Genome-enabled prediction using probabilistic neural network classifiers.
Journal:
BMC genomics
Published Date:
Mar 9, 2016
Abstract
BACKGROUND: Multi-layer perceptron (MLP) and radial basis function neural networks (RBFNN) have been shown to be effective in genome-enabled prediction. Here, we evaluated and compared the classification performance of an MLP classifier versus that of a probabilistic neural network (PNN), to predict the probability of membership of one individual in a phenotypic class of interest, using genomic and phenotypic data as input variables. We used 16 maize and 17 wheat genomic and phenotypic datasets with different trait-environment combinations (sample sizes ranged from 290 to 300 individuals) with 1.4 k and 55 k SNP chips. Classifiers were tested using continuous traits that were categorized into three classes (upper, middle and lower) based on the empirical distribution of each trait, constructed on the basis of two percentiles (15-85 % and 30-70 %). We focused on the 15 and 30 % percentiles for the upper and lower classes for selecting the best individuals, as commonly done in genomic selection. Wheat datasets were also used with two classes. The criteria for assessing the predictive accuracy of the two classifiers were the area under the receiver operating characteristic curve (AUC) and the area under the precision-recall curve (AUCpr). Parameters of both classifiers were estimated by optimizing the AUC for a specific class of interest.