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Probabilistic Methods/Gaussian Processes

Jihao Andreas Lin, Javier Antorán, Shreyas Padhy, David Janz, José Miguel Hernández-Lobato, Alexander Terenin

Gaussian processes are a powerful framework for quantifying uncertainty and for sequential decision-making but are limited by the requirement of solving linear systems. In general, this has a cubic cost in dataset size and is sensitive to conditioning. We explore stochastic gradient algorithms as a computationally efficient method of approximately solving these linear systems: we develop low-variance optimization objectives for sampling from the posterior and extend these to inducing points. Counterintuitively, stochastic gradient descent often produces accurate predictions, even in cases where it does not converge quickly to the optimum. We explain this through a spectral characterization of the implicit bias from non-convergence. We show that stochastic gradient descent produces predictive distributions close to the true posterior both in regions with sufficient data coverage, and in regions sufficiently far away from the data. Experimentally, stochastic gradient descent achieves state-of-the-art performance on sufficiently large-scale or ill-conditioned regression tasks. Its uncertainty estimates match the performance of significantly more expensive baselines on a large-scale Bayesian~optimization~task.

Probabilistic Methods/Gaussian Processes

mu niu, Zhenwen Dai, Pokman Cheung, Yizhu Wang

This article presents a novel approach to construct Intrinsic Gaussian Processes for regression on unknown manifolds with probabilistic metrics (GPUM) in point clouds. In many real world applications, one often encounters high dimensional data (e.g.‘point cloud data’) centered around some lower dimensional unknown manifolds. The geometry of manifold is in general different from the usual Euclidean geometry. Naively applying traditional smoothing methods such as Euclidean Gaussian Processes (GPs) to manifold-valued data and so ignoring the geometry of the space can potentially lead to highly misleading predictions and inferences. A manifold embedded in a high dimensional Euclidean space can be well described by a probabilistic mapping function and the corresponding latent space. We investigate the geometrical structure of the unknown manifolds using the Bayesian Gaussian Processes latent variable models(B-GPLVM) and Riemannian geometry. The distribution of the metric tensor is learned using B-GPLVM. The boundary of the resulting manifold is defined based on the uncertainty quantification of the mapping. We use the probabilistic metric tensor to simulate Brownian Motion paths on the unknown manifold. The heat kernel is estimated as the transition density of Brownian Motion and used as the covariance functions of GPUM. The applications of GPUM are illustrated in the simulation studies on the Swiss roll, high dimensional real datasets of WiFi signals and image data examples. Its performance is compared with the Graph Laplacian GP, Graph Mat\'{e}rn GP and Euclidean GP.

Probabilistic Methods/Gaussian Processes

Robert Allison, Anthony Stephenson, Samuel F, Edward O Pyzer-Knapp

The accurate predictions and principled uncertainty measures provided by GP regression incur $O(n^3)$ cost which is prohibitive for modern-day large-scale applications. This has motivated extensive work on computationally efficient approximations. We introduce a new perspective by exploring robustness properties and limiting behaviour of GP nearest-neighbour (GPnn) prediction. We demonstrate through theory and simulation that as the data-size $n$ increases, accuracy of estimated parameters and GP model assumptions become increasingly irrelevant to GPnn predictive accuracy. Consequently, it is sufficient to spend small amounts of work on parameter estimation in order to achieve high MSE accuracy, even in the presence of gross misspecification. In contrast, as $n \rightarrow \infty$, uncertainty calibration and NLL are shown to remain sensitive to just one parameter, the additive noise-variance; but we show that this source of inaccuracy can be corrected for, thereby achieving both well-calibrated uncertainty measures and accurate predictions at remarkably low computational cost. We exhibit a very simple GPnn regression algorithm with stand-out performance compared to other state-of-the-art GP approximations as measured on large UCI datasets. It operates at a small fraction of those other methods' training costs, for example on a basic laptop taking about 30 seconds to train on a dataset of size $n = 1.6 \times 10^6$.

