arXiv subjects

Shiwei Lan

Publications and source records attributed to Shiwei Lan.

At least 19 recordsLinked to original sources

arXiv2025

Bayesian Bridge Gaussian Process Regression

The performance of Gaussian Process (GP) regression is often hampered by the curse of dimensionality, which inflates computational cost and reduces predictive power in high-dimensional problems. Variable selection is thus crucial for building efficient and accurate GP models. Inspired by Bayesian bridge regression, we propose the Bayesian Bridge Gaussian Process Regression (B\textsuperscript{2}GPR) model. This framework places $\ell_q$-norm constraints on key GP parameters to automatically induce sparsity and identify active variables. We formulate two distinct versions: one for $q=2$ using conjugate Gaussian priors, and another for $0<q<2$ that employs constrained flat priors, leading to non-standard, norm-constrained posterior distributions. To enable posterior inference, we design a Gibbs sampling algorithm that integrates Spherical Hamiltonian Monte Carlo (SphHMC) to efficiently sample from the constrained posteriors when $0<q<2$. Simulations and a real-data application confirm that B\textsuperscript{2}GPR offers superior variable selection and prediction compared to alternative approaches.

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arXiv2024

The Reconstruction of the Space-Dependent Thermal Conductivity from Sparse Temperature Measurements

We present a novel method for reconstructing the thermal conductivity coefficient in 1D and 2D heat equations using moving sensors that dynamically traverse the domain to record sparse and noisy temperature measurements. We significantly reduce the computational cost associated with forward PDE evaluations by employing automatic differentiation, enabling a more efficient and scalable reconstruction process. This allows the inverse problem to be solved with fewer sensors and observations. Specifically, we demonstrate the successful reconstruction of thermal conductivity on the 1D circle and 2D torus, using one and four moving sensors, respectively, with their positions recorded over time. Our method incorporates sampling algorithms to compute confidence intervals for the reconstructed conductivity, improving robustness against measurement noise. Extensive numerical simulations of heat dynamics validate the efficacy of our approach, confirming both the accuracy and stability of the reconstructed thermal conductivity. Additionally, the method is thoroughly tested using large datasets from machine learning, allowing us to evaluate its performance across various scenarios and ensure its reliability. This approach provides a cost-effective and flexible solution for conductivity reconstruction from sparse measurements, making it a robust tool for solving inverse problems in complex domains.

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arXiv2024

Deep Q-Exponential Processes

Motivated by deep neural networks, the deep Gaussian process (DGP) generalizes the standard GP by stacking multiple layers of GPs. Despite the enhanced expressiveness, GP, as an $L_2$ regularization prior, tends to be over-smooth and sub-optimal for inhomogeneous subjects, such as images with edges. Recently, Q-exponential process (Q-EP) has been proposed as an $L_q$ relaxation to GP and demonstrated with more desirable regularization properties through a parameter $q>0$ with $q=2$ corresponding to GP. Sharing the similar tractability of posterior and predictive distributions with GP, Q-EP can also be stacked to improve its modeling flexibility. In this paper, we generalize Q-EP to deep Q-EP to enjoy both proper regularization and improved expressiveness. The generalization is realized by introducing shallow Q-EP as a latent variable model and then building a hierarchy of the shallow Q-EP layers. Sparse approximation by inducing points and scalable variational strategy are applied to facilitate the inference. We demonstrate the numerical advantages of the proposed deep Q-EP model by comparing with multiple state-of-the-art deep probabilistic models.

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arXiv2023

Scaling Up Bayesian Neural Networks with Neural Networks

Bayesian Neural Networks (BNNs) offer a principled and natural framework for proper uncertainty quantification in the context of deep learning. They address the typical challenges associated with conventional deep learning methods, such as data insatiability, ad-hoc nature, and susceptibility to overfitting. However, their implementation typically either relies on Markov chain Monte Carlo (MCMC) methods, which are characterized by their computational intensity and inefficiency in a high-dimensional space, or variational inference methods, which tend to underestimate uncertainty. To address this issue, we propose a novel Calibration-Emulation-Sampling (CES) strategy to significantly enhance the computational efficiency of BNN. In this framework, during the initial calibration stage, we collect a small set of samples from the parameter space. These samples serve as training data for the emulator, which approximates the map between parameters and posterior probability. The trained emulator is then used for sampling from the posterior distribution at substantially higher speed compared to the standard BNN. Using simulated and real data, we demonstrate that our proposed method improves computational efficiency of BNN, while maintaining similar performance in terms of prediction accuracy and uncertainty quantification.

