Normalizing constant (also called partition function, Bayesian evidence, or marginal likelihood) is one of the central goals of Bayesian inference, yet most of the existing methods are both expensive and inaccurate. Here we develop a new approach, starting from posterior samples obtained with a standard Markov Chain Monte Carlo (MCMC). We apply a novel Normalizing Flow (NF) approach to obtain an analytic density estimator from these samples, followed by Optimal Bridge Sampling (OBS) to obtain the normalizing constant. We compare our method which we call Gaussianized Bridge Sampling (GBS) to existing methods such as Nested Sampling (NS) and Annealed Importance Sampling (AIS) on several examples, showing our method is both significantly faster and substantially more accurate than these methods, and comes with a reliable error estimation.
Neural Tangents is a library designed to enable research into infinite-width neural networks. It provides a high-level API for specifying complex and hierarchical neural network architectures. These networks can then be trained and evaluated either at finite-width as usual or in their infinite-width limit. Infinite-width networks can be trained analytically using exact Bayesian inference or using gradient descent via the Neural Tangent Kernel. Additionally, Neural Tangents provides tools to study gradient descent training dynamics of wide but finite networks in either function space or weight space. The entire library runs out-of-the-box on CPU, GPU, or TPU. All computations can be automatically distributed over multiple accelerators with near-linear scaling in the number of devices. Neural Tangents is available at www.github.com/google/neural-tangents. We also provide an accompanying interactive Colab notebook.
The complex and computationally expensive nature of landscape evolution models pose significant challenges in the inference and optimisation of unknown parameters. Bayesian inference provides a methodology for estimation and uncertainty quantification of unknown model parameters. In our previous work, we developed parallel tempering Bayeslands as a framework for parameter estimation and uncertainty quantification for the Badlands landscape evolution model. Parallel tempering Bayeslands features high-performance computing with dozens of processing cores running in parallel to enhance computational efficiency. Although we use parallel computing, the procedure remains computationally challenging since thousands of samples need to be drawn and evaluated. \textcolor{black}{In large-scale landscape and basin evolution problems, a single model evaluation can take from several minutes to hours, and in some instances, even days. Surrogate-assisted optimisation has been used for several computationally expensive engineering problems which motivate its use in optimisation and inference of complex geoscientific models.} The use of surrogate models can speed up parallel tempering Bayeslands by developing computationally inexpensive models to mimic expensive ones. In this paper, we apply surrogate-assisted parallel tempering where that surrogate mimics a landscape evolution model by estimating the likelihood function from the model. \textcolor{black}{We employ a neural network-based surrogate model that learns from the history of samples generated. } The entire framework is developed in a parallel computing infrastructure to take advantage of parallelism. The results show that the proposed methodology is effective in lowering the overall computational cost significantly while retaining the quality of solutions.
In many real-world applications of machine learning, data are distributed across many clients and cannot leave the devices they are stored on. Furthermore, each client's data, computational resources and communication constraints may be very different. This setting is known as federated learning, in which privacy is a key concern. Differential privacy is commonly used to provide mathematical privacy guarantees. This work, to the best of our knowledge, is the first to consider federated, differentially private, Bayesian learning. We build on Partitioned Variational Inference (PVI) which was recently developed to support approximate Bayesian inference in the federated setting. We modify the client-side optimisation of PVI to provide an (${\epsilon}$, ${\delta}$)-DP guarantee. We show that it is possible to learn moderately private logistic regression models in the federated setting that achieve similar performance to models trained non-privately on centralised data.
Empirical research in Natural Language Processing (NLP) has adopted a narrow set of principles for assessing hypotheses, relying mainly on p-value computation, which suffers from several known issues. While alternative proposals have been well-debated and adopted in other fields, they remain rarely discussed or used within the NLP community. We address this gap by contrasting various hypothesis assessment techniques, especially those not commonly used in the field (such as evaluations based on Bayesian inference). Since these statistical techniques differ in the hypotheses they can support, we argue that practitioners should first decide their target hypothesis before choosing an assessment method. This is crucial because common fallacies, misconceptions, and misinterpretation surrounding hypothesis assessment methods often stem from a discrepancy between what one would like to claim versus what the method used actually assesses. Our survey reveals that these issues are omnipresent in the NLP research community. As a step forward, we provide best practices and guidelines tailored to NLP research, as well as an easy-to-use package called 'HyBayes' for Bayesian assessment of hypotheses, complementing existing tools.
