{"id":"W2310742968","doi":"10.1534/g3.115.021667","title":"LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms","year":2015,"lang":"en","type":"article","venue":"G3 Genes Genomes Genetics","topic":"Genetic and phenotypic traits in livestock","field":"Biochemistry, Genetics and Molecular Biology","cited_by":481,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"Canada Research Chairs; Genome Canada","keywords":"Imputation (statistics); Genotyping; Genotype; Missing data; Biology; Genomic selection; Genome-wide association study; Genome; Genomics; Computational biology; Genetics; Computer science; Single-nucleotide polymorphism; Gene; Machine learning","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0002031659,0.0003012174,0.0002207847,0.00005557574,0.0001343586,0.0000895647,0.0002831512,0.000265693,0.000005818537],"category_scores_gemma":[0.00001253788,0.0003046253,0.00007405172,0.00009920914,0.0001158646,0.00000735564,0.0002141754,0.00007203705,0.00001572622],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001955238,"about_ca_system_score_gemma":0.0002671015,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000004142227,"about_ca_topic_score_gemma":0.00001524586,"domain_scores_codex":[0.9984562,0.00004692006,0.0003267897,0.000574558,0.000171677,0.0004237892],"domain_scores_gemma":[0.9988247,0.0000182598,0.000130005,0.0004362414,0.0003017762,0.0002889841],"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":[0.0001702107,0.0000728703,0.002062157,0.00005976734,0.0001327743,6.839214e-7,0.0007611032,0.0373529,0.06801879,0.001206623,0.001340197,0.8888219],"study_design_scores_gemma":[0.007821559,0.006596269,0.01359478,0.0000266901,0.0004681462,0.000198346,0.001573216,0.01403051,0.15683,0.03688418,0.759136,0.002840301],"study_design_candidate":"design_other","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.243737,0.1901244,0.5641885,0.0001328939,0.0006320923,0.0007044995,0.0001057724,0.00003588808,0.0003388945],"genre_scores_gemma":[0.5829669,0.01206673,0.4000536,0.0005876491,0.00148224,0.00009482809,0.0004896499,0.0001295738,0.00212891],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.8859816,"threshold_uncertainty_score":0.9999406,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02402387547798219,"score_gpt":0.2646507965306267,"score_spread":0.2406269210526445,"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."}}