arXiv subjects

Noemi Petra

Publications and source records attributed to Noemi Petra.

18 recordsLinked to original sources

arXiv2025

Taylor Approximation Variance Reduction for Approximation Errors in PDE-constrained Bayesian Inverse Problems

In numerous applications, surrogate models are used as a replacement for accurate parameter-to-observable mappings when solving large-scale inverse problems governed by partial differential equations (PDEs). The surrogate model may be a computationally cheaper alternative to the accurate parameter-to-observable mappings and/or may ignore additional unknowns or sources of uncertainty. The Bayesian approximation error (BAE) approach provides a means to account for the induced uncertainties and approximation errors (between the accurate parameter-to-observable mapping and the surrogate). The statistics of these errors are in general unknown a priori, and are thus calculated using Monte Carlo sampling. Although the sampling is typically carried out offline the process can still represent a computational bottleneck. In this work, we develop a scalable computational approach for reducing the costs associated with the sampling stage of the BAE approach. Specifically, we consider the Taylor expansion of the accurate and surrogate forward models with respect to the uncertain parameter fields either as a control variate for variance reduction or as a means to efficiently approximate the mean and covariance of the approximation errors. We propose efficient methods for evaluating the expressions for the mean and covariance of the Taylor approximations based on linear(-ized) PDE solves. Furthermore, the proposed approach is independent of the dimension of the uncertain parameter, depending instead on the intrinsic dimension of the data, ensuring scalability to high-dimensional problems. The potential benefits of the proposed approach are demonstrated for two high-dimensional inverse problems governed by PDE examples, namely for the estimation of a distributed Robin boundary coefficient in a linear diffusion problem, and for a coefficient estimation problem governed by a nonlinear diffusion problem.

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arXiv2024

A Scalable Interior-Point Gauss-Newton Method for PDE-Constrained Optimization with Bound Constraints

We present a scalable approach to solve a class of elliptic partial differential equation (PDE)-constrained optimization problems with bound constraints. This approach utilizes a robust full-space interior-point (IP)-Gauss-Newton optimization method. To cope with the poorly-conditioned IP-Gauss-Newton saddle-point linear systems that need to be solved, once per optimization step, we propose two spectrally related preconditioners. These preconditioners leverage the limited informativeness of data in regularized PDE-constrained optimization problems. A block Gauss-Seidel preconditioner is proposed for the GMRES-based solution of the IP-Gauss-Newton linear systems. It is shown, for a large-class of PDE- and bound-constrained optimization problems, that the spectrum of the block Gauss-Seidel preconditioned IP-Gauss-Newton matrix is asymptotically independent of discretization and is not impacted by the ill-conditioning that notoriously plagues interior-point methods. We propose a regularization and log-barrier Hessian preconditioner for the preconditioned conjugate gradient (PCG)-based solution of the related IP-Gauss-Newton-Schur complement linear systems. The scalability of the approach is demonstrated on an example problem with bound and nonlinear elliptic PDE constraints. The numerical solution of the optimization problem is shown to require a discretization independent number of IP-Gauss-Newton linear solves. Furthermore, the linear systems are solved in a discretization and IP ill-conditioning independent number of preconditioned Krylov subspace iterations. The parallel scalability of preconditioner and linear system matrix applies, achieved with algebraic multigrid based solvers, and the aforementioned algorithmic scalability permits a parallel scalable means to compute solutions of a large class of PDE- and bound-constrained problems.

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arXiv2024

Democratizing Uncertainty Quantification

Uncertainty Quantification (UQ) is vital to safety-critical model-based analyses, but the widespread adoption of sophisticated UQ methods is limited by technical complexity. In this paper, we introduce UM-Bridge (the UQ and Modeling Bridge), a high-level abstraction and software protocol that facilitates universal interoperability of UQ software with simulation codes. It breaks down the technical complexity of advanced UQ applications and enables separation of concerns between experts. UM-Bridge democratizes UQ by allowing effective interdisciplinary collaboration, accelerating the development of advanced UQ methods, and making it easy to perform UQ analyses from prototype to High Performance Computing (HPC) scale. In addition, we present a library of ready-to-run UQ benchmark problems, all easily accessible through UM-Bridge. These benchmarks support UQ methodology research, enabling reproducible performance comparisons. We demonstrate UM-Bridge with several scientific applications, harnessing HPC resources even using UQ codes not designed with HPC support.

