{"id":"W2997640910","doi":"10.1186/s12859-019-3266-7","title":"A systematic evaluation of copy number alterations detection methods on real SNP array and deep sequencing data","year":2019,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"Genomic variations and chromosomal abnormalities","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Natural Science Foundation of China; McGill University; National Science Foundation","keywords":"Computer science; Benchmark (surveying); Data mining; SNP array; SNP; Scale (ratio); Computational biology; Biology; Single-nucleotide polymorphism; Genetics; Gene","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.01449177,0.002166827,0.001626032,0.005110533,0.001129809,0.001870143,0.002378397,0.001773177,0.0008632935],"category_scores_gemma":[0.02267872,0.0004331205,0.001799201,0.003034592,0.0008272219,0.00196625,0.001761769,0.001108192,0.0007547353],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001286205,"about_ca_system_score_gemma":0.001989321,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.008532277,"about_ca_topic_score_gemma":0.01502905,"domain_scores_codex":[0.9826695,0.004537955,0.0017978,0.004745547,0.005645589,0.0006036757],"domain_scores_gemma":[0.9792271,0.009490418,0.001489873,0.002791097,0.006396424,0.0006050856],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.003045376,0.001320453,0.2671569,0.00720231,0.004166959,0.001139442,0.0006017209,0.06602665,0.04910032,0.002408098,0.0695961,0.5282357],"study_design_scores_gemma":[0.0006646842,0.00269483,0.2570019,0.000981787,0.001775463,0.003169761,0.001386108,0.5733733,0.1000677,0.00482922,0.05356617,0.0004890834],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7455041,0.03056359,0.1523722,0.001505906,0.001766841,0.00151187,0.04792215,0.01102722,0.007826171],"genre_scores_gemma":[0.6265913,0.002698762,0.2416788,0.0009513278,0.0002880552,0.0008592346,0.122943,0.0006334228,0.003356208],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01449177,"threshold_uncertainty_score":0.07664073,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05793704564169391,"score_gpt":0.3418176645331231,"score_spread":0.2838806188914292,"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."}}