{"id":"W2914184348","doi":"10.1093/bioinformatics/btz080","title":"ChimeraUGEM: unsupervised gene expression modeling in any given organism","year":2019,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Gene Regulatory Network Analysis","field":"Biochemistry, Genetics and Molecular Biology","cited_by":13,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Azrieli Foundation; Tel Aviv University; Ministry of Science, Technology and Space","keywords":"Organism; Chlamydomonas reinhardtii; Model organism; Gene; Computational biology; Source code; Computer science; Biology; Gene expression; Coding (social sciences); Software; Coding region; Genetics; Programming language","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001710992,0.0001646089,0.0001890882,0.00008901865,0.00004112441,0.00002520046,0.000225631,0.0001717331,0.00006234898],"category_scores_gemma":[0.0000142878,0.0001527184,0.00008875956,0.0001675694,0.00001580534,0.00001148054,0.0001554669,0.00008052021,0.0001285565],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002251507,"about_ca_system_score_gemma":0.00005994044,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000006530954,"about_ca_topic_score_gemma":0.000007232082,"domain_scores_codex":[0.9989831,0.00002747107,0.0003646666,0.0001836592,0.0001663458,0.0002747665],"domain_scores_gemma":[0.9992847,0.000003963618,0.00008238291,0.0005000157,0.00005121531,0.00007775164],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00004032758,0.00006714364,0.01032087,0.00008007565,0.0000641681,0.000001583525,0.000449238,0.08117989,0.9053103,0.00001400849,0.0009358963,0.001536473],"study_design_scores_gemma":[0.00105784,0.0001153068,0.0008103151,0.00004599927,0.00002637974,0.000009341361,0.0003697564,0.7099062,0.2843537,0.00005097852,0.002845762,0.0004084435],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9906202,0.0003420092,0.007649002,0.00003464357,0.00009756563,0.0001921137,0.000005625429,0.00001634155,0.001042505],"genre_scores_gemma":[0.984704,0.0001435236,0.01433806,0.0001537304,0.00009094241,0.000005957198,0.0001679222,0.00002314385,0.0003727424],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6287262,"threshold_uncertainty_score":0.6227677,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01067659054947601,"score_gpt":0.2116643274055728,"score_spread":0.2009877368560968,"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."}}