153,"about_ca_topic_score_gemma":0.001464862,"domain_scores_codex":[0.9424884,0.02482212,0.008781665,0.005239038,0.01705891,0.001609748],"domain_scores_gemma":[0.6384319,0.2697543,0.01001903,0.01638626,0.06053703,0.004871474],"domain_codex":null,"domain_gemma":"methods","domain_candidate":"methods","domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"observational","study_design_scores_codex":[0.006809186,0.0007599667,0.2113846,0.005102562,0.001971395,0.00173303,0.005105865,0.02422738,0.08440257,0.01080491,0.03740694,0.6102916],"study_design_scores_gemma":[0.0006924981,0.004179097,0.2070554,0.003243922,0.002632065,0.003438361,0.005457837,0.4091554,0.2376939,0.0305371,0.09479058,0.001123951],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7394027,0.01216993,0.1925863,0.007516634,0.00198821,0.001262708,0.01009862,0.01621568,0.01875924],"genre_scores_gemma":[0.8109388,0.001477767,0.1722805,0.0007481251,0.0002487189,0.0004754746,0.009260041,0.003110616,0.001459945],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9285827,"threshold_uncertainty_score":0.3776953,"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."}}