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arXiv2023

Spatiotemporal Besov Priors for Bayesian Inverse Problems

Fast development in science and technology has driven the need for proper statistical tools to capture special data features such as abrupt changes or sharp contrast. Many inverse problems in data science require spatiotemporal solutions derived from a sequence of time-dependent objects with these spatial features, e.g., the dynamic reconstruction of computerized tomography (CT) images with edges. Conventional methods based on Gaussian processes (GP) often fall short in providing satisfactory solutions since they tend to offer oversmooth priors. Recently, the Besov process (BP), defined by wavelet expansions with random coefficients, has emerged as a more suitable prior for Bayesian inverse problems of this nature. While BP excels in handling spatial inhomogeneity, it does not automatically incorporate temporal correlation inherited in the dynamically changing objects. In this paper, we generalize BP to a novel spatiotemporal Besov process (STBP) by replacing the random coefficients in the series expansion with stochastic time functions as Q-exponential process (Q-EP) which governs the temporal correlation structure. We thoroughly investigate the mathematical and statistical properties of STBP. Simulations, two limited-angle CT reconstruction examples, a highly non-linear inverse problem involving Navier-Stokes equation, and a spatiotemporal temperature imputation problem are used to demonstrate the advantage of the proposed STBP compared with the classic STGP and a time-uncorrelated approach.

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arXiv2022

Bayesian Learning via Q-Exponential Process

Regularization is one of the most fundamental topics in optimization, statistics and machine learning. To get sparsity in estimating a parameter $u\in\mathbb{R}^d$, an $\ell_q$ penalty term, $\Vert u\Vert_q$, is usually added to the objective function. What is the probabilistic distribution corresponding to such $\ell_q$ penalty? What is the correct stochastic process corresponding to $\Vert u\Vert_q$ when we model functions $u\in L^q$? This is important for statistically modeling large dimensional objects, e.g. images, with penalty to preserve certainty properties, e.g. edges in the image. In this work, we generalize the $q$-exponential distribution (with density proportional to) $\exp{(- \frac{1}{2}|u|^q)}$ to a stochastic process named $Q$-exponential (Q-EP) process that corresponds to the $L_q$ regularization of functions. The key step is to specify consistent multivariate $q$-exponential distributions by choosing from a large family of elliptic contour distributions. The work is closely related to Besov process which is usually defined by the expanded series. Q-EP can be regarded as a definition of Besov process with explicit probabilistic formulation and direct control on the correlation length. From the Bayesian perspective, Q-EP provides a flexible prior on functions with sharper penalty ($q<2$) than the commonly used Gaussian process (GP). We compare GP, Besov and Q-EP in modeling functional data, reconstructing images, and solving inverse problems and demonstrate the advantage of our proposed methodology.

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arXiv2022

Sampling Constrained Continuous Probability Distributions: A Review

The problem of sampling constrained continuous distributions has frequently appeared in many machine/statistical learning models. Many Monte Carlo Markov Chain (MCMC) sampling methods have been adapted to handle different types of constraints on the random variables. Among these methods, Hamilton Monte Carlo (HMC) and the related approaches have shown significant advantages in terms of computational efficiency compared to other counterparts. In this article, we first review HMC and some extended sampling methods, and then we concretely explain three constrained HMC-based sampling methods, reflection, reformulation, and spherical HMC. For illustration, we apply these methods to solve three well-known constrained sampling problems, truncated multivariate normal distributions, Bayesian regularized regression, and nonparametric density estimation. In this review, we also connect constrained sampling with another similar problem in the statistical design of experiments of constrained design space.

