{"id":"W2148930557","doi":"10.1101/gr.118414.110","title":"Estimation of rearrangement phylogeny for cancer genomes","year":2011,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomic variations and chromosomal abnormalities","field":"Biochemistry, Genetics and Molecular Biology","cited_by":132,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Cancer Agency","funders":"Medical Research Council; Cancer Research UK; Wellcome Trust","keywords":"Biology; Genome; Computational biology; Genetics; Karyotype; Somatic cell; Gene rearrangement; Genomics; Evolutionary biology; Gene; Chromosome","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":[0.0004715158,0.00006512268,0.00008759557,0.00007367165,0.00009863864,0.000008084044,0.0001749583,0.00006039965,0.0001939063],"category_scores_gemma":[0.00002642849,0.00006158732,0.00005399927,0.00008446808,0.00007699853,0.00000256175,0.00009042733,0.00004161398,0.000009038747],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002375683,"about_ca_system_score_gemma":0.0001159402,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001499781,"about_ca_topic_score_gemma":0.00003730309,"domain_scores_codex":[0.9992314,0.00004640937,0.000158897,0.0001818939,0.0001331006,0.0002483217],"domain_scores_gemma":[0.9994432,0.00001023741,0.00004210255,0.0002348727,0.0002248916,0.00004465363],"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":[0.0001583297,0.0001046515,0.001839641,0.0001437387,0.0001235947,4.861966e-7,0.001093245,0.0003291343,0.9785295,0.002060449,0.0004136644,0.01520361],"study_design_scores_gemma":[0.0009814396,0.001236209,0.04761633,0.00001933996,0.00003434924,0.000004783027,0.001338503,0.0003909033,0.8657387,0.003195663,0.07912891,0.0003148428],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9901682,0.002621601,0.002830271,0.00005425902,0.00005985349,0.0004551728,0.0001362173,0.000004639096,0.003669803],"genre_scores_gemma":[0.9930103,0.0005101786,0.004355581,0.00001316452,0.000122678,0.0002366569,0.00008559795,0.00001355807,0.001652256],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1127907,"threshold_uncertainty_score":0.2511458,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.104520587350761,"score_gpt":0.3543059501946551,"score_spread":0.249785362843894,"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."}}