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arXiv2024

Optimal design of large-scale nonlinear Bayesian inverse problems under model uncertainty

We consider optimal experimental design (OED) for Bayesian nonlinear inverse problems governed by partial differential equations (PDEs) under model uncertainty. Specifically, we consider inverse problems in which, in addition to the inversion parameters, the governing PDEs include secondary uncertain parameters. We focus on problems with infinite-dimensional inversion and secondary parameters and present a scalable computational framework for optimal design of such problems. The proposed approach enables Bayesian inversion and OED under uncertainty within a unified framework. We build on the Bayesian approximation error (BAE) approach, to incorporate modeling uncertainties in the Bayesian inverse problem, and methods for A-optimal design of infinite-dimensional Bayesian nonlinear inverse problems. Specifically, a Gaussian approximation to the posterior at the maximum a posteriori probability point is used to define an uncertainty aware OED objective that is tractable to evaluate and optimize. In particular, the OED objective can be computed at a cost, in the number of PDE solves, that does not grow with the dimension of the discretized inversion and secondary parameters. The OED problem is formulated as a binary bilevel PDE constrained optimization problem and a greedy algorithm, which provides a pragmatic approach, is used to find optimal designs. We demonstrate the effectiveness of the proposed approach for a model inverse problem governed by an elliptic PDE on a three-dimensional domain. Our computational results also highlight the pitfalls of ignoring modeling uncertainties in the OED and/or inference stages.

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arXiv2024

Point spread function approximation of high rank Hessians with locally supported non-negative integral kernels

We present an efficient matrix-free point spread function (PSF) method for approximating operators that have locally supported non-negative integral kernels. The method computes impulse responses at scattered points, and interpolates these impulse responses to approximate integral kernel entries. Impulse responses are computed by applying the operator to Dirac comb batches of point sources, which are chosen via an ellipsoid packing procedure. Evaluation of kernel entries allows us to construct a hierarchical matrix approximation of the operator, which is used for further matrix computations. We illustrate the end-to-end method on a blur problem, then use the method to build preconditioners for the Hessian in two inverse problems governed by partial differential equations (PDEs): inversion for the basal friction coefficient in an ice sheet flow problem and for the initial condition in an advective-diffusive transport problem. While for many ill-posed inverse problems the Hessian of the data misfit term exhibits a low rank structure, and hence a low rank approximation is suitable, for many problems of practical interest the numerical rank of the Hessian is still large. But Hessian impulse responses typically become more local as the numerical rank increases, which benefits the PSF method. Numerical results reveal that the PSF preconditioner clusters the spectrum of the preconditioned Hessian near one, yielding roughly 5x-10x reductions in the required number of PDE solves, as compared to regularization preconditioning and no preconditioning. We also present a numerical study for the influence of various parameters (that control the shape of the impulse responses) on the effectiveness of the advection-diffusion Hessian approximation. The results show that the PSF-based preconditioners are able to form good approximations of high-rank Hessians using a small number of operator applications.

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arXiv2023

Further analysis of multilevel Stein variational gradient descent with an application to the Bayesian inference of glacier ice models

Multilevel Stein variational gradient descent is a method for particle-based variational inference that leverages hierarchies of surrogate target distributions with varying costs and fidelity to computationally speed up inference. The contribution of this work is twofold. First, an extension of a previous cost complexity analysis is presented that applies even when the exponential convergence rate of single-level Stein variational gradient descent depends on iteration-varying parameters. Second, multilevel Stein variational gradient descent is applied to a large-scale Bayesian inverse problem of inferring discretized basal sliding coefficient fields of the Arolla glacier ice. The numerical experiments demonstrate that the multilevel version achieves orders of magnitude speedups compared to its single-level version.

