results for au:Marzouk_Y in:stat

- We study Bayesian inference methods for solving linear inverse problems, focusing on hierarchical formulations where the prior or the likelihood function depend on unspecified hyperparameters. In practice, these hyperparameters are often determined via an empirical Bayesian method that maximizes the marginal likelihood function, i.e., the probability density of the data conditional on the hyperparameters. Evaluating the marginal likelihood, however, is computationally challenging for large-scale problems. In this work, we present a method to approximately evaluate marginal likelihood functions, based on a low-rank approximation of the update from the prior covariance to the posterior covariance. We show that this approximation is optimal in a minimax sense. Moreover, we provide an efficient algorithm to implement the proposed method, based on a combination of the randomized SVD and a spectral approximation method to compute square roots of the prior covariance matrix. Several numerical examples demonstrate good performance of the proposed method.
- The development of chemical reaction models aids system design and optimization, along with fundamental understanding, in areas including combustion, catalysis, electrochemistry, and biology. A systematic approach to building reaction network models uses available data not only to estimate unknown parameters, but also to learn the model structure. Bayesian inference provides a natural approach to this data-driven construction of models. Traditional Bayesian model inference methodology is based on evaluating a multidimensional integral for each model. This approach is often infeasible for nonlinear reaction network inference, as the number of plausible models can be combinatorially large. An alternative approach based on model-space sampling can enable large-scale network inference, but its efficient implementation presents many challenges. In this paper, we present new computational methods that make large-scale nonlinear network inference tractable. Firstly, we exploit the network-based interactions of species to design improved "between-model" proposals for Markov chain Monte Carlo (MCMC). We then introduce a sensitivity-based determination of move types which, when combined with the network-aware proposals, yields further sampling efficiency. These algorithms are tested on example problems with up to 1024 plausible models. We find that our new algorithms yield significant gains in sampling performance, thus providing a means for tractable inference over a large number reaction models with physics-based nonlinear species interactions.
- Integration against an intractable probability measure is among the fundamental challenges of statistical inference, particularly in the Bayesian setting. A principled approach to this problem seeks a deterministic coupling of the measure of interest with a tractable "reference" measure (e.g., a standard Gaussian). This coupling is induced by a transport map, and enables direct simulation from the desired measure simply by evaluating the transport map at samples from the reference. Yet characterizing such a map---e.g., representing and evaluating it---grows challenging in high dimensions. The central contribution of this paper is to establish a link between the Markov properties of the target measure and the existence of certain low-dimensional couplings, induced by transport maps that are sparse or decomposable. Our analysis not only facilitates the construction of couplings in high-dimensional settings, but also suggests new inference methodologies. For instance, in the context of nonlinear and non-Gaussian state space models, we describe new variational algorithms for online filtering, smoothing, and parameter estimation. These algorithms implicitly characterize---via a transport map---the full posterior distribution of the sequential inference problem using local operations only incrementally more complex than regular filtering, while avoiding importance sampling or resampling.
- Mar 16 2017 stat.CO arXiv:1703.04866v1In this article we develop a new sequential Monte Carlo (SMC) method for multilevel (ML) Monte Carlo estimation. In particular, the method can be used to estimate expectations with respect to a target probability distribution over an infinite-dimensional and non-compact space as given, for example, by a Bayesian inverse problem with Gaussian random field prior. Under suitable assumptions the MLSMC method has the optimal $O(\epsilon^{-2})$ bound on the cost to obtain a mean-square error of $O(\epsilon^2)$. The algorithm is accelerated by dimension-independent likelihood-informed (DILI) proposals designed for Gaussian priors, leveraging a novel variation which uses empirical sample covariance information in lieu of Hessian information, hence eliminating the requirement for gradient evaluations. The efficiency of the algorithm is illustrated on two examples: inversion of noisy pressure measurements in a PDE model of Darcy flow to recover the posterior distribution of the permeability field, and inversion of noisy measurements of the solution of an SDE to recover the posterior path measure.
