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Comparing Genomic Prediction Models by Means of Cross Validation.

ABSTRACT: In the two decades of continuous development of genomic selection, a great variety of models have been proposed to make predictions from the information available in dense marker panels. Besides deciding which particular model to use, practitioners also need to make many minor choices for those parameters in the model which are not typically estimated by the data (so called "hyper-parameters"). When the focus is placed on predictions, most of these decisions are made in a direction sought to optimize predictive accuracy. Here we discuss and illustrate using publicly available crop datasets the use of cross validation to make many such decisions. In particular, we emphasize the importance of paired comparisons to achieve high power in the comparison between candidate models, as well as the need to define notions of relevance in the difference between their performances. Regarding the latter, we borrow the idea of equivalence margins from clinical research and introduce new statistical tests. We conclude that most hyper-parameters can be learnt from the data by either minimizing REML or by using weakly-informative priors, with good predictive results. In particular, the default options in a popular software are generally competitive with the optimal values. With regard to the performance assessments themselves, we conclude that the paired k-fold cross validation is a generally applicable and statistically powerful methodology to assess differences in model accuracies. Coupled with the definition of equivalence margins based on expected genetic gain, it becomes a useful tool for breeders.

SUBMITTER: Schrauf MF

PROVIDER: S-EPMC8639521 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundGenerally, QSAR modelling requires both model selection and validation since there is no a priori knowledge about the optimal QSAR model. Prediction errors (PE) are frequently used to select and to assess the models under study. Reliable estimation of prediction errors is challenging - especially under model uncertainty - and requires independent test objects. These test objects must not be involved in model building nor in model selection. Double cross-validation, sometimes also termed nested cross-validation, offers an attractive possibility to generate test data and to select QSAR models since it uses the data very efficiently. Nevertheless, there is a controversy in the literature with respect to the reliability of double cross-validation under model uncertainty. Moreover, systematic studies investigating the adequate parameterization of double cross-validation are still missing. Here, the cross-validation design in the inner loop and the influence of the test set size in the outer loop is systematically studied for regression models in combination with variable selection.MethodsSimulated and real data are analysed with double cross-validation to identify important factors for the resulting model quality. For the simulated data, a bias-variance decomposition is provided.ResultsThe prediction errors of QSAR/QSPR regression models in combination with variable selection depend to a large degree on the parameterization of double cross-validation. While the parameters for the inner loop of double cross-validation mainly influence bias and variance of the resulting models, the parameters for the outer loop mainly influence the variability of the resulting prediction error estimate.ConclusionsDouble cross-validation reliably and unbiasedly estimates prediction errors under model uncertainty for regression models. As compared to a single test set, double cross-validation provided a more realistic picture of model quality and should be preferred over a single test set.

Project description:BackgroundGenomic prediction is becoming a daily tool for plant breeders. It makes use of genotypic information to make predictions used for selection decisions. The accuracy of the predictions depends on the number of genotypes used in the calibration; hence, there is a need of combining data across years. A proper phenotypic analysis is a crucial prerequisite for accurate calibration of genomic prediction procedures. We compared stage-wise approaches to analyse a real dataset of a multi-environment trial (MET) in rye, which was connected between years only through one check, and used different spatial models to obtain better estimates, and thus, improved predictive abilities for genomic prediction. The aims of this study were to assess the advantage of using spatial models for the predictive abilities of genomic prediction, to identify suitable procedures to analyse a MET weakly connected across years using different stage-wise approaches, and to explore genomic prediction as a tool for selection of models for phenotypic data analysis.ResultsUsing 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 case of MET poorly connected between years, analysing each year separately and fitting year as a fixed effect in the genomic prediction stage yielded the most realistic predictive abilities. Predictive abilities can also be used to select models for phenotypic data analysis. The trend of the predictive abilities was not the same as the traditionally used Akaike information criterion, but favoured in the end the same models.ConclusionsMaking predictions using weakly linked datasets is of utmost interest for plant breeders. We provide an example with suggestions on how to handle such cases. Rather than relying on checks we show how to use year means across all entries for integrating data across years. It is further shown that fitting of row and column effects captures most of the heterogeneity in the field trials analysed.

Project description:A major application of genomic prediction (GP) in plant breeding is the identification of superior inbred lines within families derived from biparental crosses. When models for various traits were trained within related or unrelated biparental families (BPFs), experimental studies found substantial variation in prediction accuracy (PA), but little is known about the underlying factors. We used SNP marker genotypes of inbred lines from either elite germplasm or landraces of maize (Zeamays L.) as parents to generate in silico 300 BPFs of doubled-haploid lines. We analyzed PA within each BPF for 50 simulated polygenic traits, using genomic best linear unbiased prediction (GBLUP) models trained with individuals from either full-sib (FSF), half-sib (HSF), or unrelated families (URF) for various sizes ([Formula: see text]) of the training set and different heritabilities ([Formula: see text] In addition, we modified two deterministic equations for forecasting PA to account for inbreeding and genetic variance unexplained by the training set. Averaged across traits, PA was high within FSF (0.41-0.97) with large variation only for [Formula: see text] and [Formula: see text] [Formula: see text] For HSF and URF, PA was on average ?40-60% lower and varied substantially among different combinations of BPFs used for model training and prediction as well as different traits. As exemplified by HSF results, PA of across-family GP can be very low if causal variants not segregating in the training set account for a sizeable proportion of the genetic variance among predicted individuals. Deterministic equations accurately forecast the PA expected over many traits, yet cannot capture trait-specific deviations. We conclude that model training within BPFs generally yields stable PA, whereas a high level of uncertainty is encountered in across-family GP. Our study shows the extent of variation in PA that must be at least reckoned with in practice and offers a starting point for the design of training sets composed of multiple BPFs.

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Comparing Genomic Prediction Models by Means of Cross Validation.

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