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Botond Szabo

Publications and source records attributed to Botond Szabo.

At least 19 recordsLinked to original sources
arXiv2024

Linear methods for non-linear inverse problems

We consider the recovery of an unknown function $f$ from a noisy observation of the solution $u_f$ to a partial differential equation that can be written in the form $\mathcal{L} u_f=c(f,u_f)$, for a differential operator $\mathcal{L}$ that is rich enough to recover $f$ from $\mathcal{L} u_f$. Examples include the time-independent Schr\"odinger equation $\Delta u_f = 2u_ff$, the heat equation with absorption term $(\partial_t -\Delta_x/2) u_f=fu_f$, and the Darcy problem $\nabla\cdot (f \nabla u_f) = h$. We transform this problem into the linear inverse problem of recovering $\mathcal{L} u_f$ under the Dirichlet boundary condition, and show that Bayesian methods with priors placed either on $u_f$ or $\mathcal{L} u_f$ for this problem yield optimal recovery rates not only for $u_f$, but also for $f$. We also derive frequentist coverage guarantees for the corresponding Bayesian credible sets. Adaptive priors are shown to yield adaptive contraction rates for $f$, thus eliminating the need to know the smoothness of this function. The results are illustrated by numerical experiments on synthetic data sets.

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arXiv2024

Vecchia Gaussian Processes: on probabilistic and statistical properties

Gaussian Processes (GPs) are widely used to model dependencies in spatial statistics and machine learning. However, exact inference is computationally intractable for GP regression, with a time complexity of $O(n^3)$. The Vecchia approximation scales up computation by introducing sparsity into the spatial dependency structure, represented by a directed acyclic graph (DAG). Despite its practical popularity, this approach lacks rigorous theoretical foundations, and the choice of DAG structure remains an open problem. In this paper, we systematically study the Vecchia approximation of the popular, isotropic Mat\'{e}rn GP as standalone stochastic process and uncover key probabilistic and statistical properties. We propose selecting parent sets as norming sets with fixed cardinality in the Vecchia approximation. On the probabilistic side, we show that the conditional distributions of Mat\'ern GPs, as well as their Vecchia approximations, can be characterized by polynomial interpolations. This enables us to establish several results on small ball probabilities and the Reproducing Kernel Hilbert Spaces (RKHSs) of Vecchia GPs. Building on these probabilistic results, we prove that in the nonparametric regression model, the corresponding posterior contracts around the truth at the optimal minimax rate, both under oracle rescaling and hierarchical tuning of the prior. We illustrate the theoretical findings through numerical experiments on synthetic datasets. Our core algorithms are implemented in C++ with an R interface.

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arXiv2024

Skew-symmetric approximations of posterior distributions

Popular deterministic approximations of posterior distributions from, e.g. the Laplace method, variational Bayes and expectation-propagation, generally rely on symmetric approximating families, often taken to be Gaussian. This choice facilitates optimization and inference, but typically affects the quality of the overall approximation. In fact, even in basic parametric models, the posterior distribution often displays asymmetries that yield bias and a reduced accuracy when considering symmetric approximations. Recent research has moved towards more flexible approximating families which incorporate skewness. However, current solutions are often model specific, lack a general supporting theory, increase the computational complexity of the optimization problem, and do not provide a broadly applicable solution to incorporate skewness in any symmetric approximation. This article addresses such a gap by introducing a general and provably optimal strategy to perturb any off-the-shelf symmetric approximation of a generic posterior distribution. This novel perturbation scheme is derived without additional optimization steps, and yields a similarly tractable approximation within the class of skew-symmetric densities that provably enhances the finite sample accuracy of the original symmetric counterpart. Furthermore, under suitable assumptions, it improves the convergence rate to the exact posterior by at least a $\sqrt{n}$ factor, in asymptotic regimes. These advancements are illustrated in numerical studies focusing on skewed perturbations of state-of-the-art Gaussian approximations.