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arXiv2023

Hierarchical off-diagonal low-rank approximation of Hessians in inverse problems, with application to ice sheet model initializaiton

Obtaining lightweight and accurate approximations of Hessian applies in inverse problems governed by partial differential equations (PDEs) is an essential task to make both deterministic and Bayesian statistical large-scale inverse problems computationally tractable. The $\mathcal{O}(N^{3})$ computational complexity of dense linear algebraic routines such as that needed for sampling from Gaussian proposal distributions and Newton solves by direct linear methods, can be reduced to log-linear complexity by utilizing hierarchical off-diagonal low-rank (HODLR) matrix approximations. In this work, we show that a class of Hessians that arise from inverse problems governed by PDEs are well approximated by the HODLR matrix format. In particular, we study inverse problems governed by PDEs that model the instantaneous viscous flow of ice sheets. In these problems, we seek a spatially distributed basal sliding parameter field such that the flow predicted by the ice sheet model is consistent with ice sheet surface velocity observations. We demonstrate the use of HODLR approximation by efficiently generating Hessian approximations that allow fast generation of samples from a Gaussianized posterior proposal distribution. Computational studies are performed which illustrate ice sheet problem regimes for which the Gauss-Newton data-misfit Hessian is more efficiently approximated by the HODLR matrix format than the low-rank (LR) format. We then demonstrate that HODLR approximations can be favorable, when compared to global low-rank approximations, for large-scale problems by studying the data-misfit Hessian associated to inverse problems governed by the Stokes flow model on the Humboldt glacier and Greenland ice sheets.

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arXiv2022

hIPPYlib-MUQ: A Bayesian Inference Software Framework for Integration of Data with Complex Predictive Models under Uncertainty

Bayesian inference provides a systematic framework for integration of data with mathematical models to quantify the uncertainty in the solution of the inverse problem. However, the solution of Bayesian inverse problems governed by complex forward models described by partial differential equations (PDEs) remains prohibitive with black-box Markov chain Monte Carlo (MCMC) methods. We present hIPPYlib-MUQ, an extensible and scalable software framework that contains implementations of state-of-the art algorithms aimed to overcome the challenges of high-dimensional, PDE-constrained Bayesian inverse problems. These algorithms accelerate MCMC sampling by exploiting the geometry and intrinsic low-dimensionality of parameter space via derivative information and low rank approximation. The software integrates two complementary open-source software packages, hIPPYlib and MUQ. hIPPYlib solves PDE-constrained inverse problems using automatically-generated adjoint-based derivatives, but it lacks full Bayesian capabilities. MUQ provides a spectrum of powerful Bayesian inversion models and algorithms, but expects forward models to come equipped with gradients and Hessians to permit large-scale solution. By combining these two libraries, we created a robust, scalable, and efficient software framework that realizes the benefits of each and allows us to tackle complex large-scale Bayesian inverse problems. To illustrate the capabilities of hIPPYlib-MUQ, we present a comparison of a number of MCMC methods on several inverse problems. These include problems with linear and nonlinear PDEs, various noise models, and different parameter dimensions. The results demonstrate that large ($\sim 50\times$) speedups over conventional black box and gradient-based MCMC algorithms can be obtained by exploiting Hessian information (from the log posterior), underscoring the power of the integrated hIPPYlib-MUQ framework.

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arXiv2020

hIPPYlib: An Extensible Software Framework for Large-Scale Inverse Problems Governed by PDEs; Part I: Deterministic Inversion and Linearized Bayesian Inference

We present an extensible software framework, hIPPYlib, for solution of large-scale deterministic and Bayesian inverse problems governed by partial differential equations (PDEs) with infinite-dimensional parameter fields (which are high-dimensional after discretization). hIPPYlib overcomes the prohibitive nature of Bayesian inversion for this class of problems by implementing state-of-the-art scalable algorithms for PDE-based inverse problems that exploit the structure of the underlying operators, notably the Hessian of the log-posterior. The key property of the algorithms implemented in hIPPYlib is that the solution of the deterministic and linearized Bayesian inverse problem is computed at a cost, measured in linearized forward PDE solves, that is independent of the parameter dimension. The mean of the posterior is approximated by the MAP point, which is found by minimizing the negative log-posterior. This deterministic nonlinear least-squares optimization problem is solved with an inexact matrix-free Newton-CG method. The posterior covariance is approximated by the inverse of the Hessian of the negative log posterior evaluated at the MAP point. This Gaussian approximation is exact when the parameter-to-observable map is linear; otherwise, its logarithm agrees to two derivatives with the log-posterior at the MAP point, and thus it can serve as a proposal for Hessian-based MCMC methods. The construction of the posterior covariance is made tractable by invoking a low-rank approximation of the Hessian of the log-likelihood. Scalable tools for sample generation are also implemented. hIPPYlib makes all of these advanced algorithms easily accessible to domain scientists and provides an environment that expedites the development of new algorithms. hIPPYlib is also a teaching tool to educate researchers and practitioners who are new to inverse problems and the Bayesian inference framework.