Probabilistic Methods/Gaussian Processes

Amir Hossein Hosseini Akbarnejad, Gilbert Bigras, Nilanjan Ray

The analogy between Gaussian processes (GPs) and deep artificial neural networks (ANNs) has received a lot of interest, and has shown promise to unbox the blackbox of deep ANNs. Existing theoretical works put strict assumptions on the ANN (e.g. requiring all intermediate layers to be wide, or using specific activation functions). Accommodating those theoretical assumptions is hard in recent deep architectures, and those theoretical conditions need refinement as new deep architectures emerge. In this paper we derive an evidence lower-bound that encourages the GP's posterior to match the ANN's output without any requirement on the ANN. Using our method we find out that on 5 datasets, only a subset of those theoretical assumptions are sufficient. Indeed, in our experiments we used a normal ResNet-18 or feed-forward backbone with a single wide layer in the end. One limitation of training GPs is the lack of scalability with respect to the number of inducing points. We use novel computational techniques that allow us to train GPs with hundreds of thousands of inducing points and with GPU acceleration. As shown in our experiments, doing so has been essential to get a close match between the GPs and the ANNs on 5 datasets. We implement our method as a publicly available tool called GPEX: https://github.com/amirakbarnejad/gpex. On 5 datasets (4 image datasets, and 1 biological dataset) and ANNs with 2 types of functionality (classifier or attention-mechanism) we were able to find GPs whose outputs closely match those of the corresponding ANNs. After matching the GPs to the ANNs, we used the GPs' kernel functions to explain the ANNs' decisions. We provide more than 200 explanations (around 30 in the paper and the rest in the supplementary) which are highly interpretable by humans and show the ability of the obtained GPs to unbox the ANNs' decisions.

Probabilistic Methods/Gaussian Processes

Luke Travis, Kolyan Ray

We study pointwise estimation and uncertainty quantification for a sparse variational Gaussian process method with eigenvector inducing variables. For a rescaled Brownian motion prior, we derive theoretical guarantees and limitations for the frequentist size and coverage of pointwise credible sets. For sufficiently many inducing variables, we precisely characterize the asymptotic frequentist coverage, deducing when credible sets from this variational method are conservative and when overconfident/misleading. We numerically illustrate the applicability of our results and discuss connections with other common Gaussian process priors.

Probabilistic Methods/Gaussian Processes

Siu Lun Chau, Krikamol Muandet, Dino Sejdinovic

We present a novel approach for explaining Gaussian processes (GPs) that can utilize the full analytical covariance structure present in GPs. Our method is based on the popular solution concept of Shapley values extended to stochastic cooperative games, resulting in explanations that are random variables. The GP explanations generated using our approach satisfy similar favorable axioms to standard Shapley values and possess a tractable covariance function across features and data observations. This covariance allows for quantifying explanation uncertainties and studying the statistical dependencies between explanations. We further extend our framework to the problem of predictive explanation, and propose a Shapley prior over the explanation function to predict Shapley values for new data based on previously computed ones. Our extensive illustrations demonstrate the effectiveness of the proposed approach.

Probabilistic Methods/Gaussian Processes

Austin Tripp, Sergio Bacallado, Sukriti Singh, José Miguel Hernández-Lobato

The Tanimoto coefficient is commonly used to measure the similarity between molecules represented as discrete fingerprints,either as a distance metric or a positive definite kernel. While many kernel methods can be accelerated using random feature approximations, at present there is a lack of such approximations for the Tanimoto kernel. In this paper we propose two kinds of novel random features to allow this kernel to scale to large datasets, and in the process discover a novel extension of the kernel to real-valued vectors. We theoretically characterize these random features, and provide error bounds on the spectral norm of the Gram matrix. Experimentally, we show that these random features are effective at approximating the Tanimoto coefficient of real-world datasetsand are useful for molecular property prediction and optimization tasks. Future updates to this work will be available at http://arxiv.org/abs/2306.14809.

Probabilistic Methods/Gaussian Processes

Hideaki Kim

Survival or time-to-event data with time-varying covariates are common in practice, and exploring the non-stationarity in covariates is essential to accurately analyzing the nonlinear dependence of time-to-event outcomes on covariates. Traditional survival analysis methods such as Cox proportional hazards model have been extended to address the time-varying covariates through a counting process formulation, although sophisticated machine learning methods that can accommodate time-varying covariates have been limited. In this paper, we propose a non-parametric Bayesian survival model to analyze the nonlinear dependence of time-to-event outcomes on time-varying covariates. We focus on a computationally feasible Cox process called permanental process, which assumes the square root of hazard function to be generated from a Gaussian process, and tailor it for survival data with time-varying covariates. We verify that the proposed model holds with the representer theorem, a beneficial property for functional analysis, which offers us a fast Bayesian estimation algorithm that scales linearly with the number of observed events without relying on Markov Chain Monte Carlo computation. We evaluate our algorithm on synthetic and real-world data, and show that it achieves comparable predictive accuracy while being tens to hundreds of times faster than state-of-the-art methods.

