Accelerating Eulerian Fluid Simulation With Convolutional Networks

Efficient simulation of the Navier-Stokes equations for fluid flow is a long standing problem in applied mathematics, for which state-of-the-art methods require large compute resources. In this work, we propose a data-driven approach that leverages the approximation power of deep-learning with the precision of standard solvers to obtain fast and highly realistic simulations. Our method solves the incompressible Euler equations using the standard operator splitting method, in which a large sparse linear system with many free parameters must be solved. We use a Convolutional Network with a highly tailored architecture, trained using a novel unsupervised learning framework to solve the linear system. We present real-time 2D and 3D simulations that outperform recently proposed data-driven methods; the obtained results are realistic and show good generalization properties.Comment: Significant revisio

Getting Started with Particle Metropolis-Hastings for Inference in Nonlinear Dynamical Models

This tutorial provides a gentle introduction to the particle Metropolis-Hastings (PMH) algorithm for parameter inference in nonlinear state-space models together with a software implementation in the statistical programming language R. We employ a step-by-step approach to develop an implementation of the PMH algorithm (and the particle filter within) together with the reader. This final implementation is also available as the package pmhtutorial in the CRAN repository. Throughout the tutorial, we provide some intuition as to how the algorithm operates and discuss some solutions to problems that might occur in practice. To illustrate the use of PMH, we consider parameter inference in a linear Gaussian state-space model with synthetic data and a nonlinear stochastic volatility model with real-world data.Comment: 41 pages, 7 figures. In press for Journal of Statistical Software. Source code for R, Python and MATLAB available at: https://github.com/compops/pmh-tutoria

Multiphase MCMC sampling for parameter inference in nonlinear ordinary differential equations

Traditionally, ODE parameter inference relies on solving the system of ODEs and assessing fit of the estimated signal with the observations. However, nonlinear ODEs often do not permit closed form solutions. Using numerical methods to solve the equations results in prohibitive computational costs, particularly when one adopts a Bayesian approach in sampling parameters from a posterior distribution. With the introduction of gradient matching, we can abandon the need to numerically solve the system of equations. Inherent in these efficient procedures is an introduction of bias to the learning problem as we no longer sample based on the exact likelihood function. This paper presents a multiphase MCMC approach that attempts to close the gap between efficiency and accuracy. By sampling using a surrogate likelihood, we accelerate convergence to the stationary distribution before sampling using the exact likelihood. We demonstrate that this method combines the efficiency of gradient matching and the accuracy of the exact likelihood scheme

A note on integrating products of linear forms over the unit simplex

Integrating a product of linear forms over the unit simplex can be done in polynomial time if the number of variables n is fixed (V. Baldoni et al., 2011). In this note, we highlight that this problem is equivalent to obtaining the normalizing constant of state probabilities for a popular class of Markov processes used in queueing network theory. In light of this equivalence, we survey existing computational algorithms developed in queueing theory that can be used for exact integration. For example, under some regularity conditions, queueing theory algorithms can exactly integrate a product of linear forms of total degree N by solving N systems of linear equations

Accelerating delayed-acceptance Markov chain Monte Carlo algorithms

Delayed-acceptance Markov chain Monte Carlo (DA-MCMC) samples from a probability distribution via a two-stages version of the Metropolis-Hastings algorithm, by combining the target distribution with a "surrogate" (i.e. an approximate and computationally cheaper version) of said distribution. DA-MCMC accelerates MCMC sampling in complex applications, while still targeting the exact distribution. We design a computationally faster, albeit approximate, DA-MCMC algorithm. We consider parameter inference in a Bayesian setting where a surrogate likelihood function is introduced in the delayed-acceptance scheme. When the evaluation of the likelihood function is computationally intensive, our scheme produces a 2-4 times speed-up, compared to standard DA-MCMC. However, the acceleration is highly problem dependent. Inference results for the standard delayed-acceptance algorithm and our approximated version are similar, indicating that our algorithm can return reliable Bayesian inference. As a computationally intensive case study, we introduce a novel stochastic differential equation model for protein folding data.Comment: 40 pages, 21 figures, 10 table

Riemannian Optimization via Frank-Wolfe Methods

We study projection-free methods for constrained Riemannian optimization. In particular, we propose the Riemannian Frank-Wolfe (RFW) method. We analyze non-asymptotic convergence rates of RFW to an optimum for (geodesically) convex problems, and to a critical point for nonconvex objectives. We also present a practical setting under which RFW can attain a linear convergence rate. As a concrete example, we specialize Rfw to the manifold of positive definite matrices and apply it to two tasks: (i) computing the matrix geometric mean (Riemannian centroid); and (ii) computing the Bures-Wasserstein barycenter. Both tasks involve geodesically convex interval constraints, for which we show that the Riemannian "linear oracle" required by RFW admits a closed-form solution; this result may be of independent interest. We further specialize RFW to the special orthogonal group and show that here too, the Riemannian "linear oracle" can be solved in closed form. Here, we describe an application to the synchronization of data matrices (Procrustes problem). We complement our theoretical results with an empirical comparison of Rfw against state-of-the-art Riemannian optimization methods and observe that RFW performs competitively on the task of computing Riemannian centroids.Comment: Under Review. Largely revised version, including an extended experimental section and an application to the special orthogonal group and the Procrustes proble