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arXiv2024

Contraction rates for conjugate gradient and Lanczos approximate posteriors in Gaussian process regression

Due to their flexibility and theoretical tractability Gaussian process (GP) regression models have become a central topic in modern statistics and machine learning. While the true posterior in these models is given explicitly, numerical evaluations depend on the inversion of the augmented kernel matrix $ K + \sigma^2 I $, which requires up to $ O(n^3) $ operations. For large sample sizes n, which are typically given in modern applications, this is computationally infeasible and necessitates the use of an approximate version of the posterior. Although such methods are widely used in practice, they typically have very limtied theoretical underpinning. In this context, we analyze a class of recently proposed approximation algorithms from the field of Probabilistic numerics. They can be interpreted in terms of Lanczos approximate eigenvectors of the kernel matrix or a conjugate gradient approximation of the posterior mean, which are particularly advantageous in truly large scale applications, as they are fundamentally only based on matrix vector multiplications amenable to the GPU acceleration of modern software frameworks. We combine result from the numerical analysis literature with state of the art concentration results for spectra of kernel matrices to obtain minimax contraction rates. Our theoretical findings are illustrated by numerical experiments.

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arXiv2023

Adaptation using spatially distributed Gaussian Processes

We consider the accuracy of an approximate posterior distribution in nonparametric regression problems by combining posterior distributions computed on subsets of the data defined by the locations of the independent variables. We show that this approximate posterior retains the rate of recovery of the full data posterior distribution, where the rate of recovery adapts to the smoothness of the true regression function. As particular examples we consider Gaussian process priors based on integrated Brownian motion and the Mat\'ern kernel augmented with a prior on the length scale. Besides theoretical guarantees we present a numerical study of the methods both on synthetic and real world data. We also propose a new aggregation technique, which numerically outperforms previous approaches. Finally, we demonstrate empirically that spatially distributed methods can adapt to local regularities, potentially outperforming the original Gaussian process.

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arXiv2023

Variational Gaussian Processes For Linear Inverse Problems

By now Bayesian methods are routinely used in practice for solving inverse problems. In inverse problems the parameter or signal of interest is observed only indirectly, as an image of a given map, and the observations are typically further corrupted with noise. Bayes offers a natural way to regularize these problems via the prior distribution and provides a probabilistic solution, quantifying the remaining uncertainty in the problem. However, the computational costs of standard, sampling based Bayesian approaches can be overly large in such complex models. Therefore, in practice variational Bayes is becoming increasingly popular. Nevertheless, the theoretical understanding of these methods is still relatively limited, especially in context of inverse problems. In our analysis we investigate variational Bayesian methods for Gaussian process priors to solve linear inverse problems. We consider both mildly and severely ill-posed inverse problems and work with the popular inducing variables variational Bayes approach proposed by Titsias in 2009. We derive posterior contraction rates for the variational posterior in general settings and show that the minimax estimation rate can be attained by correctly tunned procedures. As specific examples we consider a collection of inverse problems including the heat equation, Volterra operator and Radon transform and inducing variable methods based on population and empirical spectral features.

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arXiv2023

Skewed Bernstein-von Mises theorem and skew-modal approximations

Gaussian approximations are routinely employed in Bayesian statistics to ease inference when the target posterior is intractable. Although these approximations are asymptotically justified by Bernstein-von Mises type results, in practice the expected Gaussian behavior may poorly represent the shape of the posterior, thus affecting approximation accuracy. Motivated by these considerations, we derive an improved class of closed-form approximations of posterior distributions which arise from a new treatment of a third-order version of the Laplace method yielding approximations in a tractable family of skew-symmetric distributions. Under general assumptions which account for misspecified models and non-i.i.d. settings, this family of approximations is shown to have a total variation distance from the target posterior whose rate of convergence improves by at least one order of magnitude the one established by the classical Bernstein-von Mises theorem. Specializing this result to the case of regular parametric models shows that the same improvement in approximation accuracy can be also derived for polynomially bounded posterior functionals. Unlike other higher-order approximations, our results prove that it is possible to derive closed-form and valid densities which are expected to provide, in practice, a more accurate, yet similarly-tractable, alternative to Gaussian approximations of the target posterior, while inheriting its limiting frequentist properties. We strengthen such arguments by developing a practical skew-modal approximation for both joint and marginal posteriors that achieves the same theoretical guarantees of its theoretical counterpart by replacing the unknown model parameters with the corresponding MAP estimate. Empirical studies confirm that our theoretical results closely match the remarkable performance observed in practice, even in finite, possibly small, sample regimes.