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arXiv2022

Learning Temporal Evolution of Spatial Dependence with Generalized Spatiotemporal Gaussian Process Models

A large number of scientific studies and engineering problems involve high-dimensional spatiotemporal data with complicated relationships. In this paper, we focus on a type of space-time interaction named \emph{temporal evolution of spatial dependence (TESD)}, which is a zero time-lag spatiotemporal covariance. For this purpose, we propose a novel Bayesian nonparametric method based on non-stationary spatiotemporal Gaussian process (STGP). The classic STGP has a covariance kernel separable in space and time, failed to characterize TESD. More recent works on non-separable STGP treat location and time together as a joint variable, which is unnecessarily inefficient. We generalize STGP (gSTGP) to introduce the time-dependence to the spatial kernel by varying its eigenvalues over time in the Mercer's representation. The resulting non-stationary non-separable covariance model bares a quasi Kronecker sum structure. Finally, a hierarchical Bayesian model for the joint covariance is proposed to allow for full flexibility in learning TESD. A simulation study and a longitudinal neuroimaging analysis on Alzheimer's patients demonstrate that the proposed methodology is (statistically) effective and (computationally) efficient in characterizing TESD. Theoretic properties of gSTGP including posterior contraction (for covariance) are also studied.

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arXiv2022

Scaling Up Bayesian Uncertainty Quantification for Inverse Problems using Deep Neural Networks

Due to the importance of uncertainty quantification (UQ), Bayesian approach to inverse problems has recently gained popularity in applied mathematics, physics, and engineering. However, traditional Bayesian inference methods based on Markov Chain Monte Carlo (MCMC) tend to be computationally intensive and inefficient for such high dimensional problems. To address this issue, several methods based on surrogate models have been proposed to speed up the inference process. More specifically, the calibration-emulation-sampling (CES) scheme has been proven to be successful in large dimensional UQ problems. In this work, we propose a novel CES approach for Bayesian inference based on deep neural network models for the emulation phase. The resulting algorithm is computationally more efficient and more robust against variations in the training set. Further, by using an autoencoder (AE) for dimension reduction, we have been able to speed up our Bayesian inference method up to three orders of magnitude. Overall, our method, henceforth called \emph{Dimension-Reduced Emulative Autoencoder Monte Carlo (DREAMC)} algorithm, is able to scale Bayesian UQ up to thousands of dimensions for inverse problems. Using two low-dimensional (linear and nonlinear) inverse problems we illustrate the validity of this approach. Next, we apply our method to two high-dimensional numerical examples (elliptic and advection-diffussion) to demonstrate its computational advantages over existing algorithms.

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arXiv2022

Bayesian Spatiotemporal Modeling for Inverse Problems

Inverse problems with spatiotemporal observations are ubiquitous in scientific studies and engineering applications. In these spatiotemporal inverse problems, observed multivariate time series are used to infer parameters of physical or biological interests. Traditional solutions for these problems often ignore the spatial or temporal correlations in the data (static model), or simply model the data summarized over time (time-averaged model). In either case, the data information that contains the spatiotemporal interactions is not fully utilized for parameter learning, which leads to insufficient modeling in these problems. In this paper, we apply Bayesian models based on spatiotemporal Gaussian processes (STGP) to the inverse problems with spatiotemporal data and show that the spatial and temporal information provides more effective parameter estimation and uncertainty quantification (UQ). We demonstrate the merit of Bayesian spatiotemporal modeling for inverse problems compared with traditional static and time-averaged approaches using a time-dependent advection-diffusion partial different equation (PDE) and three chaotic ordinary differential equations (ODE). We also provide theoretic justification for the superiority of spatiotemporal modeling to fit the trajectories even it appears cumbersome (e.g. for chaotic dynamics).

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arXiv2020

Calibrate, Emulate, Sample

Many parameter estimation problems arising in applications are best cast in the framework of Bayesian inversion. This allows not only for an estimate of the parameters, but also for the quantification of uncertainties in the estimates. Often in such problems the parameter-to-data map is very expensive to evaluate, and computing derivatives of the map, or derivative-adjoints, may not be feasible. Additionally, in many applications only noisy evaluations of the map may be available. We propose an approach to Bayesian inversion in such settings that builds on the derivative-free optimization capabilities of ensemble Kalman inversion methods. The overarching approach is to first use ensemble Kalman sampling (EKS) to calibrate the unknown parameters to fit the data; second, to use the output of the EKS to emulate the parameter-to-data map; third, to sample from an approximate Bayesian posterior distribution in which the parameter-to-data map is replaced by its emulator. This results in a principled approach to approximate Bayesian inference that requires only a small number of evaluations of the (possibly noisy approximation of the) parameter-to-data map. It does not require derivatives of this map, but instead leverages the documented power of ensemble Kalman methods. Furthermore, the EKS has the desirable property that it evolves the parameter ensembles towards the regions in which the bulk of the parameter posterior mass is located, thereby locating them well for the emulation phase of the methodology. In essence, the EKS methodology provides a cheap solution to the design problem of where to place points in parameter space to efficiently train an emulator of the parameter-to-data map for the purposes of Bayesian inversion.

