“Noisy beets”: impact of phenotyping errors on genomic predictions for binary traits in Beta vulgaris
Year: 2016
Type: article
Abstract: BACKGROUND: Noise (errors) in scientific data is endemic and may have a detrimental effect on statistical analyses and experimental results. The effects of noisy data have been assessed in genome-wide association studies for case-control experiments in human medicine. Little is known, however, on the impact of noisy data on genomic predictions, a widely used statistical application in plant and animal breeding. RESULTS: In this study, the sensitivity to noise in the data of five classification methods (K-nearest neighbours-KNN, random forest-RF, ridge logistic regression-LR, and support vector machines with linear or radial basis function kernels) was investigated. A sugar beet population of 123 plants phenotyped for a binary trait and genotyped for 192 SNP (single nucleotide polymorphism) markers was used. Labels (0/1 phenotype) were randomly sampled to generate noise. From the base scenario without errors in the labels, increasing proportions of noisy labels-up to 50 %-were generated and introduced in the data. CONCLUSIONS: Local classification methods-KNN and RF-showed higher tolerance to noisy labels compared to methods that leverage global data properties-LR and the two SVM models. In particular, KNN outperformed all other classifiers with AUC (area under the ROC curve) higher than 0.95 up to 20 % noisy labels. The runner-up method, RF, had an AUC of 0.941 with 20 % noise.
Source: Plant Methods
Language: English
Subfield: Genetics
Domain: Life Sciences
SDG: Zero hunger
Open Access status: gold
Estimated APC paid: $3,090
OpenAlex ID: W2496723281