Probabilistic Methods/Gaussian Processes

Daniel Augusto de Souza, Alexander Nikitin, ST John, Magnus Ross, Mauricio A Álvarez, Marc Deisenroth, João Paulo Gomes, Diego Mesquita, César Lincoln Mattos

Gaussian processes (GPs) can provide a principled approach to uncertainty quantification with easy-to-interpret kernel hyperparameters, such as the lengthscale, which controls the correlation distance of function values.However, selecting an appropriate kernel can be challenging.Deep GPs avoid manual kernel engineering by successively parameterizing kernels with GP layers, allowing them to learn low-dimensional embeddings of the inputs that explain the output data.Following the architecture of deep neural networks, the most common deep GPs warp the input space layer-by-layer but lose all the interpretability of shallow GPs. An alternative construction is to successively parameterize the lengthscale of a kernel, improving the interpretability but ultimately giving away the notion of learning lower-dimensional embeddings. Unfortunately, both methods are susceptible to particular pathologies which may hinder fitting and limit their interpretability.This work proposes a novel synthesis of both previous approaches: {Thin and Deep GP} (TDGP). Each TDGP layer defines locally linear transformations of the original input data maintaining the concept of latent embeddings while also retaining the interpretation of lengthscales of a kernel. Moreover, unlike the prior solutions, TDGP induces non-pathological manifolds that admit learning lower-dimensional representations.We show with theoretical and experimental results that i) TDGP is, unlike previous models, tailored to specifically discover lower-dimensional manifolds in the input data, ii) TDGP behaves well when increasing the number of layers, and iii) TDGP performs well in standard benchmark datasets.

Probabilistic Methods/Gaussian Processes

Paul Rosa, Slava Borovitskiy, Alexander Terenin, Judith Rousseau

Gaussian processes are used in many machine learning applications that rely on uncertainty quantification. Recently, computational tools for working with these models in geometric settings, such as when inputs lie on a Riemannian manifold, have been developed. This raises the question: can these intrinsic models be shown theoretically to lead to better performance, compared to simply embedding all relevant quantities into $\mathbb{R}^d$ and using the restriction of an ordinary Euclidean Gaussian process? To study this, we prove optimal contraction rates for intrinsic Matérn Gaussian processes defined on compact Riemannian manifolds. We also prove analogous rates for extrinsic processes using trace and extension theorems between manifold and ambient Sobolev spaces: somewhat surprisingly, the rates obtained turn out to coincide with those of the intrinsic processes, provided that their smoothness parameters are matched appropriately. We illustrate these rates empirically on a number of examples, which, mirroring prior work, show that intrinsic processes can achieve better performance in practice. Therefore, our work shows that finer-grained analyses are needed to distinguish between different levels of data-efficiency of geometric Gaussian processes, particularly in settings which involve small data set sizes and non-asymptotic behavior.

Probabilistic Methods/Gaussian Processes

Kaiwen Wu, Kyurae Kim, Roman Garnett, Jacob Gardner

A recent development in Bayesian optimization is the use of local optimization strategies, which can deliver strong empirical performance on high-dimensional problems compared to traditional global strategies. The "folk wisdom" in the literature is that the focus on local optimization sidesteps the curse of dimensionality; however, little is known concretely about the expected behavior or convergence of Bayesian local optimization routines. We first study the behavior of the local approach, and find that the statistics of individual local solutions of Gaussian process sample paths are surprisingly good compared to what we would expect to recover from global methods. We then present the first rigorous analysis of such a Bayesian local optimization algorithm recently proposed by Müller et al. (2021), and derive convergence rates in both the noisy and noiseless settings.