We address the problem of continual learning in multi-task Gaussian process (GP) models for handling sequential input-output observations. Our approach extends the existing prior-posterior recursion of online Bayesian inference, i.e.\ past posterior discoveries become future prior beliefs, to the infinite functional space setting of GP. For a reason of scalability, we introduce variational inference together with an sparse approximation based on inducing inputs. As a consequence, we obtain tractable continual lower-bounds where two novel Kullback-Leibler (KL) divergences intervene in a natural way. The key technical property of our method is the recursive reconstruction of conditional GP priors conditioned on the variational parameters learned so far. To achieve this goal, we introduce a novel factorization of past variational distributions, where the predictive GP equation propagates the posterior uncertainty forward. We then demonstrate that it is possible to derive GP models over many types of sequential observations, either discrete or continuous and amenable to stochastic optimization. The continual inference approach is also applicable to scenarios where potential multi-channel or heterogeneous observations might appear. Extensive experiments demonstrate that the method is fully scalable, shows a reliable performance and is robust to uncertainty error propagation over a plenty of synthetic and real-world datasets.
Bayesian inference in state-space models is challenging due to high-dimensional state trajectories. A viable approach is particle Markov chain Monte Carlo, combining MCMC and sequential Monte Carlo to form "exact approximations" to otherwise intractable MCMC methods. The performance of the approximation is limited to that of the exact method. We focus on particle Gibbs and particle Gibbs with ancestor sampling, improving their performance beyond that of the underlying Gibbs sampler (which they approximate) by marginalizing out one or more parameters. This is possible when the parameter prior is conjugate to the complete data likelihood. Marginalization yields a non-Markovian model for inference, but we show that, in contrast to the general case, this method still scales linearly in time. While marginalization can be cumbersome to implement, recent advances in probabilistic programming have enabled its automation. We demonstrate how the marginalized methods are viable as efficient inference backends in probabilistic programming, and demonstrate with examples in ecology and epidemiology.
Stein variational gradient descent (SVGD) is a particle-based inference algorithm that leverages gradient information for efficient approximate inference. In this work, we enhance SVGD by leveraging preconditioning matrices, such as the Hessian and Fisher information matrix, to incorporate geometric information into SVGD updates. We achieve this by presenting a generalization of SVGD that replaces the scalar-valued kernels in vanilla SVGD with more general matrix-valued kernels. This yields a significant extension of SVGD, and more importantly, allows us to flexibly incorporate various preconditioning matrices to accelerate the exploration in the probability landscape. Empirical results show that our method outperforms vanilla SVGD and a variety of baseline approaches over a range of real-world Bayesian inference tasks.
Deep learning has been successfully applied to the segmentation of 3D Computed Tomography (CT) scans. Establishing the credibility of these segmentations requires uncertainty quantification (UQ) to identify untrustworthy predictions. Recent UQ architectures include Monte Carlo dropout networks (MCDNs), which approximate deep Gaussian processes, and Bayesian neural networks (BNNs), which learn the distribution of the weight space. BNNs are advantageous over MCDNs for UQ but are thought to be computationally infeasible in high dimension, and neither architecture has produced interpretable geometric uncertainty maps. We propose a novel 3D Bayesian convolutional neural network (BCNN), the first deep learning method which generates statistically credible geometric uncertainty maps and scales for application to 3D data. We present experimental results on CT scans of graphite electrodes and laser-welded metals and show that our BCNN outperforms an MCDN in recent uncertainty metrics. The geometric uncertainty maps generated by our BCNN capture distributions of sigmoid values that are interpretable as confidence intervals, critical for applications that rely on deep learning for high-consequence decisions. Code available at https://github.com/sandialabs/bcnn.