- Performing Bayesian inference via Markov chain Monte Carlo (MCMC) can be exceedingly expensive when posterior evaluations invoke the evaluation of a computationally expensive model, such as a system of partial differential equations. In recent work [Conrad et al. JASA 2015, arXiv:1402.1694] we described a framework for constructing and refining local approximations of such models during an MCMC simulation. These posterior--adapted approximations harness regularity of the model to reduce the computational cost of inference while preserving asymptotic exactness of the Markov chain. Here we describe two extensions of that work. First, focusing on the Metropolis--adjusted Langevin algorithm, we describe how a proposal distribution can successfully employ gradients and other relevant information extracted from the approximation. Second, we prove that samplers running in parallel can collaboratively construct a shared posterior approximation while ensuring ergodicity of each associated chain, providing a novel opportunity for exploiting parallel computation in MCMC. We investigate the practical performance of our strategies using two challenging inference problems, the first in subsurface hydrology and the second in glaciology. Using local approximations constructed via parallel chains, we successfully reduce the run time needed to characterize the posterior distributions in these problems from days to hours and from months to days, respectively, dramatically improving the tractability of Bayesian inference.
- We propose optimal dimensionality reduction techniques for the solution of goal-oriented linear-Gaussian inverse problems, where the quantity of interest (QoI) is a function of the inversion parameters. These approximations are suitable for large-scale applications. In particular, we study the approximation of the posterior covariance of the QoI as a low-rank negative update of its prior covariance, and prove optimality of this update with respect to the natural geodesic distance on the manifold of symmetric positive definite matrices. Assuming exact knowledge of the posterior mean of the QoI, the optimality results extend to optimality in distribution with respect to the Kullback-Leibler divergence and the Hellinger distance between the associated distributions. We also propose approximation of the posterior mean of the QoI as a low-rank linear function of the data, and prove optimality of this approximation with respect to a weighted Bayes risk. Both of these optimal approximations avoid the explicit computation of the full posterior distribution of the parameters and instead focus on directions that are well informed by the data and relevant to the QoI. These directions stem from a balance among all the components of the goal-oriented inverse problem: prior information, forward model, measurement noise, and ultimate goals. We illustrate the theory using a high-dimensional inverse problem in heat transfer.
- Jul 08 2016 stat.CO arXiv:1607.01904v2Prior distributions for Bayesian inference that rely on the $l_1$-norm of the parameters are of considerable interest, in part because they promote parameter fields with less regularity than Gaussian priors (e.g., discontinuities and blockiness). These $l_1$-type priors include the total variation (TV) prior and the Besov $B^s_{1,1}$ space prior, and in general yield non-Gaussian posterior distributions. Sampling from these posteriors is challenging, particularly in the inverse problem setting where the parameter space is high-dimensional and the forward problem may be nonlinear. This paper extends the randomize-then-optimize (RTO) method, an optimization-based sampling algorithm developed for Bayesian inverse problems with Gaussian priors, to inverse problems with $l_1$-type priors. We use a variable transformation to convert an $l_1$-type prior to a standard Gaussian prior, such that the posterior distribution of the transformed parameters is amenable to Metropolized sampling via RTO. We demonstrate this approach on several deconvolution problems and an elliptic PDE inverse problem, using TV or Besov $B^s_{1,1}$ space priors. Our results show that the transformed RTO algorithm characterizes the correct posterior distribution and can be more efficient than other sampling algorithms. The variable transformation can also be extended to other non-Gaussian priors.
- The design of multiple experiments is commonly undertaken via suboptimal strategies, such as batch (open-loop) design that omits feedback or greedy (myopic) design that does not account for future effects. This paper introduces new strategies for the optimal design of sequential experiments. First, we rigorously formulate the general sequential optimal experimental design (sOED) problem as a dynamic program. Batch and greedy designs are shown to result from special cases of this formulation. We then focus on sOED for parameter inference, adopting a Bayesian formulation with an information theoretic design objective. To make the problem tractable, we develop new numerical approaches for nonlinear design with continuous parameter, design, and observation spaces. We approximate the optimal policy by using backward induction with regression to construct and refine value function approximations in the dynamic program. The proposed algorithm iteratively generates trajectories via exploration and exploitation to improve approximation accuracy in frequently visited regions of the state space. Numerical results are verified against analytical solutions in a linear-Gaussian setting. Advantages over batch and greedy design are then demonstrated on a nonlinear source inversion problem where we seek an optimal policy for sequential sensing.