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arXiv2020

Optimal design of large-scale Bayesian linear inverse problems under reducible model uncertainty: good to know what you don't know

We consider optimal design of infinite-dimensional Bayesian linear inverse problems governed by partial differential equations that contain secondary reducible model uncertainties, in addition to the uncertainty in the inversion parameters. By reducible uncertainties we refer to parametric uncertainties that can be reduced through parameter inference. We seek experimental designs that minimize the posterior uncertainty in the primary parameters, while accounting for the uncertainty in secondary parameters. We accomplish this by deriving a marginalized A-optimality criterion and developing an efficient computational approach for its optimization. We illustrate our approach for estimating an uncertain time-dependent source in a contaminant transport model with an uncertain initial state as secondary uncertainty. Our results indicate that accounting for additional model uncertainty in the experimental design process is crucial.

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arXiv2019

Statistical Treatment of Inverse Problems Constrained by Differential Equations-Based Models with Stochastic Terms

This paper introduces a statistical treatment of inverse problems constrained by models with stochastic terms. The solution of the forward problem is given by a distribution represented numerically by an ensemble of simulations. The goal is to formulate the inverse problem, in particular the objective function, to find the closest forward distribution (i.e., the output of the stochastic forward problem) that best explains the distribution of the observations in a certain metric. We use proper scoring rules, a concept employed in statistical forecast verification, namely energy, variogram, and hybrid (i.e., combination of the two) scores. We study the performance of the proposed formulation in the context of two applications: a coefficient field inversion for subsurface flow governed by an elliptic partial differential equation (PDE) with a stochastic source and a parameter inversion for power grid governed by differential-algebraic equations (DAEs). In both cases we show that the variogram and the hybrid scores show better parameter inversion results than does the energy score, whereas the energy score leads to better probabilistic predictions.

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arXiv2018

Estimation of the Robin coefficient field in a Poisson problem with uncertain conductivity field

We consider the reconstruction of a heterogeneous coefficient field in a Robin boundary condition on an inaccessible part of the boundary in a Poisson problem with an uncertain (or unknown) inhomogeneous conductivity field in the interior of the domain. To account for model errors that stem from the uncertainty in the conductivity coefficient, we treat the unknown conductivity as a nuisance parameter and carry out approximative premarginalization over it, and invert for the Robin coefficient field only. We approximate the related modelling errors via the Bayesian approximation error (BAE) approach. The uncertainty analysis presented here relies on a local linearization of the parameter-to-observable map at the maximum a posteriori (MAP) estimates, which leads to a normal (Gaussian) approximation of the parameter posterior density. To compute the MAP point we apply an inexact Newton conjugate gradient approach based on the adjoint methodology. The construction of the covariance is made tractable by invoking a low-rank approximation of the data misfit component of the Hessian. Two numerical experiments are considered: one where the prior covariance on the conductivity is isotropic, and one where the prior covariance on the conductivity is anisotropic. Results are compared to those based on standard error models, with particular emphasis on the feasibility of the posterior uncertainty estimates. We show that the BAE approach is a feasible one in the sense that the predicted posterior uncertainty is consistent with the actual estimation errors, while neglecting the related modelling error yields infeasible estimates for the Robin coefficient. In addition, we demonstrate that the BAE approach is approximately as computationally expensive (measured in the number of PDE solves) as the conventional error approach.