Markov chain Monte Carlo (MCMC) methods have not been broadly adopted in Bayesian neural networks (BNNs). This paper initially reviews the main challenges in sampling from the parameter posterior of a neural network via MCMC. Such challenges culminate to lack of convergence to the parameter posterior. Nevertheless, this paper shows that a non-converged Markov chain, generated via MCMC sampling from the parameter space of a neural network, can yield via Bayesian marginalization a valuable posterior predictive distribution of the output of the neural network. Classification examples based on multilayer perceptrons showcase highly accurate posterior predictive distributions. The postulate of limited scope for MCMC developments in BNNs is partially valid; an asymptotically exact parameter posterior seems less plausible, yet an accurate posterior predictive distribution is a tenable research avenue.
We introduce a recent symplectic integration scheme derived for solving physically motivated systems with non-separable Hamiltonians. We show its relevance to Riemannian manifold Hamiltonian Monte Carlo (RMHMC) and provide an alternative to the currently used generalised leapfrog symplectic integrator, which relies on solving multiple fixed point iterations to convergence. Via this approach, we are able to reduce the number of higher-order derivative calculations per leapfrog step. We explore the implications of this integrator and demonstrate its efficacy in reducing the computational burden of RMHMC. Our code is provided in a new open-source Python package, hamiltorch.
Recently, different machine learning methods have been introduced to tackle the challenging few-shot learning scenario that is, learning from a small labeled dataset related to a specific task. Common approaches have taken the form of meta-learning: learning to learn on the new problem given the old. Following the recognition that meta-learning is implementing learning in a multi-level model, we present a Bayesian treatment for the meta-learning inner loop through the use of deep kernels. As a result we can learn a kernel that transfers to new tasks; we call this Deep Kernel Transfer (DKT). This approach has many advantages: is straightforward to implement as a single optimizer, provides uncertainty quantification, and does not require estimation of task-specific parameters. We empirically demonstrate that DKT outperforms several state-of-the-art algorithms in few-shot classification, and is the state of the art for cross-domain adaptation and regression. We conclude that complex meta-learning routines can be replaced by a simpler Bayesian model without loss of accuracy.
Likelihood-free inference involves inferring parameter values given observed data and a simulator model. The simulator is computer code which takes parameters, performs stochastic calculations, and outputs simulated data. In this work, we view the simulator as a function whose inputs are (1) the parameters and (2) a vector of pseudo-random draws. We attempt to infer all these inputs conditional on the observations. This is challenging as the resulting posterior can be high dimensional and involve strong dependence. We approximate the posterior using normalizing flows, a flexible parametric family of densities. Training data is generated by likelihood-free importance sampling with a large bandwidth value epsilon, which makes the target similar to the prior. The training data is "distilled" by using it to train an updated normalizing flow. The process is iterated, using the updated flow as the importance sampling proposal, and slowly reducing epsilon so the target becomes closer to the posterior. Unlike most other likelihood-free methods, we avoid the need to reduce data to low dimensional summary statistics, and hence can achieve more accurate results. We illustrate our method in two challenging examples, on queuing and epidemiology.
Variational inference has become an increasingly attractive fast alternative to Markov chain Monte Carlo methods for approximate Bayesian inference. However, a major obstacle to the widespread use of variational methods is the lack of post-hoc accuracy measures that are both theoretically justified and computationally efficient. In this paper, we provide rigorous bounds on the error of posterior mean and uncertainty estimates that arise from full-distribution approximations, as in variational inference. Our bounds are widely applicable, as they require only that the approximating and exact posteriors have polynomial moments. Our bounds are also computationally efficient for variational inference because they require only standard values from variational objectives, straightforward analytic calculations, and simple Monte Carlo estimates. We show that our analysis naturally leads to a new and improved workflow for validated variational inference. Finally, we demonstrate the utility of our proposed workflow and error bounds on a robust regression problem and on a real-data example with a widely used multilevel hierarchical model.
