{"id":"W4409705160","doi":"10.1101/2025.04.22.650035","title":"Programmatic design and editing of cis-regulatory elements","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Viral Infectious Diseases and Gene Expression in Insects","field":"Biochemistry, Genetics and Molecular Biology","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Waterloo","funders":"Österreichische Forschungsförderungsgesellschaft","keywords":"Computer science","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":[],"consensus_categories":[],"category_scores_codex":[0.0009057618,0.0005063398,0.0003495615,0.0002983379,0.0003168792,0.0007376507,0.0009846189,0.0004729721,0.002258021],"category_scores_gemma":[0.00188486,0.0004736389,0.000573371,0.000272724,0.0006587555,0.0006815753,0.0007185654,0.001155659,0.000578472],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005017864,"about_ca_system_score_gemma":0.0005124901,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006020419,"about_ca_topic_score_gemma":0.001514161,"domain_scores_codex":[0.9994748,0.0001072242,0.00003413661,0.0002176779,0.0001169958,0.00004915143],"domain_scores_gemma":[0.9992673,0.0003597364,0.00009651233,0.0001783834,0.00005796605,0.00004004709],"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":[0.0003041509,0.0002542686,0.002855611,0.0004931384,0.0000938185,0.0002752157,0.0002997166,0.3145167,0.4571473,0.07392678,0.001768252,0.148065],"study_design_scores_gemma":[0.0000602788,0.0002632394,0.0006945194,0.00002935136,0.00005319347,0.0001942338,0.00006544844,0.62255,0.3178885,0.03393036,0.02422178,0.00004915741],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.09022005,0.0002214833,0.9006597,0.0001767352,0.00006878568,0.0000899698,0.0001758217,0.002745477,0.005642002],"genre_scores_gemma":[0.601418,0.0003920888,0.3915709,0.0002035735,0.00002453705,0.0002472933,0.0003567089,0.0007095689,0.005077441],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.002258021,"threshold_uncertainty_score":0.007553875,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01058352727552564,"score_gpt":0.2374982108326785,"score_spread":0.2269146835571529,"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."}}