Bayesian Neural Networks (BNNs) place priors over the parameters in a neural network. Inference in BNNs, however, is difficult; all inference methods for BNNs are approximate. In this work, we empirically compare the quality of predictive uncertainty estimates for 10 common inference methods on both regression and classification tasks. Our experiments demonstrate that commonly used metrics (e.g. test log-likelihood) can be misleading. Our experiments also indicate that inference innovations designed to capture structure in the posterior do not necessarily produce high quality posterior approximations.
In literature, posteriors for Bayesian Neural Network models obtained by Hamiltonian Monte Carlo (HMC) @cite_12 are frequently used as ground truth. However, HMC scales poorly on high dimensional parameter space and large datasets @cite_0 @cite_4 . Mini-batched versions of HMC, such as Stochastic Gradient Langevin Dynamics (SGLD) @cite_0 and Stochastic Gadient HMC @cite_5 , have been introduced to address the issue of scalability. However, these methods still suffer from lower mixing rate and are not theoretically guaranteed to converge to the true posterior when model assumptions are not met (e.g. when the true model of the gradient noise is not well-estimated).
@cite_0 @cite_5 @cite_4 @cite_12
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Hamiltonian Monte Carlo (HMC) sampling methods provide a mechanism for defining distant proposals with high acceptance probabilities in a Metropolis-Hastings framework, enabling more efficient exploration of the state space than standard random-walk proposals. The popularity of such methods has grown significantly in recent years. However, a limitation of HMC methods is the required gradient computation for simulation of the Hamiltonian dynamical system--such computation is infeasible in problems involving a large sample size or streaming data. Instead, we must rely on a noisy gradient estimate computed from a subset of the data. In this paper, we explore the properties of such a stochastic gradient HMC approach. Surprisingly, the natural implementation of the stochastic approximation can be arbitrarily bad. To address this problem we introduce a variant that uses second-order Langevin dynamics with a friction term that counteracts the effects of the noisy gradient, maintaining the desired target distribution as the invariant distribution. Results on simulated data validate our theory. We also provide an application of our methods to a classification task using neural networks and to online Bayesian matrix factorization. Hamiltonian Monte Carlo (HMC) is a widely deployed method to sample from high-dimensional distributions in Statistics and Machine learning. HMC is known to run very efficiently in practice and its popular second-order "leapfrog" implementation has long been conjectured to run in @math gradient evaluations. Here we show that this conjecture is true when sampling from strongly log-concave target distributions that satisfy a weak third-order regularity property associated with the input data. Our regularity condition is weaker than the Lipschitz Hessian property and allows us to show faster convergence bounds for a much larger class of distributions than would be possible with the usual Lipschitz Hessian constant alone. Important distributions that satisfy our regularity condition include posterior distributions used in Bayesian logistic regression for which the data satisfies an "incoherence" property. Our result compares favorably with the best available bounds for the class of strongly log-concave distributions, which grow like @math gradient evaluations with the dimension. Moreover, our simulations on synthetic data suggest that, when our regularity condition is satisfied, leapfrog HMC performs better than its competitors -- both in terms of accuracy and in terms of the number of gradient evaluations it requires. Recent advances in Bayesian learning with large-scale data have witnessed emergence of stochastic gradient MCMC algorithms (SG-MCMC), such as stochastic gradient Langevin dynamics (SGLD), stochastic gradient Hamiltonian MCMC (SGHMC), and the stochastic gradient thermostat. While finite-time convergence properties of the SGLD with a 1st-order Euler integrator have recently been studied, corresponding theory for general SG-MCMCs has not been explored. In this paper we consider general SG-MCMCs with high-order integrators, and develop theory to analyze finite-time convergence properties and their asymptotic invariant measures. Our theoretical results show faster convergence rates and more accurate invariant measures for SG-MCMCs with higher-order integrators. For example, with the proposed efficient 2nd-order symmetric splitting integrator, the mean square error (MSE) of the posterior average for the SGHMC achieves an optimal convergence rate of L-4 5 at L iterations, compared to L-2 3 for the SGHMC and SGLD with 1st-order Euler integrators. Furthermore, convergence results of decreasing-step-size SG-MCMCs are also developed, with the same convergence rates as their fixed-step-size counterparts for a specific decreasing sequence. Experiments on both synthetic and real datasets verify our theory, and show advantages of the proposed method in two large-scale real applications. Recently, Stochastic Gradient Markov Chain Monte Carlo (SG-MCMC) methods have been proposed for scaling up Monte Carlo computations to large data problems. Whilst these approaches have proven useful in many applications, vanilla SG-MCMC might suffer from poor mixing rates when random variables exhibit strong couplings under the target densities or big scale differences. In this study, we propose a novel SG-MCMC method that takes the local geometry into account by using ideas from Quasi-Newton optimization methods. These second order methods directly approximate the inverse Hessian by using a limited history of samples and their gradients. Our method uses dense approximations