{"id":"W4386438154","doi":"10.1158/0008-5472.can-23-0816","title":"Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal","year":2023,"lang":"en","type":"article","venue":"Cancer Research","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":853,"is_retracted":false,"has_abstract":true,"ca_institutions":"Princess Margaret Cancer Centre; University Health Network","funders":"National Center for Research Resources; Stand Up To Cancer; Ben and Catherine Ivy Foundation; Instituto Tecnológico de Costa Rica; Adenoid Cystic Carcinoma Research Foundation; Parker Institute for Cancer Immunotherapy; National Cancer Institute; Robertson Foundation; Memorial Sloan-Kettering Cancer Center; Breast Cancer Research Foundation; American Association for Cancer Research; Prostate Cancer Foundation; Cholangiocarcinoma Foundation","keywords":"Cancer; Medicine; Genomics; Visualization; Data science; Bioinformatics; Computer science; Data mining; Genome; Internal medicine; Biology; Genetics; Gene","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0009819373,0.00006926564,0.0001559211,0.0001216316,0.00006656176,0.00003840968,0.0002384522,0.00007280431,0.00001397503],"category_scores_gemma":[0.0002911082,0.00005611201,0.00002456674,0.001004604,0.0002914694,0.00000469915,0.0006094968,0.00009914581,0.000001342678],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001900923,"about_ca_system_score_gemma":0.0003958303,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002840033,"about_ca_topic_score_gemma":0.008569904,"domain_scores_codex":[0.9988762,0.0001555604,0.000226349,0.0004206022,0.0001461666,0.0001751441],"domain_scores_gemma":[0.9991743,0.0001944935,0.00005803509,0.0003805114,0.0001480416,0.0000446177],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0002054234,0.00003063316,0.9223732,0.00001251907,0.0003456422,0.000006627994,0.0001476387,0.00003504251,0.07151181,0.0000231161,0.003334542,0.001973778],"study_design_scores_gemma":[0.0007574066,0.0001537103,0.9825905,0.00001360158,0.0001245147,5.310425e-7,0.0005111512,0.002526668,0.008502602,0.00004336077,0.004667051,0.0001088984],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9935532,0.004652169,0.00005275095,0.0001729137,0.00005157473,0.0002675847,0.00122539,0.000002484666,0.00002195827],"genre_scores_gemma":[0.965838,0.03300256,0.0000335614,0.00002949926,0.000174657,0.00002788453,0.00085514,0.000009870665,0.000028846],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06300921,"threshold_uncertainty_score":0.4782207,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.157915453429175,"score_gpt":0.5056920842015609,"score_spread":0.3477766307723859,"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."}}