Probabilistic Methods/Gaussian Processes

Jonathan Schmidt, Philipp Hennig, Jörg Nick, Filip Tronarp

Inference and simulation in the context of high-dimensional dynamical systems remain computationally challenging problems.Some form of dimensionality reduction is required to make the problem tractable in general.In this paper, we propose a novel approximate Gaussian filtering and smoothing methodwhich propagates low-rank approximations of the covariance matrices.This is accomplished by projecting the Lyapunov equations associated with the prediction step to a manifold of low-rank matrices,which are then solved by a recently developed, numerically stable, dynamical low-rank integrator.Meanwhile, the update steps are made tractable by noting that the covariance update only transforms the column space of the covariance matrix, which is low-rank by construction.The algorithm differentiates itself from existing ensemble-based approaches in thatthe low-rank approximations of the covariance matrices are deterministic, rather than stochastic.Crucially, this enables the method to reproduce the exact Kalman filter as the low-rank dimension approaches the true dimensionality of the problem.Our method reduces computational complexity from cubic (for the Kalman filter) to quadratic in the state-space size in the worst-case, and can achieve linear complexity if the state-space model satisfies certain criteria.Through a set of experiments in classical data-assimilation and spatio-temporal regression, we show that the proposed method consistently outperforms the ensemble-based methods in terms of error in the mean and covariance with respect to the exact Kalman filter. This comes at no additional cost in terms of asymptotic computational complexity.

Probabilistic Methods/Gaussian Processes

Jiawen Chen, Wancen Mu, Yun Li, Didong Li

In this paper, we critically examine the prevalent practice of using additive mixtures of Mat\'ern kernels in single-output Gaussian process (GP) models and explore the properties of multiplicative mixtures of Mat\'ern kernels for multi-output GP models. For the single-output case, we derive a series of theoretical results showing that the smoothness of a mixture of Mat\'ern kernels is determined by the least smooth component and that a GP with such a kernel is effectively equivalent to the least smooth kernel component. Furthermore, we demonstrate that none of the mixing weights or parameters within individual kernel components are identifiable. We then turn our attention to multi-output GP models and analyze the identifiability of the covariance matrix $A$ in the multiplicative kernel $K(x,y) = AK_0(x,y)$, where $K_0$ is a standard single output kernel such as Mat\'ern. We show that $A$ is identifiable up to a multiplicative constant, suggesting that multiplicative mixtures are well suited for multi-output tasks. Our findings are supported by extensive simulations and real applications for both single- and multi-output settings. This work provides insight into kernel selection and interpretation for GP models, emphasizing the importance of choosing appropriate kernel structures for different tasks.

Probabilistic Methods/Gaussian Processes

Nathanael Bosch, Philipp Hennig, Filip Tronarp

Probabilistic solvers provide a flexible and efficient framework for simulation, uncertainty quantification, and inference in dynamical systems. However, like standard solvers, they suffer performance penalties for certain stiff systems, where small steps are required not for reasons of numerical accuracy but for the sake of stability. This issue is greatly alleviated in semi-linear problems by the probabilistic exponential integrators developed in this paper. By including the fast, linear dynamics in the prior, we arrive at a class of probabilistic integrators with favorable properties. Namely, they are proven to be L-stable, and in a certain case reduce to a classic exponential integrator---with the added benefit of providing a probabilistic account of the numerical error. The method is also generalized to arbitrary non-linear systems by imposing piece-wise semi-linearity on the prior via Jacobians of the vector field at the previous estimates, resulting in probabilistic exponential Rosenbrock methods. We evaluate the proposed methods on multiple stiff differential equations and demonstrate their improved stability and efficiency over established probabilistic solvers. The present contribution thus expands the range of problems that can be effectively tackled within probabilistic numerics.

Probabilistic Methods/Gaussian Processes

Bernardo Fichera, Slava Borovitskiy, Andreas Krause, Aude G Billard

Gaussian process regression is widely used because of its ability to provide well-calibrated uncertainty estimates and handle small or sparse datasets. However, it struggles with high-dimensional data. One possible way to scale this technique to higher dimensions is to leverage the implicit low-dimensional manifold upon which the data actually lies, as postulated by the manifold hypothesis. Prior work ordinarily requires the manifold structure to be explicitly provided though, i.e. given by a mesh or be known to be one of the well-known manifolds like the sphere. In contrast, in this paper we propose a Gaussian process regression technique capable of inferring implicit structure directly from data (labeled and unlabeled) in a fully differentiable way. For the resulting model, we discuss its convergence to the Matérn Gaussian process on the assumed manifold. Our technique scales up to hundreds of thousands of data points, and improves the predictive performance and calibration of the standard Gaussian process regression in some high-dimensional settings.