Hamiltonian ABC

Approximate Bayesian computation (ABC) is a powerful and elegant framework for performing inference in simulation-based models. However, due to the difficulty in scaling likelihood estimates, ABC remains useful for relatively low-dimensional problems. We introduce Hamiltonian ABC (HABC), a set of likelihood-free algorithms that apply recent advances in scaling Bayesian learning using Hamiltonian Monte Carlo (HMC) and stochastic gradients. We find that a small number forward simulations can effectively approximate the ABC gradient, allowing Hamiltonian dynamics to efficiently traverse parameter spaces. We also describe a new simple yet general approach of incorporating random seeds into the state of the Markov chain, further reducing the random walk behavior of HABC. We demonstrate HABC on several typical ABC problems, and show that HABC samples comparably to regular Bayesian inference using true gradients on a high-dimensional problem from machine learning.Comment: Submission to UAI 201

A spatial analysis of multivariate output from regional climate models

Climate models have become an important tool in the study of climate and climate change, and ensemble experiments consisting of multiple climate-model runs are used in studying and quantifying the uncertainty in climate-model output. However, there are often only a limited number of model runs available for a particular experiment, and one of the statistical challenges is to characterize the distribution of the model output. To that end, we have developed a multivariate hierarchical approach, at the heart of which is a new representation of a multivariate Markov random field. This approach allows for flexible modeling of the multivariate spatial dependencies, including the cross-dependencies between variables. We demonstrate this statistical model on an ensemble arising from a regional-climate-model experiment over the western United States, and we focus on the projected change in seasonal temperature and precipitation over the next 50 years.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS369 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

An empirical Bayes approach to identification of modules in dynamic networks

We present a new method of identifying a specific module in a dynamic network, possibly with feedback loops. Assuming known topology, we express the dynamics by an acyclic network composed of two blocks where the first block accounts for the relation between the known reference signals and the input to the target module, while the second block contains the target module. Using an empirical Bayes approach, we model the first block as a Gaussian vector with covariance matrix (kernel) given by the recently introduced stable spline kernel. The parameters of the target module are estimated by solving a marginal likelihood problem with a novel iterative scheme based on the Expectation-Maximization algorithm. Additionally, we extend the method to include additional measurements downstream of the target module. Using Markov Chain Monte Carlo techniques, it is shown that the same iterative scheme can solve also this formulation. Numerical experiments illustrate the effectiveness of the proposed methods

Data-Driven Model Reduction for the Bayesian Solution of Inverse Problems

One of the major challenges in the Bayesian solution of inverse problems governed by partial differential equations (PDEs) is the computational cost of repeatedly evaluating numerical PDE models, as required by Markov chain Monte Carlo (MCMC) methods for posterior sampling. This paper proposes a data-driven projection-based model reduction technique to reduce this computational cost. The proposed technique has two distinctive features. First, the model reduction strategy is tailored to inverse problems: the snapshots used to construct the reduced-order model are computed adaptively from the posterior distribution. Posterior exploration and model reduction are thus pursued simultaneously. Second, to avoid repeated evaluations of the full-scale numerical model as in a standard MCMC method, we couple the full-scale model and the reduced-order model together in the MCMC algorithm. This maintains accurate inference while reducing its overall computational cost. In numerical experiments considering steady-state flow in a porous medium, the data-driven reduced-order model achieves better accuracy than a reduced-order model constructed using the classical approach. It also improves posterior sampling efficiency by several orders of magnitude compared to a standard MCMC method