{"id":"W953912505","doi":"10.1038/nmeth.3440","title":"Pathway and network analysis of cancer genomes","year":2015,"lang":"en","type":"article","venue":"Nature Methods","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":358,"is_retracted":false,"has_abstract":false,"ca_institutions":"Ontario Institute for Cancer Research; University of Toronto","funders":"National Institute of General Medical Sciences; National Cancer Institute; National Human Genome Research Institute; Canadian Institutes of Health Research","keywords":"Genome; Computational biology; Gene; Biology; Cancer; Genetics; Pathway analysis; Genomics; Gene expression","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":[0.000749907,0.00009067239,0.000221832,0.00004808595,0.0000226989,0.000009419575,0.00009988521,0.0003046959,0.000009121391],"category_scores_gemma":[0.00004101724,0.00007358255,0.00008226375,0.00028505,0.00004532354,0.000001536933,0.00009236672,0.0001442453,1.971451e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000006488213,"about_ca_system_score_gemma":0.00005888031,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001317558,"about_ca_topic_score_gemma":0.00006568984,"domain_scores_codex":[0.9993951,0.00008511382,0.0001652509,0.0001442238,0.00006809446,0.0001422459],"domain_scores_gemma":[0.9994864,0.00002145991,0.00009852161,0.0002217214,0.00008857155,0.00008325552],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0002087548,0.00004527215,0.04353847,0.00005556456,0.00462989,0.000001719655,0.0006072781,0.01638024,0.04535914,0.003416978,0.01511741,0.8706393],"study_design_scores_gemma":[0.001001264,0.0002875681,0.02249447,0.00001930329,0.001462923,0.00000536986,0.0002204426,0.02272259,0.04119328,0.003894816,0.9061036,0.0005943479],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"empirical","genre_scores_codex":[0.3921141,0.3934259,0.2009073,0.0004406733,0.001491509,0.0003668129,0.0001193062,0.00002302849,0.01111133],"genre_scores_gemma":[0.6717016,0.001467128,0.3246649,0.0009018188,0.0005602147,0.00001186355,0.0001091766,0.00001683392,0.0005665398],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.8909862,"threshold_uncertainty_score":0.3000609,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01404375712307823,"score_gpt":0.3479617190518691,"score_spread":0.3339179619287909,"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."}}