- We present the fundamentals of a measure transport approach to sampling. The idea is to construct a deterministic coupling---i.e., a transport map---between a complex "target" probability measure of interest and a simpler reference measure. Given a transport map, one can generate arbitrarily many independent and unweighted samples from the target simply by pushing forward reference samples through the map. We consider two different and complementary scenarios: first, when only evaluations of the unnormalized target density are available, and second, when the target distribution is known only through a finite collection of samples. We show that in both settings the desired transports can be characterized as the solutions of variational problems. We then address practical issues associated with the optimization--based construction of transports: choosing finite-dimensional parameterizations of the map, enforcing monotonicity, quantifying the error of approximate transports, and refining approximate transports by enriching the corresponding approximation spaces. Approximate transports can also be used to "Gaussianize" complex distributions and thus precondition conventional asymptotically exact sampling schemes. We place the measure transport approach in broader context, describing connections with other optimization--based samplers, with inference and density estimation schemes using optimal transport, and with alternative transformation--based approaches to simulation. We also sketch current work aimed at the construction of transport maps in high dimensions, exploiting essential features of the target distribution (e.g., conditional independence, low-rank structure). The approaches and algorithms presented here have direct applications to Bayesian computation and to broader problems of stochastic simulation.
- Two major bottlenecks to the solution of large-scale Bayesian inverse problems are the scaling of posterior sampling algorithms to high-dimensional parameter spaces and the computational cost of forward model evaluations. Yet incomplete or noisy data, the state variation and parameter dependence of the forward model, and correlations in the prior collectively provide useful structure that can be exploited for dimension reduction in this setting--both in the parameter space of the inverse problem and in the state space of the forward model. To this end, we show how to jointly construct low-dimensional subspaces of the parameter space and the state space in order to accelerate the Bayesian solution of the inverse problem. As a byproduct of state dimension reduction, we also show how to identify low-dimensional subspaces of the data in problems with high-dimensional observations. These subspaces enable approximation of the posterior as a product of two factors: (i) a projection of the posterior onto a low-dimensional parameter subspace, wherein the original likelihood is replaced by an approximation involving a reduced model; and (ii) the marginal prior distribution on the high-dimensional complement of the parameter subspace. We present and compare several strategies for constructing these subspaces using only a limited number of forward and adjoint model simulations. The resulting posterior approximations can rapidly be characterized using standard sampling techniques, e.g., Markov chain Monte Carlo. Two numerical examples demonstrate the accuracy and efficiency of our approach: inversion of an integral equation in atmospheric remote sensing, where the data dimension is very high; and the inference of a heterogeneous transmissivity field in a groundwater system, which involves a partial differential equation forward model with high dimensional state and parameters.
- A priori dimension reduction is a widely adopted technique for reducing the computational complexity of stationary inverse problems. In this setting, the solution of an inverse problem is parameterized by a low-dimensional basis that is often obtained from the truncated Karhunen-Loeve expansion of the prior distribution. For high-dimensional inverse problems equipped with smoothing priors, this technique can lead to drastic reductions in parameter dimension and significant computational savings. In this paper, we extend the concept of a priori dimension reduction to non-stationary inverse problems, in which the goal is to sequentially infer the state of a dynamical system. Our approach proceeds in an offline-online fashion. We first identify a low-dimensional subspace in the state space before solving the inverse problem (the offline phase), using either the method of "snapshots" or regularized covariance estimation. Then this subspace is used to reduce the computational complexity of various filtering algorithms - including the Kalman filter, extended Kalman filter, and ensemble Kalman filter - within a novel subspace-constrained Bayesian prediction-and-update procedure (the online phase). We demonstrate the performance of our new dimension reduction approach on various numerical examples. In some test cases, our approach reduces the dimensionality of the original problem by orders of magnitude and yields up to two orders of magnitude in computational savings.
