{"id":"W2898449026","doi":"10.1093/bioinformatics/bty888","title":"Alignment-free clustering of UMI tagged DNA molecules","year":2018,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":44,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; Simon Fraser University","funders":"","keywords":"Barcode; Cluster analysis; Computer science; DNA sequencing; Computational biology; Genomics; Data mining; Biology; DNA; Genetics; Genome; Gene; Artificial intelligence","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":[0.000100595,0.0001160673,0.000121661,0.00003746167,0.0000503248,0.00002041632,0.0002926886,0.00009056979,0.00002170079],"category_scores_gemma":[0.0001444728,0.0001135535,0.00006474803,0.00005899469,0.0001237513,0.000004260255,0.0003275985,0.000030001,0.00002198718],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001385954,"about_ca_system_score_gemma":0.00006409667,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001490812,"about_ca_topic_score_gemma":0.000050924,"domain_scores_codex":[0.999272,0.000007528797,0.0003118311,0.0001003558,0.0001193606,0.000188918],"domain_scores_gemma":[0.9991451,0.00001092736,0.0001443776,0.0005354761,0.00009831951,0.00006583714],"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":[0.000346893,0.0002286473,0.002009294,0.0004708632,0.0003403453,0.000004141646,0.001840873,0.0005358016,0.8346651,0.002480258,0.1288846,0.02819318],"study_design_scores_gemma":[0.001458714,0.0009088978,0.0007701541,0.00005274051,0.00004455487,0.00001742471,0.0004407951,0.01171554,0.8624481,0.0003096015,0.1214354,0.0003981403],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8615527,0.0005282364,0.1020448,0.0002207283,0.0008751983,0.0004144227,0.0003162829,0.00003112069,0.03401651],"genre_scores_gemma":[0.9455326,0.0003930255,0.05226706,0.000846898,0.000487809,0.00001124675,0.0001335136,0.0000294071,0.0002984716],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.08397984,"threshold_uncertainty_score":0.4630576,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00933349121835504,"score_gpt":0.2314702039192874,"score_spread":0.2221367127009323,"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."}}