TorchLIMIX: GPU-accelerated multivariate genome-wideassociation studies (opens in new tab)

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 strat...