- In many inverse problems, model parameters cannot be precisely determined from observational data. Bayesian inference provides a mechanism for capturing the resulting parameter uncertainty, but typically at a high computational cost. This work introduces a multiscale decomposition that exploits conditional independence across scales, when present in certain classes of inverse problems, to decouple Bayesian inference into two stages: (1) a computationally tractable coarse-scale inference problem; and (2) a mapping of the low-dimensional coarse-scale posterior distribution into the original high-dimensional parameter space. This decomposition relies on a characterization of the non-Gaussian joint distribution of coarse- and fine-scale quantities via optimal transport maps. We demonstrate our approach on a sequence of inverse problems arising in subsurface flow, using the multiscale finite element method to discretize the steady state pressure equation. We compare the multiscale strategy with full-dimensional Markov chain Monte Carlo on a problem of moderate dimension (100 parameters) and then use it to infer a conductivity field described by over 10,000 parameters.
- This paper examines experimental design procedures used to develop surrogates of computational models, exploring the interplay between experimental designs and approximation algorithms. We focus on two widely used approximation approaches, Gaussian process (GP) regression and non-intrusive polynomial approximation. First, we introduce algorithms for minimizing a posterior integrated variance (IVAR) design criterion for GP regression. Our formulation treats design as a continuous optimization problem that can be solved with gradient-based methods on complex input domains, without resorting to greedy approximations. We show that minimizing IVAR in this way yields point sets with good interpolation properties, and that it enables more accurate GP regression than designs based on entropy minimization or mutual information maximization. Second, using a Mercer kernel/eigenfunction perspective on GP regression, we identify conditions under which GP regression coincides with pseudospectral polynomial approximation. Departures from these conditions can be understood as changes either to the kernel or to the experimental design itself. We then show how IVAR-optimal designs, while sacrificing discrete orthogonality of the kernel eigenfunctions, can yield lower approximation error than orthogonalizing point sets. Finally, we compare the performance of adaptive Gaussian process regression and adaptive pseudospectral approximation for several classes of target functions, identifying features that are favorable to the GP + IVAR approach.
- Dec 18 2014 stat.CO arXiv:1412.5492v3We introduce a new framework for efficient sampling from complex probability distributions, using a combination of optimal transport maps and the Metropolis-Hastings rule. The core idea is to use continuous transportation to transform typical Metropolis proposal mechanisms (e.g., random walks, Langevin methods) into non-Gaussian proposal distributions that can more effectively explore the target density. Our approach adaptively constructs a lower triangular transport map-an approximation of the Knothe-Rosenblatt rearrangement-using information from previous MCMC states, via the solution of an optimization problem. This optimization problem is convex regardless of the form of the target distribution. It is solved efficiently using a Newton method that requires no gradient information from the target probability distribution; the target distribution is instead represented via samples. Sequential updates enable efficient and parallelizable adaptation of the map even for large numbers of samples. We show that this approach uses inexact or truncated maps to produce an adaptive MCMC algorithm that is ergodic for the exact target distribution. Numerical demonstrations on a range of parameter inference problems show order-of-magnitude speedups over standard MCMC techniques, measured by the number of effectively independent samples produced per target density evaluation and per unit of wallclock time.