of the inverse Hessian while keeping the time and memory complexities linear with the dimension of the problem. We provide a formal theoretical analysis where we show that the proposed method is asymptotically unbiased and consistent with the posterior expectations. We illustrate the effectiveness of the approach on both synthetic and real datasets. Our experiments on two challenging applications show that our method achieves fast convergence rates similar to Riemannian approaches while at the same time having low computational requirements similar to diagonal preconditioning approaches. Stimulus reconstruction or decoding methods provide an important tool for understanding how sensory and motor information is represented in neural activity. We discuss Bayesian decoding methods based on an encoding generalized linear model (GLM) that accurately describes how stimuli are transformed into the spike trains of a group of neurons. The form of the GLM likelihood ensures that the posterior distribution over the stimuli that caused an observed set of spike trains is log concave so long as the prior is. This allows the maximum a posteriori (MAP) stimulus estimate to be obtained using efficient optimization algorithms. Unfortunately, the MAP estimate can have a relatively large average error when the posterior is highly nongaussian. Here we compare several Markov chain Monte Carlo (MCMC) algorithms that allow for the calculation of general Bayesian estimators involving posterior expectations (conditional on model parameters). An efficient version of the hybrid Monte Carlo (HMC) algorithm was significantly superior to other MCMC methods for gaussian priors. When the prior distribution has sharp edges and corners, on the other hand, the “hit-and-run” algorithm performed better than other MCMC methods. Using these algorithms, we show that for this latter class of priors, the posterior mean estimate can have a considerably lower average error than MAP, whereas for gaussian priors, the two estimators have roughly equal efficiency. We also address the application of MCMC methods for extracting nonmarginal properties of the posterior distribution. For example, by using MCMC to calculate the mutual information between the stimulus and response, we verify the validity of a computationally efficient Laplace approximation to this quantity for gaussian priors in a wide range of model parameters; this makes direct model-based computation of the mutual information tractable even in the case of large observed neural populations, where methods based on binning the spike train fail. Finally, we consider the effect of uncertainty in the GLM parameters on the posterior estimators. We present a general-purpose method to train Markov chain Monte Carlo kernels, parameterized by deep neural networks, that converge and mix quickly to their target distribution. Our method generalizes Hamiltonian Monte Carlo and is trained to maximize expected squared jumped distance, a proxy for mixing speed. We demonstrate large empirical gains on a collection of simple but challenging distributions, for instance achieving a 106x improvement in effective sample size in one case, and mixing when standard HMC makes no measurable progress in a second. Finally, we show quantitative and qualitative gains on a real-world task: latent-variable generative modeling. Python source code will be open-sourced with the camera-ready paper. The paper proposes Metropolis adjusted Langevin and Hamiltonian Monte Carlo sampling methods defined on the Riemann manifold to resolve the shortcomings of existing Monte Carlo algorithms when sampling from target densities that may be high dimensional and exhibit strong correlations. The methods provide fully automated adaptation mechanisms that circumvent the costly pilot runs that are required to tune proposal densities for Metropolis–Hastings or indeed Hamiltonian Monte Carlo and Metropolis adjusted Langevin algorithms. This allows for highly efficient sampling even in very high dimensions where different scalings may be required for the transient and stationary phases of the Markov chain. The methodology proposed exploits the Riemann geometry of the parameter space of statistical models and thus automatically adapts to the local structure when simulating paths across this manifold, providing highly efficient convergence and exploration of the target density. The performance of these Riemann manifold Monte Carlo methods is rigorously assessed by performing inference on logistic regression models, log-Gaussian Cox point processes, stochastic volatility models and Bayesian estimation of dynamic systems described by non-linear differential equations. Substantial improvements in the time-normalized effective sample size are reported when compared with alternative sampling approaches. MATLAB code that is available from http: www.ucl.ac.uk statistics research rmhmc allows replication of all the results reported. In human-robot collaborative tasks, incorporating qualitative information provided by humans can greatly enhance the robustness and efficacy of robot state estimation. We introduce an algorithmic framework to model qualitative information as quantitative constraints on and between states. Our approach, named Sequentially Constrained Hamiltonian Monte Carlo, integrates Hamiltonian dynamics into Sequentially Constrained Monte Carlo sampling. We are able to generate samples that satisfy arbitrarily complex, non-smooth and discontinuous constraints, which in turn allows us to support a wide range of qualitative information. We evaluate our approach for constrained sampling qualitatively and quantitatively with several classes of constraints. SCHMC significantly outperforms the Metropolis-Hastings algorithm (a standard Markov Chain Monte Carlo (MCMC) method) and the Hamiltonian Monte Carlo (HMC) method, in terms of both the accuracy of the sampling (for satisfying constraints) and the quality of approximation. Compared to