{"id":"W3089452289","doi":"10.1101/2020.09.30.320465","title":"Negative controls of chemical probes can be misleading","year":2020,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Click Chemistry and Applications","field":"Chemistry","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Structural Genomics Consortium; University of Toronto","funders":"Ministero dello Sviluppo Economico; Fundação de Amparo à Pesquisa do Estado de São Paulo; Ontario Ministry of Economic Development and Innovation; Ontario Genomics Institute; European Federation of Pharmaceutical Industries and Associations; Novartis Pharma; Wellcome Trust; Genome Canada; Ontario Genomics; Natural Sciences and Engineering Research Council of Canada; Pfizer","keywords":"Phenotype; Computational biology; Gene; Ligand (biochemistry); Confounding; Chemical biology; Function (biology); Biology; Target protein; Loss function; Genetics; Negative control; Chemistry; Receptor; Medicine","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"],"consensus_categories":[],"category_scores_codex":[0.0001407316,0.0005809183,0.0008409607,0.00004982191,0.00008956383,0.00009167876,0.0008573852,0.0006872778,0.0002735891],"category_scores_gemma":[0.0006359969,0.0006703708,0.0002761858,0.0003005954,0.0002647608,0.00005190192,0.0005553366,0.00113029,0.00001458327],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002267211,"about_ca_system_score_gemma":0.0005307292,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005201043,"about_ca_topic_score_gemma":7.738026e-7,"domain_scores_codex":[0.997339,0.00002502821,0.0007332402,0.001064844,0.0003731846,0.0004647626],"domain_scores_gemma":[0.9971194,0.0002123747,0.0006918526,0.001215865,0.0003940267,0.0003665113],"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":[0.00003476265,0.0001529682,0.0006020264,0.001291623,0.0002260207,0.00001233946,0.00003023573,0.00001003763,0.9965692,0.0005670821,0.0005027582,9.170829e-7],"study_design_scores_gemma":[0.0005888619,0.000007216567,0.000171495,0.0004879682,0.0001788872,1.430009e-8,0.00001050249,0.0002436173,0.9948667,0.00001746153,0.002815287,0.0006119853],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9949452,0.0002104288,0.000127921,0.001882833,0.0000928483,0.0003904799,0.001670228,0.0004008839,0.0002791265],"genre_scores_gemma":[0.9965084,0.00004094684,0.002063943,0.0001851313,0.0006168462,0.0004513065,0.000003001091,0.0001141903,0.00001620795],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002312528,"threshold_uncertainty_score":0.9995747,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02122445277969168,"score_gpt":0.2363639131645986,"score_spread":0.2151394603849069,"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."}}