The Fast Kernel Transform

John Ryan · Sebastian Ament · Carla Gomes · Anil Damle


Kernel methods are a highly effective and widely used collection of modern machine learning algorithms. A fundamental limitation of virtually all such methods are computations involving the kernel matrix that naïvely scale quadratically (e.g., matrix-vector multiplication) or cubically (solving linear systems) with the size of the dataset N. We propose the Fast Kernel Transform (FKT), a general algorithm to compute matrix-vector multiplications (MVMs) for datasets in moderate dimensions with quasilinear complexity. Typically, analytically grounded fast multiplication methods require specialized development for specific kernels. In contrast, our scheme is based on auto-differentiation and automated symbolic computations that leverage the analytical structure of the underlying kernel. This allows the FKT to be easily applied to a broad class of kernels, including Gaussian, Matérn, and Rational Quadratic covariance functions and Green's functions, including those of the Laplace and Helmholtz equations. Furthermore, the FKT maintains a high, quantifiable, and controllable level of accuracy---properties that many acceleration methods lack. We illustrate the efficacy and versatility of the FKT by providing timing and accuracy benchmarks with comparisons to adjacent methods, and by applying it to scale the stochastic neighborhood embedding (t-SNE) and Gaussian processes to large real-world datasets.

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