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arXiv2019

Deep Markov Chain Monte Carlo

We propose a new computationally efficient sampling scheme for Bayesian inference involving high dimensional probability distributions. Our method maps the original parameter space into a low-dimensional latent space, explores the latent space to generate samples, and maps these samples back to the original space for inference. While our method can be used in conjunction with any dimension reduction technique to obtain the latent space, and any standard sampling algorithm to explore the low-dimensional space, here we specifically use a combination of auto-encoders (for dimensionality reduction) and Hamiltonian Monte Carlo (HMC, for sampling). To this end, we first run an HMC to generate some initial samples from the original parameter space, and then use these samples to train an auto-encoder. Next, starting with an initial state, we use the encoding part of the autoencoder to map the initial state to a point in the low-dimensional latent space. Using another HMC, this point is then treated as an initial state in the latent space to generate a new state, which is then mapped to the original space using the decoding part of the auto-encoder. The resulting point can be treated as a Metropolis-Hasting (MH) proposal, which is either accepted or rejected. While the induced dynamics in the parameter space is no longer Hamiltonian, it remains time reversible, and the Markov chain could still converge to the canonical distribution using a volume correction term. Dropping the volume correction step results in convergence to an approximate but reasonably accurate distribution. The empirical results based on several high-dimensional problems show that our method could substantially reduce the computational cost of Bayesian inference.

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arXiv2019

Adaptive Dimension Reduction to Accelerate Infinite-Dimensional Geometric Markov Chain Monte Carlo

Bayesian inverse problems highly rely on efficient and effective inference methods for uncertainty quantification (UQ). Infinite-dimensional MCMC algorithms, directly defined on function spaces, are robust under refinement of physical models. Recent development of this class of algorithms has started to incorporate the geometry of the posterior informed by data so that they are capable of exploring complex probability structures. However, the required geometric quantities are usually expensive to obtain in high dimensions. On the other hand, most geometric information of the unknown parameter space in this setting is concentrated in an \emph{intrinsic} finite-dimensional subspace. To mitigate the computational intensity and scale up the applications of infinite-dimensional geometric MCMC ($\infty$-GMC), we apply geometry-informed algorithms to the intrinsic subspace to probe its complex structure, and simpler methods like preconditioned Crank-Nicolson (pCN) to its geometry-flat complementary subspace. In this work, we take advantage of dimension reduction techniques to accelerate the original $\infty$-GMC algorithms. More specifically, partial spectral decomposition of the (prior or posterior) covariance operator is used to identify certain number of principal eigen-directions as a basis for the intrinsic subspace. The combination of dimension-independent algorithms, geometric information, and dimension reduction yields more efficient implementation, \emph{(adaptive) dimension-reduced infinite-dimensional geometric MCMC}. With a small amount of computational overhead, we can achieve over 70 times speed-up compared to pCN using a simulated elliptic inverse problem and an inverse problem involving turbulent combustion. A number of error bounds comparing various MCMC proposals are presented to predict the asymptotic behavior of the proposed dimension-reduced algorithms.

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arXiv2019

Flexible Bayesian Dynamic Modeling of Correlation and Covariance Matrices

Modeling correlation (and covariance) matrices can be challenging due to the positive-definiteness constraint and potential high-dimensionality. Our approach is to decompose the covariance matrix into the correlation and variance matrices and propose a novel Bayesian framework based on modeling the correlations as products of unit vectors. By specifying a wide range of distributions on a sphere (e.g. the squared-Dirichlet distribution), the proposed approach induces flexible prior distributions for covariance matrices (that go beyond the commonly used inverse-Wishart prior). For modeling real-life spatio-temporal processes with complex dependence structures, we extend our method to dynamic cases and introduce unit-vector Gaussian process priors in order to capture the evolution of correlation among components of a multivariate time series. To handle the intractability of the resulting posterior, we introduce the adaptive $Δ$-Spherical Hamiltonian Monte Carlo. We demonstrate the validity and flexibility of our proposed framework in a simulation study of periodic processes and an analysis of rat's local field potential activity in a complex sequence memory task.