- Many Bayesian inference problems require exploring the posterior distribution of high-dimensional parameters that represent the discretization of an underlying function. This work introduces a family of Markov chain Monte Carlo (MCMC) samplers that can adapt to the particular structure of a posterior distribution over functions. Two distinct lines of research intersect in the methods developed here. First, we introduce a general class of operator-weighted proposal distributions that are well defined on function space, such that the performance of the resulting MCMC samplers is independent of the discretization of the function. Second, by exploiting local Hessian information and any associated low-dimensional structure in the change from prior to posterior distributions, we develop an inhomogeneous discretization scheme for the Langevin stochastic differential equation that yields operator-weighted proposals adapted to the non-Gaussian structure of the posterior. The resulting dimension-independent, likelihood-informed (DILI) MCMC samplers may be useful for a large class of high-dimensional problems where the target probability measure has a density with respect to a Gaussian reference measure. Two nonlinear inverse problems are used to demonstrate the efficiency of these DILI samplers: an elliptic PDE coefficient inverse problem and path reconstruction in a conditioned diffusion.
- In the Bayesian approach to inverse problems, data are often informative, relative to the prior, only on a low-dimensional subspace of the parameter space. Significant computational savings can be achieved by using this subspace to characterize and approximate the posterior distribution of the parameters. We first investigate approximation of the posterior covariance matrix as a low-rank update of the prior covariance matrix. We prove optimality of a particular update, based on the leading eigendirections of the matrix pencil defined by the Hessian of the negative log-likelihood and the prior precision, for a broad class of loss functions. This class includes the FĂ¶rstner metric for symmetric positive definite matrices, as well as the Kullback-Leibler divergence and the Hellinger distance between the associated distributions. We also propose two fast approximations of the posterior mean and prove their optimality with respect to a weighted Bayes risk under squared-error loss. These approximations are deployed in an offline-online manner, where a more costly but data-independent offline calculation is followed by fast online evaluations. As a result, these approximations are particularly useful when repeated posterior mean evaluations are required for multiple data sets. We demonstrate our theoretical results with several numerical examples, including high-dimensional X-ray tomography and an inverse heat conduction problem. In both of these examples, the intrinsic low-dimensional structure of the inference problem can be exploited while producing results that are essentially indistinguishable from solutions computed in the full space.
- The intrinsic dimensionality of an inverse problem is affected by prior information, the accuracy and number of observations, and the smoothing properties of the forward operator. From a Bayesian perspective, changes from the prior to the posterior may, in many problems, be confined to a relatively low-dimensional subspace of the parameter space. We present a dimension reduction approach that defines and identifies such a subspace, called the "likelihood-informed subspace" (LIS), by characterizing the relative influences of the prior and the likelihood over the support of the posterior distribution. This identification enables new and more efficient computational methods for Bayesian inference with nonlinear forward models and Gaussian priors. In particular, we approximate the posterior distribution as the product of a lower-dimensional posterior defined on the LIS and the prior distribution marginalized onto the complementary subspace. Markov chain Monte Carlo sampling can then proceed in lower dimensions, with significant gains in computational efficiency. We also introduce a Rao-Blackwellization strategy that de-randomizes Monte Carlo estimates of posterior expectations for additional variance reduction. We demonstrate the efficiency of our methods using two numerical examples: inference of permeability in a groundwater system governed by an elliptic PDE, and an atmospheric remote sensing problem based on Global Ozone Monitoring System (GOMOS) observations.
- 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.
- We construct a new framework for accelerating Markov chain Monte Carlo in posterior sampling problems where standard methods are limited by the computational cost of the likelihood, or of numerical models embedded therein. Our approach introduces local approximations of these models into the Metropolis-Hastings kernel, borrowing ideas from deterministic approximation theory, optimization, and experimental design. Previous efforts at integrating approximate models into inference typically sacrifice either the sampler's exactness or efficiency; our work seeks to address these limitations by exploiting useful convergence characteristics of local approximations. We prove the ergodicity of our approximate Markov chain, showing that it samples asymptotically from the \emphexact posterior distribution of interest. We describe variations of the algorithm that employ either local polynomial approximations or local Gaussian process regressors. Our theoretical results reinforce the key observation underlying this paper: when the likelihood has some \emphlocal regularity, the number of model evaluations per MCMC step can be greatly reduced without biasing the Monte Carlo average. Numerical experiments demonstrate multiple order-of-magnitude reductions in the number of forward model evaluations used in representative ODE and PDE inference problems, with both synthetic and real data.
