Measurement error occurs when a covariate influencing a response variable is corrupted by noise. This can lead to misleading inference outcomes, particularly in problems where accurately estimating the relationship between covariates and response variables is crucial, such as causal effect estimation. Existing methods for dealing with measurement error often rely on strong assumptions such as knowledge of the error distribution or its variance and availability of replicated measurements of the covariates. We propose a Bayesian Nonparametric Learning framework that is robust to mismeasured covariates, does not require the preceding assumptions, and can incorporate prior beliefs about the error distribution. This approach gives rise to a general framework that is suitable for both Classical and Berkson error models via the appropriate specification of the prior centering measure of a Dirichlet Process (DP). Moreover, it offers flexibility in the choice of loss function depending on the type of regression model. We provide bounds on the generalization error based on the Maximum Mean Discrepancy (MMD) loss which allows for generalization to non-Gaussian distributed errors and nonlinear covariate-response relationships. We showcase the effectiveness of the proposed framework versus prior art in real-world problems containing either Berkson or Classical measurement errors.
This paper proposes a step toward approximate Bayesian inference in on-policy actor-critic deep reinforcement learning. It is implemented through three changes to the Asynchronous Advantage Actor-Critic (A3C) algorithm: (1) applying a ReLU function to advantage estimates, (2) spectral normalization of actor-critic weights, and (3) incorporating \emph{dropout as a Bayesian approximation}. We prove under standard assumptions that restricting policy updates to positive advantages optimizes for value by maximizing a lower bound on the value function plus an additive term. We show that the additive term is bounded proportional to the Lipschitz constant of the value function, which offers theoretical grounding for spectral normalization of critic weights. Finally, our application of dropout corresponds to approximate Bayesian inference over both the actor and critic parameters, which enables \textit{adaptive state-aware} exploration around the modes of the actor via Thompson sampling. We demonstrate significant improvements for median and interquartile mean metrics over A3C, PPO, SAC, and TD3 on the MuJoCo continuous control benchmark and improvement over PPO in the challenging ProcGen generalization benchmark.
The success of Bayesian inference with MCMC depends critically on Markov chains rapidly reaching the posterior distribution. Despite the plentitude of inferential theory for posteriors in Bayesian non-parametrics, convergence properties of MCMC algorithms that simulate from such ideal inferential targets are not thoroughly understood. This work focuses on the Bayesian CART algorithm which forms a building block of Bayesian Additive Regression Trees (BART). We derive upper bounds on mixing times for typical posteriors under various proposal distributions. Exploiting the wavelet representation of trees, we provide sufficient conditions for Bayesian CART to mix well (polynomially) under certain hierarchical connectivity restrictions on the signal. We also derive a negative result showing that Bayesian CART (based on simple grow and prune steps) cannot reach deep isolated signals in faster than exponential mixing time. To remediate myopic tree exploration, we propose Twiggy Bayesian CART which attaches/detaches entire twigs (not just single nodes) in the proposal distribution. We show polynomial mixing of Twiggy Bayesian CART without assuming that the signal is connected on a tree. Going further, we show that informed variants achieve even faster mixing. A thorough simulation study highlights discrepancies between spike-and-slab priors and Bayesian CART under a variety of proposals.
In this study, we explore the emergence of symbols during interactions between individuals through an experimental semiotic study. Previous studies investigate how humans organize symbol systems through communication using artificially designed subjective experiments. In this study, we have focused on a joint attention-naming game (JA-NG) in which participants independently categorize objects and assign names while assuming their joint attention. In the theory of the Metropolis-Hastings naming game (MHNG), listeners accept provided names according to the acceptance probability computed using the Metropolis-Hastings (MH) algorithm. The theory of MHNG suggests that symbols emerge as an approximate decentralized Bayesian inference of signs, which is represented as a shared prior variable if the conditions of MHNG are satisfied. This study examines whether human participants exhibit behavior consistent with MHNG theory when playing JA-NG. By comparing human acceptance decisions of a partner's naming with acceptance probabilities computed in the MHNG, we tested whether human behavior is consistent with the MHNG theory. The main contributions of this study are twofold. First, we reject the null hypothesis that humans make acceptance judgments with a constant probability, regardless of the acceptance probability calculated by the MH algorithm. This result suggests that people followed the acceptance probability computed by the MH algorithm to some extent. Second, the MH-based model predicted human acceptance/rejection behavior more accurately than the other four models: Constant, Numerator, Subtraction, and Binary. This result indicates that symbol emergence in JA-NG can be explained using MHNG and is considered an approximate decentralized Bayesian inference.
