{"id":"W2158270456","doi":"10.1101/gr.140665.112","title":"Spark: A navigational paradigm for genomic data exploration","year":2012,"lang":"en","type":"article","venue":"Genome Research","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":35,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; Simon Fraser University; Canada's Michael Smith Genome Sciences Centre; BC Cancer Agency","funders":"National Institute on Drug Abuse; Natural Sciences and Engineering Research Council of Canada; National Institute of Environmental Health Sciences; Canadian Institutes of Health Research; National Institutes of Health; National Human Genome Research Institute; Michael Smith Health Research BC","keywords":"Biology; SPARK (programming language); Computational biology; Epigenomics; Visualization; Genome browser; Genome; Data science; Genomics; DECIPHER; Bioinformatics; Genetics; Computer science; Artificial intelligence; DNA methylation; Gene","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":[],"consensus_categories":[],"category_scores_codex":[0.002007511,0.00007982946,0.00007295142,0.00006450052,0.000216635,0.00004256089,0.0003486901,0.00009912287,0.00002822585],"category_scores_gemma":[0.0001685509,0.00008103269,0.00003146729,0.0001064379,0.0000682996,0.0000176463,0.0003053718,0.00008947823,0.00006564234],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002865204,"about_ca_system_score_gemma":0.0001182129,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009950223,"about_ca_topic_score_gemma":0.000008699584,"domain_scores_codex":[0.99874,0.0001150468,0.0001600284,0.0003040729,0.0002430251,0.0004378543],"domain_scores_gemma":[0.9990193,0.00004867793,0.00003623774,0.0006323612,0.0001357977,0.0001275895],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0000690598,0.00007423446,0.002135083,0.00002102327,0.00003733202,1.659503e-7,0.0001217025,0.0001223572,0.9904308,0.001251999,0.001106536,0.00462976],"study_design_scores_gemma":[0.0005934607,0.0002798283,0.01981182,0.00000499868,0.00001305107,0.000002379328,0.0001249086,0.0006561716,0.1012243,0.004468983,0.8725629,0.0002571574],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9160826,0.01366515,0.06673797,0.0008067784,0.0002254653,0.0008879332,0.0003024456,0.00001149619,0.001280158],"genre_scores_gemma":[0.9876397,0.000792568,0.004412832,0.00002678055,0.001507241,0.0001209421,0.004914621,0.00002604003,0.000559262],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8892065,"threshold_uncertainty_score":0.3304417,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.3287976332125653,"score_gpt":0.4549301667804081,"score_spread":0.1261325335678428,"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."}}