{"id":"W4415588730","doi":"10.1101/2025.10.23.683559","title":"Design principles underlying nearly-homeostatic biological networks","year":2025,"lang":"","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Gene Regulatory Network Analysis","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Process (computing); Design elements and principles; Systems design; State (computer science); Complex system; Biological network; Design process; Work (physics)","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":["metaepi_narrow","research_integrity"],"consensus_categories":["metaepi_narrow"],"category_scores_codex":[0.002584253,0.002207169,0.002084757,0.0005702644,0.0009279716,0.0006591213,0.002331199,0.003367594,0.0001413353],"category_scores_gemma":[0.0005722975,0.002385903,0.001096232,0.001770102,0.0007918235,0.0000282183,0.002722961,0.001716593,0.00009744665],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005341692,"about_ca_system_score_gemma":0.002520848,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003173818,"about_ca_topic_score_gemma":0.000005178577,"domain_scores_codex":[0.9887657,0.001848939,0.002176926,0.004132472,0.0007297994,0.002346189],"domain_scores_gemma":[0.991793,0.0002867843,0.001478663,0.00431021,0.001191088,0.0009402812],"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":[0.0004319993,0.000636054,0.01418481,0.0006519661,0.004275976,0.000124307,0.000015417,0.2670498,0.7113008,0.0004623409,0.0008211193,0.00004536561],"study_design_scores_gemma":[0.004817756,0.001871568,0.1173519,0.00310011,0.004562255,4.070262e-7,0.00005176601,0.2562111,0.537577,0.00001841691,0.06301767,0.01142005],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.50335,0.02637678,0.4645201,0.0002532981,0.00233353,0.002621906,0.0001799736,0.0003325231,0.00003186596],"genre_scores_gemma":[0.9632919,0.01108268,0.02314798,0.0005061443,0.00112576,0.0004897335,0.000006915287,0.0002500506,0.00009877255],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.459942,"threshold_uncertainty_score":0.9990668,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03874484699966224,"score_gpt":0.2483714863922347,"score_spread":0.2096266393925725,"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."}}