Model-based disease mapping remains a fundamental policy-informing tool in the fields of public health and disease surveillance. Hierarchical Bayesian models have emerged as the state-of-the-art approach for disease mapping since they are able to both capture structure in the data and robustly characterise uncertainty. When working with areal data, e.g.~aggregates at the administrative unit level such as district or province, current models rely on the adjacency structure of areal units to account for spatial correlations and perform shrinkage. The goal of disease surveillance systems is to track disease outcomes over time. This task is especially challenging in crisis situations which often lead to redrawn administrative boundaries, meaning that data collected before and after the crisis are no longer directly comparable. Moreover, the adjacency-based approach ignores the continuous nature of spatial processes and cannot solve the change-of-support problem, i.e.~when estimates are required to be produced at different administrative levels or levels of aggregation. We present a novel, practical, and easy to implement solution to solve these problems relying on a methodology combining deep generative modelling and fully Bayesian inference: we build on the recently proposed PriorVAE method able to encode spatial priors over small areas with variational autoencoders by encoding aggregates over administrative units. We map malaria prevalence in Kenya, a country in which administrative boundaries changed in 2010.
In the studies on symbol emergence and emergent communication in a population of agents, a computational model was employed in which agents participate in various language games. Among these, the Metropolis-Hastings naming game (MHNG) possesses a notable mathematical property: symbol emergence through MHNG is proven to be a decentralized Bayesian inference of representations shared by the agents. However, the previously proposed MHNG is limited to a two-agent scenario. This paper extends MHNG to an N-agent scenario. The main contributions of this paper are twofold: (1) we propose the recursive Metropolis-Hastings naming game (RMHNG) as an N-agent version of MHNG and demonstrate that RMHNG is an approximate Bayesian inference method for the posterior distribution over a latent variable shared by agents, similar to MHNG; and (2) we empirically evaluate the performance of RMHNG on synthetic and real image data, enabling multiple agents to develop and share a symbol system. Furthermore, we introduce two types of approximations -- one-sample and limited-length -- to reduce computational complexity while maintaining the ability to explain communication in a population of agents. The experimental findings showcased the efficacy of RMHNG as a decentralized Bayesian inference for approximating the posterior distribution concerning latent variables, which are jointly shared among agents, akin to MHNG. Moreover, the utilization of RMHNG elucidated the agents' capacity to exchange symbols. Furthermore, the study discovered that even the computationally simplified version of RMHNG could enable symbols to emerge among the agents.
We propose an efficient online approximate Bayesian inference algorithm for estimating the parameters of a nonlinear function from a potentially non-stationary data stream. The method is based on the extended Kalman filter (EKF), but uses a novel low-rank plus diagonal decomposition of the posterior precision matrix, which gives a cost per step which is linear in the number of model parameters. In contrast to methods based on stochastic variational inference, our method is fully deterministic, and does not require step-size tuning. We show experimentally that this results in much faster (more sample efficient) learning, which results in more rapid adaptation to changing distributions, and faster accumulation of reward when used as part of a contextual bandit algorithm.
During the last decades macroecology has identified broad-scale patterns of abundances and diversity of microbial communities and put forward some potential explanations for them. However, these advances are not paralleled by a full understanding of the dynamical processes behind them. In particular, abundance fluctuations of different species are found to be correlated, both across time and across communities in metagenomic samples. Reproducing such correlations through appropriate population models remains an open challenge. The present paper tackles this problem and points to sparse species interactions as a necessary mechanism to account for them. Specifically, we discuss several possibilities to include interactions in population models and recognize Lotka-Volterra constants as a successful ansatz. For this, we design a Bayesian inference algorithm to extract sets of interaction constants able to reproduce empirical probability distributions of pairwise correlations for diverse biomes. Importantly, the inferred models still reproduce well-known single-species macroecological patterns concerning abundance fluctuations across both species and communities. Endorsed by the agreement with the empirically observed phenomenology, our analyses provide insights on the properties of the networks of microbial interactions, revealing that sparsity is a crucial feature.
In this paper, we propose a new Bayesian inference method for a high-dimensional sparse factor model that allows both the factor dimensionality and the sparse structure of the loading matrix to be inferred. The novelty is to introduce a certain dependence between the sparsity level and the factor dimensionality, which leads to adaptive posterior concentration while keeping computational tractability. We show that the posterior distribution asymptotically concentrates on the true factor dimensionality, and more importantly, this posterior consistency is adaptive to the sparsity level of the true loading matrix and the noise variance. We also prove that the proposed Bayesian model attains the optimal detection rate of the factor dimensionality in a more general situation than those found in the literature. Moreover, we obtain a near-optimal posterior concentration rate of the covariance matrix. Numerical studies are conducted and show the superiority of the proposed method compared with other competitors.