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arXiv2017

Mean-variance risk-averse optimal control of systems governed by PDEs with random parameter fields using quadratic approximations

We present a method for optimal control of systems governed by partial differential equations (PDEs) with uncertain parameter fields. We consider an objective function that involves the mean and variance of the control objective, leading to a risk-averse optimal control problem. To make the problem tractable, we invoke a quadratic Taylor series approximation of the control objective with respect to the uncertain parameter. This enables deriving explicit expressions for the mean and variance of the control objective in terms of its gradients and Hessians with respect to the uncertain parameter. The risk-averse optimal control problem is then formulated as a PDE-constrained optimization problem with constraints given by the forward and adjoint PDEs defining these gradients and Hessians. The expressions for the mean and variance of the control objective under the quadratic approximation involve the trace of the (preconditioned) Hessian and are thus prohibitive to evaluate. To address this, we employ trace estimators that only require a modest number of Hessian-vector products. We illustrate our approach with two problems: the control of a semilinear elliptic PDE with an uncertain boundary source term, and the control of a linear elliptic PDE with an uncertain coefficient field. For the latter problem, we derive adjoint-based expressions for efficient computation of the gradient of the risk-averse objective with respect to the controls. Our method ensures that the cost of computing the risk-averse objective and its gradient with respect to the control, measured in the number of PDE solves, is independent of the (discretized) parameter and control dimensions, and depends only on the number of random vectors employed in the trace estimation. Finally, we present a comprehensive numerical study of an optimal control problem for fluid flow in a porous medium with uncertain permeability field.

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arXiv2016

A Bayesian Approach for Parameter Estimation with Uncertainty for Dynamic Power Systems

We address the problem of estimating the uncertainty in the solution of power grid inverse problems within the framework of Bayesian inference. We investigate two approaches, an adjoint-based method and a stochastic spectral method. These methods are used to estimate the maximum a posteriori point of the parameters and their variance, which quantifies their uncertainty. Within this framework we estimate several parameters of the dynamic power system, such as generator inertias, which are not quantifiable in steady-state models. We illustrate the performance of these approaches on a 9-bus power grid example and analyze the dependence on measurement frequency, estimation horizon, perturbation size, and measurement noise. We assess the computational efficiency, and discuss the expected performance when these methods are applied to large systems.

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arXiv2015

A Fast and Scalable Method for A-Optimal Design of Experiments for Infinite-dimensional Bayesian Nonlinear Inverse Problems

We address the problem of optimal experimental design (OED) for Bayesian nonlinear inverse problems governed by PDEs. The goal is to find a placement of sensors, at which experimental data are collected, so as to minimize the uncertainty in the inferred parameter field. We formulate the OED objective function by generalizing the classical A-optimal experimental design criterion using the expected value of the trace of the posterior covariance. We seek a method that solves the OED problem at a cost (measured in the number of forward PDE solves) that is independent of both the parameter and sensor dimensions. To facilitate this, we construct a Gaussian approximation to the posterior at the maximum a posteriori probability (MAP) point, and use the resulting covariance operator to define the OED objective function. We use randomized trace estimation to compute the trace of this (implicitly defined) covariance operator. The resulting OED problem includes as constraints the PDEs characterizing the MAP point, and the PDEs describing the action of the covariance operator to vectors. The sparsity of the sensor configurations is controlled using sparsifying penalty functions. We elaborate our OED method for the problem of determining the sensor placement to best infer the coefficient of an elliptic PDE. Adjoint methods are used to compute the gradient of the PDE-constrained OED objective function. We provide numerical results for inference of the permeability field in a porous medium flow problem, and demonstrate that the number of PDE solves required for the evaluation of the OED objective function and its gradient is essentially independent of both the parameter and sensor dimensions. The number of quasi-Newton iterations for computing an OED also exhibits the same dimension invariance properties.

