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One of the most efficient methods to solve L2-regularized primal problems, such as logistic regression and linear support vector machine (SVM) classification, is the widely used trust region Newton algorithm, TRON. While TRON has recently been shown to enjoy substantial speedups on shared-memory multi-core systems, exploiting graphical processing units (GPUs) to speed up the method is significantly more difficult, owing to the highly complex and heavily sequential nature of the algorithm. In this work, we show that using judicious GPU-optimization principles, TRON training time for different losses and feature representations may be drastically reduced. For sparse feature sets, we show that using GPUs to train logistic regression classifiers in LIBLINEAR is up to an order-of-magnitude faster than solely using multithreading. For dense feature sets--which impose far more stringent memory constraints--we show that GPUs substantially reduce the lengthy SVM learning times required for state-of-the-art proteomics analysis, leading to dramatic improvements over recently proposed speedups. Furthermore, we show how GPU speedups may be mixed with multithreading to enable such speedups when the dataset is too large for GPU memory requirements; on a massive dense proteomics dataset of nearly a quarter-billion data instances, these mixed-architecture speedups reduce SVM analysis time from over half a week to less than a single day while using limited GPU memory.