Sequentially Constrained Monte Carlo (SCMC), which supports similar kinds of constraints, our SCHMC approach has faster convergence rates and lower parameter sensitivity. Despite having various attractive qualities such as high prediction accuracy and the ability to quantify uncertainty and avoid over-fitting, Bayesian Matrix Factorization has not been widely adopted because of the prohibitive cost of inference. In this paper, we propose a scalable distributed Bayesian matrix factorization algorithm using stochastic gradient MCMC. Our algorithm, based on Distributed Stochastic Gradient Langevin Dynamics, can not only match the prediction accuracy of standard MCMC methods like Gibbs sampling, but at the same time is as fast and simple as stochastic gradient descent. In our experiments, we show that our algorithm can achieve the same level of prediction accuracy as Gibbs sampling an order of magnitude faster. We also show that our method reduces the prediction error as fast as distributed stochastic gradient descent, achieving a 4.1 improvement in RMSE for the Netflix dataset and an 1.8 for the Yahoo music dataset. We obtain several quantitative bounds on the mixing properties of the Hamiltonian Monte Carlo (HMC) algorithm for a strongly log-concave target distribution @math on @math , showing that HMC mixes quickly in this setting. One of our main results is a dimension-free bound on the mixing of an "ideal" HMC chain, which is used to show that the usual leapfrog implementation of HMC can sample from @math using only @math gradient evaluations. This dependence on dimension is sharp, and our results significantly extend and improve previous quantitative bounds on the mixing of HMC. Stochastic gradient Markov chain Monte Carlo (SG-MCMC) methods are Bayesian analogs to popular stochastic optimization methods; however, this connection is not well studied. We explore this relationship by applying simulated annealing to an SGMCMC algorithm. Furthermore, we extend recent SG-MCMC methods with two key components: i) adaptive preconditioners (as in ADAgrad or RMSprop), and ii) adaptive element-wise momentum weights. The zerotemperature limit gives a novel stochastic optimization method with adaptive elementwise momentum weights, while conventional optimization methods only have a shared, static momentum weight. Under certain assumptions, our theoretical analysis suggests the proposed simulated annealing approach converges close to the global optima. Experiments on several deep neural network models show state-of-the-art results compared to related stochastic optimization algorithms. The posteriors over neural network weights are high dimensional and multimodal. Each mode typically characterizes a meaningfully different representation of the data. We develop Cyclical Stochastic Gradient MCMC (SG-MCMC) to automatically explore such distributions. In particular, we propose a cyclical stepsize schedule, where larger steps discover new modes, and smaller steps characterize each mode. We prove that our proposed learning rate schedule provides faster convergence to samples from a stationary distribution than SG-MCMC with standard decaying schedules. Moreover, we provide extensive experimental results to demonstrate the effectiveness of cyclical SG-MCMC in learning complex multimodal distributions, especially for fully Bayesian inference with modern deep neural networks. We describe a Bayesian method, for fitting curves to data drawn from an exponential family, that uses splines for which the number and locations of knots are free parameters. The method uses reversible jump Markov chain Monte Carlo to change the knot configurations and a locality heuristic to speed up mixing. For nonnormal models, we approximate the integrated likelihood ratios needed to compute acceptance probabilities by using the Bayesian information criterion, BIC, under priors that make this approximation accurate. Our technique is based on a marginalised chain on the knot number and locations, but we provide methods for inference about the regression coefficients, and functions of them, in both normal and nonnormal models. Simulation results suggest that the method performs well, and we illustrate the method in two neuroscience applications. Bayesian treatments of learning in neural networks are typically based either on a local Gaussian approximation to a mode of the posterior weight distribution, or on Markov chain Monte Carlo simulations. A third approach, called ensemble learning, was introduced by Hinton and van Camp (1993). It aims to approximate the posterior distribution by minimizing the Kullback-Leibler divergence between the true posterior and a parametric approximating distribution. The original derivation of a deterministic algorithm relied on the use of a Gaussian approximating distribution with a diagonal covariance matrix and hence was unable to capture the posterior correlations between parameters. In this chapter we show how the ensemble learning approach can be extended to full-covariance Gaussian distributions while remaining computationally tractable. We also extend the framework to deal with hyperparameters, leading to a simple re-estimation procedure. One of the benefits of our approach is that it yields a strict lower bound on the marginal likelihood, in contrast to other approximate procedures. In many multivariate domains, we are interested in analyzing the dependency structure of the underlying distribution, e.g., whether two variables are in direct interaction. We can represent dependency structures using Bayesian network models. To analyze a given data set, Bayesian model selection attempts to find the most likely (MAP) model, and uses its structure to answer these questions. However, when the amount of available data is modest, there might be many models that have non-negligible posterior. Thus, we want compute the Bayesian posterior of a feature, i.e., the total posterior probability of all models that contain it. In this