- The Bayesian approach to inverse problems typically relies on posterior sampling approaches, such as Markov chain Monte Carlo, for which the generation of each sample requires one or more evaluations of the parameter-to-observable map or forward model. When these evaluations are computationally intensive, approximations of the forward model are essential to accelerating sample-based inference. Yet the construction of globally accurate approximations for nonlinear forward models can be computationally prohibitive and in fact unnecessary, as the posterior distribution typically concentrates on a small fraction of the support of the prior distribution. We present a new approach that uses stochastic optimization to construct polynomial approximations over a sequence of measures adaptively determined from the data, eventually concentrating on the posterior distribution. The approach yields substantial gains in efficiency and accuracy over prior-based surrogates, as demonstrated via application to inverse problems in partial differential equations.
- Optimal experimental design (OED) seeks experiments expected to yield the most useful data for some purpose. In practical circumstances where experiments are time-consuming or resource-intensive, OED can yield enormous savings. We pursue OED for nonlinear systems from a Bayesian perspective, with the goal of choosing experiments that are optimal for parameter inference. Our objective in this context is the expected information gain in model parameters, which in general can only be estimated using Monte Carlo methods. Maximizing this objective thus becomes a stochastic optimization problem. This paper develops gradient-based stochastic optimization methods for the design of experiments on a continuous parameter space. Given a Monte Carlo estimator of expected information gain, we use infinitesimal perturbation analysis to derive gradients of this estimator. We are then able to formulate two gradient-based stochastic optimization approaches: (i) Robbins-Monro stochastic approximation, and (ii) sample average approximation combined with a deterministic quasi-Newton method. A polynomial chaos approximation of the forward model accelerates objective and gradient evaluations in both cases. We discuss the implementation of these optimization methods, then conduct an empirical comparison of their performance. To demonstrate design in a nonlinear setting with partial differential equation forward models, we use the problem of sensor placement for source inversion. Numerical results yield useful guidelines on the choice of algorithm and sample sizes, assess the impact of estimator bias, and quantify tradeoffs of computational cost versus solution quality and robustness.
- We present a new approach to Bayesian inference that entirely avoids Markov chain simulation, by constructing a map that pushes forward the prior measure to the posterior measure. Existence and uniqueness of a suitable measure-preserving map is established by formulating the problem in the context of optimal transport theory. We discuss various means of explicitly parameterizing the map and computing it efficiently through solution of an optimization problem, exploiting gradient information from the forward model when possible. The resulting algorithm overcomes many of the computational bottlenecks associated with Markov chain Monte Carlo. Advantages of a map-based representation of the posterior include analytical expressions for posterior moments and the ability to generate arbitrary numbers of independent posterior samples without additional likelihood evaluations or forward solves. The optimization approach also provides clear convergence criteria for posterior approximation and facilitates model selection through automatic evaluation of the marginal likelihood. We demonstrate the accuracy and efficiency of the approach on nonlinear inverse problems of varying dimension, involving the inference of parameters appearing in ordinary and partial differential equations.
- The optimal selection of experimental conditions is essential to maximizing the value of data for inference and prediction, particularly in situations where experiments are time-consuming and expensive to conduct. We propose a general mathematical framework and an algorithmic approach for optimal experimental design with nonlinear simulation-based models; in particular, we focus on finding sets of experiments that provide the most information about targeted sets of parameters. Our framework employs a Bayesian statistical setting, which provides a foundation for inference from noisy, indirect, and incomplete data, and a natural mechanism for incorporating heterogeneous sources of information. An objective function is constructed from information theoretic measures, reflecting expected information gain from proposed combinations of experiments. Polynomial chaos approximations and a two-stage Monte Carlo sampling method are used to evaluate the expected information gain. Stochastic approximation algorithms are then used to make optimization feasible in computationally intensive and high-dimensional settings. These algorithms are demonstrated on model problems and on nonlinear parameter estimation problems arising in detailed combustion kinetics.