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For different MAF bins, we obtained the highest predictive ability for three traits with MAF bin 0.01 0.1.
The GBM model exhibited the highest predictive ability with R2 0 test and RMSEtest values of 0.79 and 0.59 pIC50 units respectively.
The highest predictive ability of (hbox {Q}^{2}=0.973) was reached for model with ({textit{cost}}=1) and ({textit{epsilon}}=10^{-4}) (Table 1).
The MS SVM ensemble with radial kernel displayed the highest predictive ability, with (R^{2}_{0 test}) and RMSEtest of 0.65 and 0.71 pIC50 unit, which only differs marginally from the minimum theoretical RMSEtest value, namely 0.68 (Figure 5).
To select the best model with the highest predictive ability, some statistical performance criteria (SPC) (coefficient of determination (R2), root mean square error (RMSE), mean relative deviation modulus (MRDM), mean of absolute values of prediction residual errors (MAVPRE) and prediction error mean (PEM)) were used.
Several models of varying complexity were created from these descriptions in order to find the model that provided the highest predictive ability and best interpretability.
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Using complex spatial models did not significantly improve the predictive ability of genomic prediction, but using row and column effects yielded the highest predictive abilities of all models.
In the training set (74 cases), the robust variables that had high predictive ability in predicting RLNM status were subjected to SVM model construction.
This implied that validation in each cluster was conducted across different breeding population means which led to higher predictive ability than when predicting the performance of each breeding population separately.
Attention was paid to identification of genomic regions that may deliver a high predictive ability for genome-enabled prediction of complex traits, with application in breeding and medicine.
Separate validation experiment at predicted optimal condition ascertained the high predictive ability of the model equation.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com