paper, we propose a new approach for this task. We first show how to efficiently compute a sum over the exponential number of networks that are consistent with a fixed order over network variables. This allows us to compute, for a given order, both the marginal probability of the data and the posterior of a feature. We then use this result as the basis for an algorithm that approximates the Bayesian posterior of a feature. Our approach uses a Markov Chain Monte Carlo (MCMC) method, but over orders rather than over network structures. The space of orders is smaller and more regular than the space of structures, and has much a smoother posterior “landscape”. We present empirical results on synthetic and real-life datasets that compare our approach to full model averaging (when possible), to MCMC over network structures, and to a non-Bayesian bootstrap approach. Sampling logconcave functions arising in statistics and machine learning has been a subject of intensive study. Recent developments include analyses for Langevin dynamics and Hamiltonian Monte Carlo (HMC). While both approaches have dimension-independent bounds for the underlying @math processes under sufficiently strong smoothness conditions, the resulting discrete algorithms have complexity and number of function evaluations growing with the dimension. Motivated by this problem, in this paper, we give a general algorithm for solving multivariate ordinary differential equations whose solution is close to the span of a known basis of functions (e.g., polynomials or piecewise polynomials). The resulting algorithm has polylogarithmic depth and essentially tight runtime - it is nearly linear in the size of the representation of the solution. We apply this to the sampling problem to obtain a nearly linear implementation of HMC for a broad class of smooth, strongly logconcave densities, with the number of iterations (parallel depth) and gradient evaluations being @math in the dimension (rather than polynomial as in previous work). This class includes the widely-used loss function for logistic regression with incoherent weight matrices and has been subject of much study recently. We also give a faster algorithm with @math for the more general and standard class of strongly convex functions with Lipschitz gradient. These results are based on (1) an improved contraction bound for the exact HMC process and (2) logarithmic bounds on the degree of polynomials that approximate solutions of the differential equations arising in implementing HMC. In this paper we investigate the use of Langevin Monte Carlo methods on the probability simplex and propose a new method, Stochastic gradient Riemannian Langevin dynamics, which is simple to implement and can be applied to large scale data. We apply this method to latent Dirichlet allocation in an online mini-batch setting, and demonstrate that it achieves substantial performance improvements over the state of the art online variational Bayesian methods. Many different methods to train deep generative models have been introduced in the past. In this paper, we propose to extend the variational auto-encoder (VAE) framework with a new type of prior which we call "Variational Mixture of Posteriors" prior, or VampPrior for short. The VampPrior consists of a mixture distribution (e.g., a mixture of Gaussians) with components given by variational posteriors conditioned on learnable pseudo-inputs. We further extend this prior to a two layer hierarchical model and show that this architecture with a coupled prior and posterior, learns significantly better models. The model also avoids the usual local optima issues related to useless latent dimensions that plague VAEs. We provide empirical studies on six datasets, namely, static and binary MNIST, OMNIGLOT, Caltech 101 Silhouettes, Frey Faces and Histopathology patches, and show that applying the hierarchical VampPrior delivers state-of-the-art results on all datasets in the unsupervised permutation invariant setting and the best results or comparable to SOTA methods for the approach with convolutional networks. Stochastic Gradient Descent with a constant learning rate (constant SGD) simulates a Markov chain with a stationary distribution. With this perspective, we derive several new results. (1) We show that constant SGD can be used as an approximate Bayesian posterior inference algorithm. Specifically, we show how to adjust the tuning parameters of constant SGD to best match the stationary distribution to a posterior, minimizing the Kullback-Leibler divergence between these two distributions. (2) We demonstrate that constant SGD gives rise to a new variational EM algorithm that optimizes hyperparameters in complex probabilistic models. (3) We also propose SGD with momentum for sampling and show how to adjust the damping coefficient accordingly. (4) We analyze MCMC algorithms. For Langevin Dynamics and Stochastic Gradient Fisher Scoring, we quantify the approximation errors due to finite learning rates. Finally (5), we use the stochastic process perspective to give a short proof of why Polyak averaging is optimal. Based on this idea, we propose a scalable approximate MCMC algorithm, the Averaged Stochastic Gradient Sampler. Hierarchical Bayesian networks and neural networks with stochastic hidden units are commonly perceived as two separate types of models. We show that either of these types of models can often be transformed into an instance of the other, by switching between centered and differentiable non-centered parameterizations of the latent variables. The choice of parameterization greatly influences the efficiency of gradient-based posterior inference; we show that they are often complementary to eachother, we clarify when each parameterization is preferred and show how inference can be made robust. In the noncentered form, a simple Monte Carlo estimator of the marginal likelihood can be used for learning the parameters. Theoretical results are supported by experiments.