Bayesian inference remains one of the most important tool-kits for any scientist, but increasingly expensive likelihood functions are required for ever-more complex experiments, raising the cost of generating a Monte Carlo sample of the posterior. Recent attention has been directed towards the use of emulators of the posterior based on Gaussian Process (GP) regression combined with active sampling to achieve comparable precision with far fewer costly likelihood evaluations. Key to this approach is the batched acquisition of proposals, so that the true posterior can be evaluated in parallel. This is usually achieved via sequential maximization of the highly multimodal acquisition function. Unfortunately, this approach parallelizes poorly and is prone to getting stuck in local maxima. Our approach addresses this issue by generating nearly-optimal batches of candidates using an almost-embarrassingly parallel Nested Sampler on the mean prediction of the GP. The resulting nearly-sorted Monte Carlo sample is used to generate a batch of candidates ranked according to their sequentially conditioned acquisition function values at little cost. The final sample can also be used for inferring marginal quantities. Our proposed implementation (NORA) demonstrates comparable accuracy to sequential conditioned acquisition optimization and efficient parallelization in various synthetic and cosmological inference problems.
In this work, we introduce a novel framework which combines physics and machine learning methods to analyse acoustic signals. Three methods are developed for this task: a Bayesian inference approach for inferring the spectral acoustics characteristics, a neural-physical model which equips a neural network with forward and backward physical losses, and the non-linear least squares approach which serves as benchmark. The inferred propagation coefficient leads to the room impulse response (RIR) quantity which can be used for relocalisation with uncertainty. The simplicity and efficiency of this framework is empirically validated on simulated data.
The shocks which hit macroeconomic models such as Vector Autoregressions (VARs) have the potential to be non-Gaussian, exhibiting asymmetries and fat tails. This consideration motivates the VAR developed in this paper which uses a Dirichlet process mixture (DPM) to model the shocks. However, we do not follow the obvious strategy of simply modeling the VAR errors with a DPM since this would lead to computationally infeasible Bayesian inference in larger VARs and potentially a sensitivity to the way the variables are ordered in the VAR. Instead we develop a particular additive error structure inspired by Bayesian nonparametric treatments of random effects in panel data models. We show that this leads to a model which allows for computationally fast and order-invariant inference in large VARs with nonparametric shocks. Our empirical results with nonparametric VARs of various dimensions shows that nonparametric treatment of the VAR errors is particularly useful in periods such as the financial crisis and the pandemic.
Neural additive models (NAMs) enhance the transparency of deep neural networks by handling input features in separate additive sub-networks. However, they lack inherent mechanisms that provide calibrated uncertainties and enable selection of relevant features and interactions. Approaching NAMs from a Bayesian perspective, we augment them in three primary ways, namely by a) providing credible intervals for the individual additive sub-networks; b) estimating the marginal likelihood to perform an implicit selection of features via an empirical Bayes procedure; and c) facilitating the ranking of feature pairs as candidates for second-order interaction in fine-tuned models. In particular, we develop Laplace-approximated NAMs (LA-NAMs), which show improved empirical performance on tabular datasets and challenging real-world medical tasks.
One of the fundamental challenges in the prediction of dynamic agents is robustness. Usually, most predictions are deterministic estimates of future states which are over-confident and prone to error. Recently, few works have addressed capturing uncertainty during forecasting of future states. However, these probabilistic estimation methods fail to account for the upstream noise in perception data during tracking. Sensors always have noise and state estimation becomes even more difficult under adverse weather conditions and occlusion. Traditionally, Bayes filters have been used to fuse information from noisy sensors to update states with associated belief. But, they fail to address non-linearities and long-term predictions. Therefore, we propose an end-to-end estimator that can take noisy sensor measurements and make robust future state predictions with uncertainty bounds while simultaneously taking into consideration the upstream perceptual uncertainty. For the current research, we consider an encoder-decoder based deep ensemble network for capturing both perception and predictive uncertainty simultaneously. We compared the current model to other approximate Bayesian inference methods. Overall, deep ensembles provided more robust predictions and the consideration of upstream uncertainty further increased the estimation accuracy for the model.