Deep learning has enjoyed much recent success, and applying state-of-the-art model learning methods to controls is an exciting prospect. However, there is a strong reluctance to use these methods on safety-critical systems, which have constraints on safety, stability, and real-time performance. We propose a framework which satisfies these constraints while allowing the use of deep neural networks for learning model uncertainties. Central to our method is the use of Bayesian model learning, which provides an avenue for maintaining appropriate degrees of caution in the face of the unknown. In the proposed approach, we develop an adaptive control framework leveraging the theory of stochastic CLFs (Control Lyapunov Functions) and stochastic CBFs (Control Barrier Functions) along with tractable Bayesian model learning via Gaussian Processes or Bayesian neural networks. Under reasonable assumptions, we guarantee stability and safety while adapting to unknown dynamics with probability 1. We demonstrate this architecture for high-speed terrestrial mobility targeting potential applications in safety-critical high-speed Mars rover missions.
To understand how rich dynamics emerge in neural populations, we require models exhibiting a wide range of activity patterns while remaining interpretable in terms of connectivity and single-neuron dynamics. However, it has been challenging to fit such mechanistic spiking networks at the single neuron scale to empirical population data. To close this gap, we propose to fit such data at a meso scale, using a mechanistic but low-dimensional and hence statistically tractable model. The mesoscopic representation is obtained by approximating a population of neurons as multiple homogeneous `pools' of neurons, and modelling the dynamics of the aggregate population activity within each pool. We derive the likelihood of both single-neuron and connectivity parameters given this activity, which can then be used to either optimize parameters by gradient ascent on the log-likelihood, or to perform Bayesian inference using Markov Chain Monte Carlo (MCMC) sampling. We illustrate this approach using a model of generalized integrate-and-fire neurons for which mesoscopic dynamics have been previously derived, and show that both single-neuron and connectivity parameters can be recovered from simulated data. In particular, our inference method extracts posterior correlations between model parameters, which define parameter subsets able to reproduce the data. We compute the Bayesian posterior for combinations of parameters using MCMC sampling and investigate how the approximations inherent to a mesoscopic population model impact the accuracy of the inferred single-neuron parameters.
Variational inference has had great success in scaling approximate Bayesian inference to big data by exploiting mini-batch training. To date, however, this strategy has been most applicable to models of independent data. We propose an extension to state space models of time series data based on a novel generative model for latent temporal states: the neural moving average model. This permits a subsequence to be sampled without drawing from the entire distribution, enabling training iterations to use mini-batches of the time series at low computational cost. We illustrate our method on autoregressive, Lotka-Volterra, FitzHugh-Nagumo and stochastic volatility models, achieving accurate parameter estimation in a short time.
Model uncertainty obtained by variational Bayesian inference with Monte Carlo dropout is prone to miscalibration. The uncertainty does not represent the model error well. In this paper, temperature scaling is extended to dropout variational inference to calibrate model uncertainty. Expected uncertainty calibration error (UCE) is presented as a metric to measure miscalibration of uncertainty. The effectiveness of this approach is evaluated on CIFAR-10/100 for recent CNN architectures. Experimental results show, that temperature scaling considerably reduces miscalibration by means of UCE and enables robust rejection of uncertain predictions. The proposed approach can easily be derived from frequentist temperature scaling and yields well-calibrated model uncertainty. It is simple to implement and does not affect the model accuracy.
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.
Neural networks are popular state-of-the-art models for many different tasks.They are often trained via back-propagation to find a value of the weights that correctly predicts the observed data. Although back-propagation has shown good performance in many applications, it cannot easily output an estimate of the uncertainty in the predictions made. Estimating the uncertainty in the predictions is a critical aspect with important applications, and one method to obtain this information is following a Bayesian approach to estimate a posterior distribution on the model parameters. This posterior distribution summarizes which parameter values are compatible with the data, but is usually intractable and has to be approximated. Several mechanisms have been considered for solving this problem. We propose here a general method for approximate Bayesian inference that is based on minimizing{\alpha}-divergences and that allows for flexible approximate distributions. The method is evaluated in the context of Bayesian neural networks on extensive experiments. The results show that, in regression problems, it often gives better performance in terms of the test log-likelihoodand sometimes in terms of the squared error. In classification problems, however, it gives competitive results.