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arXiv2022

Uncertainty quantification for sparse spectral variational approximations in Gaussian process regression

We investigate the frequentist guarantees of the variational sparse Gaussian process regression model. In the theoretical analysis, we focus on the variational approach with spectral features as inducing variables. We derive guarantees and limitations for the frequentist coverage of the resulting variational credible sets. We also derive sufficient and necessary lower bounds for the number of inducing variables required to achieve minimax posterior contraction rates. The implications of these results are demonstrated for different choices of priors. In a numerical analysis we consider a wider range of inducing variable methods and observe similar phenomena beyond the scope of our theoretical findings.

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arXiv2021

Contraction rates for sparse variational approximations in Gaussian process regression

We study the theoretical properties of a variational Bayes method in the Gaussian Process regression model. We consider the inducing variables method introduced by Titsias (2009a) and derive sufficient conditions for obtaining contraction rates for the corresponding variational Bayes (VB) posterior. As examples we show that for three particular covariance kernels (Mat\'ern, squared exponential, random series prior) the VB approach can achieve optimal, minimax contraction rates for a sufficiently large number of appropriately chosen inducing variables. The theoretical findings are demonstrated by numerical experiments.

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arXiv2021

Spike and slab variational Bayes for high dimensional logistic regression

Variational Bayes (VB) is a popular scalable alternative to Markov chain Monte Carlo for Bayesian inference. We study a mean-field spike and slab VB approximation of widely used Bayesian model selection priors in sparse high-dimensional logistic regression. We provide non-asymptotic theoretical guarantees for the VB posterior in both $\ell_2$ and prediction loss for a sparse truth, giving optimal (minimax) convergence rates. Since the VB algorithm does not depend on the unknown truth to achieve optimality, our results shed light on effective prior choices. We confirm the improved performance of our VB algorithm over common sparse VB approaches in a numerical study.

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arXiv2021

Analyzing hierarchical multi-view MRI data with StaPLR: An application to Alzheimer's disease classification

Multi-view data refers to a setting where features are divided into feature sets, for example because they correspond to different sources. Stacked penalized logistic regression (StaPLR) is a recently introduced method that can be used for classification and automatically selecting the views that are most important for prediction. We introduce an extension of this method to a setting where the data has a hierarchical multi-view structure. We also introduce a new view importance measure for StaPLR, which allows us to compare the importance of views at any level of the hierarchy. We apply our extended StaPLR algorithm to Alzheimer's disease classification where different MRI measures have been calculated from three scan types: structural MRI, diffusion-weighted MRI, and resting-state fMRI. StaPLR can identify which scan types and which derived MRI measures are most important for classification, and it outperforms elastic net regression in classification performance.

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arXiv2020

Variational Bayes for high-dimensional linear regression with sparse priors

We study a mean-field spike and slab variational Bayes (VB) approximation to Bayesian model selection priors in sparse high-dimensional linear regression. Under compatibility conditions on the design matrix, oracle inequalities are derived for the mean-field VB approximation, implying that it converges to the sparse truth at the optimal rate and gives optimal prediction of the response vector. The empirical performance of our algorithm is studied, showing that it works comparably well as other state-of-the-art Bayesian variable selection methods. We also numerically demonstrate that the widely used coordinate-ascent variational inference (CAVI) algorithm can be highly sensitive to the parameter updating order, leading to potentially poor performance. To mitigate this, we propose a novel prioritized updating scheme that uses a data-driven updating order and performs better in simulations. The variational algorithm is implemented in the R package 'sparsevb'.

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arXiv2020

View selection in multi-view stacking: Choosing the meta-learner

Multi-view stacking is a framework for combining information from different views (i.e. different feature sets) describing the same set of objects. In this framework, a base-learner algorithm is trained on each view separately, and their predictions are then combined by a meta-learner algorithm. In a previous study, stacked penalized logistic regression, a special case of multi-view stacking, has been shown to be useful in identifying which views are most important for prediction. In this article we expand this research by considering seven different algorithms to use as the meta-learner, and evaluating their view selection and classification performance in simulations and two applications on real gene-expression data sets. Our results suggest that if both view selection and classification accuracy are important to the research at hand, then the nonnegative lasso, nonnegative adaptive lasso and nonnegative elastic net are suitable meta-learners. Exactly which among these three is to be preferred depends on the research context. The remaining four meta-learners, namely nonnegative ridge regression, nonnegative forward selection, stability selection and the interpolating predictor, show little advantages in order to be preferred over the other three.

