Improving machine learning reproducibility in genetic association studies with proportional instance cross validation (PICV)

Abstract

Background: Machine learning methods and conventions are increasingly employed for the analysis of large, complex biomedical data sets, including genome-wide association studies (GWAS). Reproducibility of machine learning analyses of GWAS can be hampered by biological and statistical factors, particularly so for the investigation of non-additive genetic interactions. Application of traditional cross validation to a GWAS data set may result in poor consistency between the training and testing data set splits due to an imbalance of the interaction genotypes relative to the data as a whole. We propose a new cross validation method, proportional instance cross validation (PICV), that preserves the original distribution of an independent variable when splitting the data set into training and testing partitions. Results: We apply PICV to simulated GWAS data with epistatic interactions of varying minor allele frequencies and prevalences and compare performance to that of a traditional cross validation procedure in which individuals are randomly allocated to training and testing partitions. Sensitivity and positive predictive value are significantly improved across all tested scenarios for PICV compared to traditional cross validation. We also apply PICV to GWAS data from a study of primary open-angle glaucoma to investigate a previously-reported interaction, which fails to significantly replicate; PICV however improves the consistency of testing and training results. Conclusions: Application of traditional machine learning procedures to biomedical data may require modifications to better suit intrinsic characteristics of the data, such as the potential for highly imbalanced genotype distributions in the case of epistasis detection. The reproducibility of genetic interaction findings can be improved by considering this variable imbalance in cross validation implementation, such as with PICV. This approach may be extended to problems in other domains in which imbalanced variable distributions are a concern.