TorchLIMIX: GPU-accelerated multivariate genome-wideassociation studies

We introduce TorchLIMIX, a GPU-accelerated PyTorch implementation of the LIMIX multivariate genome-wide association study pipeline. By leveraging batched GPU linear algebra, TorchLIMIX achieves speedups of up to two orders of magnitude over the original CPU-based implementation while maintaining numerically equivalent results and full concordance of significantly associated loci. In simulation studies, replacing the default initialization of the genetic covariance factor with a QR-based strategy reduces genomic inflation factors to near-unity values under the common and interaction effect null hypotheses, ensuring well-calibrated type I error control. Applying TorchLIMIX to metabolic traits of Arabidopsis thaliana measured in two experiments uncovered 37 additional associated SNPs at the same significance threshold used in the original univariate GWAS.