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arXiv2015

Scalable and efficient algorithms for the propagation of uncertainty from data through inference to prediction for large-scale problems, with application to flow of the Antarctic ice sheet

The majority of research on efficient and scalable algorithms in computational science and engineering has focused on the forward problem: given parameter inputs, solve the governing equations to determine output quantities of interest. In contrast, here we consider the broader question: given a (large-scale) model containing uncertain parameters, (possibly) noisy observational data, and a prediction quantity of interest, how do we construct efficient and scalable algorithms to (1) infer the model parameters from the data (the deterministic inverse problem), (2) quantify the uncertainty in the inferred parameters (the Bayesian inference problem), and (3) propagate the resulting uncertain parameters through the model to issue predictions with quantified uncertainties (the forward uncertainty propagation problem)? We present efficient and scalable algorithms for this end-to-end, data-to-prediction process under the Gaussian approximation and in the context of modeling the flow of the Antarctic ice sheet and its effect on sea level. The ice is modeled as a viscous, incompressible, creeping, shear-thinning fluid. The observational data come from InSAR satellite measurements of surface ice flow velocity, and the uncertain parameter field to be inferred is the basal sliding parameter. The prediction quantity of interest is the present-day ice mass flux from the Antarctic continent to the ocean. We show that the work required for executing this data-to-prediction process is independent of the state dimension, parameter dimension, data dimension, and number of processor cores. The key to achieving this dimension independence is to exploit the fact that the observational data typically provide only sparse information on model parameters. This property can be exploited to construct a low rank approximation of the linearized parameter-to-observable map.

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arXiv2014

A-optimal design of experiments for infinite-dimensional Bayesian linear inverse problems with regularized $\ell_0$-sparsification

We present an efficient method for computing A-optimal experimental designs for infinite-dimensional Bayesian linear inverse problems governed by partial differential equations (PDEs). Specifically, we address the problem of optimizing the location of sensors (at which observational data are collected) to minimize the uncertainty in the parameters estimated by solving the inverse problem, where the uncertainty is expressed by the trace of the posterior covariance. Computing optimal experimental designs (OEDs) is particularly challenging for inverse problems governed by computationally expensive PDE models with infinite-dimensional (or, after discretization, high-dimensional) parameters. To alleviate the computational cost, we exploit the problem structure and build a low-rank approximation of the parameter-to-observable map, preconditioned with the square root of the prior covariance operator. This relieves our method from expensive PDE solves when evaluating the optimal experimental design objective function and its derivatives. Moreover, we employ a randomized trace estimator for efficient evaluation of the OED objective function. We control the sparsity of the sensor configuration by employing a sequence of penalty functions that successively approximate the $\ell_0$-"norm"; this results in binary designs that characterize optimal sensor locations. We present numerical results for inference of the initial condition from spatio-temporal observations in a time-dependent advection-diffusion problem in two and three space dimensions. We find that an optimal design can be computed at a cost, measured in number of forward PDE solves, that is independent of the parameter and sensor dimensions. We demonstrate numerically that $\ell_0$-sparsified experimental designs obtained via a continuation method outperform $\ell_1$-sparsified designs.

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arXiv2014

A computational framework for infinite-dimensional Bayesian inverse problems: Part II. Stochastic Newton MCMC with application to ice sheet flow inverse problems

We address the numerical solution of infinite-dimensional inverse problems in the framework of Bayesian inference. In the Part I companion to this paper (arXiv.org:1308.1313), we considered the linearized infinite-dimensional inverse problem. Here in Part II, we relax the linearization assumption and consider the fully nonlinear infinite-dimensional inverse problem using a Markov chain Monte Carlo (MCMC) sampling method. To address the challenges of sampling high-dimensional pdfs arising from Bayesian inverse problems governed by PDEs, we build on the stochastic Newton MCMC method. This method exploits problem structure by taking as a proposal density a local Gaussian approximation of the posterior pdf, whose construction is made tractable by invoking a low-rank approximation of its data misfit component of the Hessian. Here we introduce an approximation of the stochastic Newton proposal in which we compute the low-rank-based Hessian at just the MAP point, and then reuse this Hessian at each MCMC step. We compare the performance of the proposed method to the original stochastic Newton MCMC method and to an independence sampler. The comparison of the three methods is conducted on a synthetic ice sheet inverse problem. For this problem, the stochastic Newton MCMC method with a MAP-based Hessian converges at least as rapidly as the original stochastic Newton MCMC method, but is far cheaper since it avoids recomputing the Hessian at each step. On the other hand, it is more expensive per sample than the independence sampler; however, its convergence is significantly more rapid, and thus overall it is much cheaper. Finally, we present extensive analysis and interpretation of the posterior distribution, and classify directions in parameter space based on the extent to which they are informed by the prior or the observations.

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