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arXiv2020

Stacked Penalized Logistic Regression for Selecting Views in Multi-View Learning

In biomedical research, many different types of patient data can be collected, such as various types of omics data and medical imaging modalities. Applying multi-view learning to these different sources of information can increase the accuracy of medical classification models compared with single-view procedures. However, collecting biomedical data can be expensive and/or burdening for patients, so that it is important to reduce the amount of required data collection. It is therefore necessary to develop multi-view learning methods which can accurately identify those views that are most important for prediction. In recent years, several biomedical studies have used an approach known as multi-view stacking (MVS), where a model is trained on each view separately and the resulting predictions are combined through stacking. In these studies, MVS has been shown to increase classification accuracy. However, the MVS framework can also be used for selecting a subset of important views. To study the view selection potential of MVS, we develop a special case called stacked penalized logistic regression (StaPLR). Compared with existing view-selection methods, StaPLR can make use of faster optimization algorithms and is easily parallelized. We show that nonnegativity constraints on the parameters of the function which combines the views play an important role in preventing unimportant views from entering the model. We investigate the performance of StaPLR through simulations, and consider two real data examples. We compare the performance of StaPLR with an existing view selection method called the group lasso and observe that, in terms of view selection, StaPLR is often more conservative and has a consistently lower false positive rate.

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arXiv2020

Fast Exact Bayesian Inference for Sparse Signals in the Normal Sequence Model

We consider exact algorithms for Bayesian inference with model selection priors (including spike-and-slab priors) in the sparse normal sequence model. Because the best existing exact algorithm becomes numerically unstable for sample sizes over n=500, there has been much attention for alternative approaches like approximate algorithms (Gibbs sampling, variational Bayes, etc.), shrinkage priors (e.g. the Horseshoe prior and the Spike-and-Slab LASSO) or empirical Bayesian methods. However, by introducing algorithmic ideas from online sequential prediction, we show that exact calculations are feasible for much larger sample sizes: for general model selection priors we reach n=25000, and for certain spike-and-slab priors we can easily reach n=100000. We further prove a de Finetti-like result for finite sample sizes that characterizes exactly which model selection priors can be expressed as spike-and-slab priors. The computational speed and numerical accuracy of the proposed methods are demonstrated in experiments on simulated data, on a differential gene expression data set, and to compare the effect of multiple hyper-parameter settings in the beta-binomial prior. In our experimental evaluation we compute guaranteed bounds on the numerical accuracy of all new algorithms, which shows that the proposed methods are numerically reliable whereas an alternative based on long division is not.

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arXiv2020

Distributed function estimation: adaptation using minimal communication

We investigate whether in a distributed setting, adaptive estimation of a smooth function at the optimal rate is possible under minimal communication. It turns out that the answer depends on the risk considered and on the number of servers over which the procedure is distributed. We show that for the $L_\infty$-risk, adaptively obtaining optimal rates under minimal communication is not possible. For the $L_2$-risk, it is possible over a range of regularities that depends on the relation between the number of local servers and the total sample size.

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arXiv2019

Debiased Bayesian inference for average treatment effects

Bayesian approaches have become increasingly popular in causal inference problems due to their conceptual simplicity, excellent performance and in-built uncertainty quantification ('posterior credible sets'). We investigate Bayesian inference for average treatment effects from observational data, which is a challenging problem due to the missing counterfactuals and selection bias. Working in the standard potential outcomes framework, we propose a data-driven modification to an arbitrary (nonparametric) prior based on the propensity score that corrects for the first-order posterior bias, thereby improving performance. We illustrate our method for Gaussian process (GP) priors using (semi-)synthetic data. Our experiments demonstrate significant improvement in both estimation accuracy and uncertainty quantification compared to the unmodified GP, rendering our approach highly competitive with the state-of-the-art.

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