We study the problem of approximate sampling from non-log-concave distributions, e.g., Gaussian mixtures, which is often challenging even in low dimensions due to their multimodality. We focus on performing this task via Markov chain Monte Carlo (MCMC) methods derived from discretizations of the overdamped Langevin diffusions, which are commonly known as Langevin Monte Carlo algorithms. Furthermore, we are also interested in two nonsmooth cases for which a large class of proximal MCMC methods have been developed: (i) a nonsmooth prior is considered with a Gaussian mixture likelihood; (ii) a Laplacian mixture distribution. Such nonsmooth and non-log-concave sampling tasks arise from a wide range of applications to Bayesian inference and imaging inverse problems such as image deconvolution. We perform numerical simulations to compare the performance of most commonly used Langevin Monte Carlo algorithms.
Agent-based modelling (ABMing) is a powerful and intuitive approach to modelling complex systems; however, the intractability of ABMs' likelihood functions and the non-differentiability of the mathematical operations comprising these models present a challenge to their use in the real world. These difficulties have in turn generated research on approximate Bayesian inference methods for ABMs and on constructing differentiable approximations to arbitrary ABMs, but little work has been directed towards designing approximate Bayesian inference techniques for the specific case of differentiable ABMs. In this work, we aim to address this gap and discuss how generalised variational inference procedures may be employed to provide misspecification-robust Bayesian parameter inferences for differentiable ABMs. We demonstrate with experiments on a differentiable ABM of the COVID-19 pandemic that our approach can result in accurate inferences, and discuss avenues for future work.
The Bayesian Synthetic Likelihood (BSL) method is a widely-used tool for likelihood-free Bayesian inference. This method assumes that some summary statistics are normally distributed, which can be incorrect in many applications. We propose a transformation, called the Wasserstein Gaussianization transformation, that uses a Wasserstein gradient flow to approximately transform the distribution of the summary statistics into a Gaussian distribution. BSL also implicitly requires compatibility between simulated summary statistics under the working model and the observed summary statistics. A robust BSL variant which achieves this has been developed in the recent literature. We combine the Wasserstein Gaussianization transformation with robust BSL, and an efficient Variational Bayes procedure for posterior approximation, to develop a highly efficient and reliable approximate Bayesian inference method for likelihood-free problems.
Many scientific models are composed of multiple discrete components, and scientists often make heuristic decisions about which components to include. Bayesian inference provides a mathematical framework for systematically selecting model components, but defining prior distributions over model components and developing associated inference schemes has been challenging. We approach this problem in a simulation-based inference framework: We define model priors over candidate components and, from model simulations, train neural networks to infer joint probability distributions over both model components and associated parameters. Our method, simulation-based model inference (SBMI), represents distributions over model components as a conditional mixture of multivariate binary distributions in the Grassmann formalism. SBMI can be applied to any compositional stochastic simulator without requiring likelihood evaluations. We evaluate SBMI on a simple time series model and on two scientific models from neuroscience, and show that it can discover multiple data-consistent model configurations, and that it reveals non-identifiable model components and parameters. SBMI provides a powerful tool for data-driven scientific inquiry which will allow scientists to identify essential model components and make uncertainty-informed modelling decisions.
Bayesian approaches for learning deep neural networks (BNN) have been received much attention and successfully applied to various applications. Particularly, BNNs have the merit of having better generalization ability as well as better uncertainty quantification. For the success of BNN, search an appropriate architecture of the neural networks is an important task, and various algorithms to find good sparse neural networks have been proposed. In this paper, we propose a new node-sparse BNN model which has good theoretical properties and is computationally feasible. We prove that the posterior concentration rate to the true model is near minimax optimal and adaptive to the smoothness of the true model. In particular the adaptiveness is the first of its kind for node-sparse BNNs. In addition, we develop a novel MCMC algorithm which makes the Bayesian inference of the node-sparse BNN model feasible in practice.
Bayesian inference usually requires running potentially costly inference procedures separately for every new observation. In contrast, the idea of amortized Bayesian inference is to initially invest computational cost in training an inference network on simulated data, which can subsequently be used to rapidly perform inference (i.e., to return estimates of posterior distributions) for new observations. This approach has been applied to many real-world models in the sciences and engineering, but it is unclear how robust the approach is to adversarial perturbations in the observed data. Here, we study the adversarial robustness of amortized Bayesian inference, focusing on simulation-based estimation of multi-dimensional posterior distributions. We show that almost unrecognizable, targeted perturbations of the observations can lead to drastic changes in the predicted posterior and highly unrealistic posterior predictive samples, across several benchmark tasks and a real-world example from neuroscience. We propose a computationally efficient regularization scheme based on penalizing the Fisher information of the conditional density estimator, and show how it improves the adversarial robustness of amortized Bayesian inference.