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arXiv2017

Earth System Modeling 2.0: A Blueprint for Models That Learn From Observations and Targeted High-Resolution Simulations

Climate projections continue to be marred by large uncertainties, which originate in processes that need to be parameterized, such as clouds, convection, and ecosystems. But rapid progress is now within reach. New computational tools and methods from data assimilation and machine learning make it possible to integrate global observations and local high-resolution simulations in an Earth system model (ESM) that systematically learns from both. Here we propose a blueprint for such an ESM. We outline how parameterization schemes can learn from global observations and targeted high-resolution simulations, for example, of clouds and convection, through matching low-order statistics between ESMs, observations, and high-resolution simulations. We illustrate learning algorithms for ESMs with a simple dynamical system that shares characteristics of the climate system; and we discuss the opportunities the proposed framework presents and the challenges that remain to realize it.

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arXiv2017

The nonparametric Fisher geometry and the chi-square process density prior

It is well known that the Fisher information induces a Riemannian geometry on parametric families of probability density functions. Following recent work, we consider the nonparametric generalization of the Fisher geometry. The resulting nonparametric Fisher geometry is shown to be equivalent to a familiar, albeit infinite-dimensional, geometric object---the sphere. By shifting focus away from density functions and toward \emph{square-root} density functions, one may calculate theoretical quantities of interest with ease. More importantly, the sphere of square-root densities is much more computationally tractable. This insight leads to a novel Bayesian nonparametric density estimation model. We construct the $χ^2$-process density prior by modeling the square-root density with a restricted Gaussian process prior. Inference over square-root densities is fast, and the model retains the flexibility characteristic of Bayesian nonparametric models. Finally, we formalize the relationship between spherical HMC in the infinite-dimensional limit and standard Riemannian HMC.

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arXiv2017

Geometric MCMC for Infinite-Dimensional Inverse Problems

Bayesian inverse problems often involve sampling posterior distributions on infinite-dimensional function spaces. Traditional Markov chain Monte Carlo (MCMC) algorithms are characterized by deteriorating mixing times upon mesh-refinement, when the finite-dimensional approximations become more accurate. Such methods are typically forced to reduce step-sizes as the discretization gets finer, and thus are expensive as a function of dimension. Recently, a new class of MCMC methods with mesh-independent convergence times has emerged. However, few of them take into account the geometry of the posterior informed by the data. At the same time, recently developed geometric MCMC algorithms have been found to be powerful in exploring complicated distributions that deviate significantly from elliptic Gaussian laws, but are in general computationally intractable for models defined in infinite dimensions. In this work, we combine geometric methods on a finite-dimensional subspace with mesh-independent infinite-dimensional approaches. Our objective is to speed up MCMC mixing times, without significantly increasing the computational cost per step (for instance, in comparison with the vanilla preconditioned Crank-Nicolson (pCN) method). This is achieved by using ideas from geometric MCMC to probe the complex structure of an intrinsic finite-dimensional subspace where most data information concentrates, while retaining robust mixing times as the dimension grows by using pCN-like methods in the complementary subspace. The resulting algorithms are demonstrated in the context of three challenging inverse problems arising in subsurface flow, heat conduction and incompressible flow control. The algorithms exhibit up to two orders of magnitude improvement in sampling efficiency when compared with the pCN method.

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arXiv2016

Geodesic Lagrangian Monte Carlo over the space of positive definite matrices: with application to Bayesian spectral density estimation

We extend the application of Hamiltonian Monte Carlo to allow for sampling from probability distributions defined over symmetric or Hermitian positive definite matrices. To do so, we exploit the Riemannian structure induced by Cartan's century-old canonical metric. The geodesics that correspond to this metric are available in closed-form and---within the context of Lagrangian Monte Carlo---provide a principled way to travel around the space of positive definite matrices. Our method improves Bayesian inference on such matrices by allowing for a broad range of priors, so we are not limited to conjugate priors only. In the context of spectral density estimation, we use the (non-conjugate) complex reference prior as an example modeling option made available by the algorithm. Results based on simulated and real-world multivariate time series are presented in this context, and future directions are outlined.

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