Empirical Bayes (EB) improves the accuracy of simultaneous inference "by learning from the experience of others" (Efron, 2012). Classical EB theory focuses on latent variables that are iid draws from a fitted prior (Efron, 2019). Modern applications, however, feature complex structure, like arrays, spatial processes, or covariates. How can we apply EB ideas to these settings? We propose a generalized approach to empirical Bayes based on the notion of probabilistic symmetry. Our method pairs a simultaneous inference problem-with an unknown prior-to a symmetry assumption on the joint distribution of the latent variables. Each symmetry implies an ergodic decomposition, which we use to derive a corresponding empirical Bayes method. We call this methodBayesian empirical Bayes (BEB). We show how BEB recovers the classical methods of empirical Bayes, which implicitly assume exchangeability. We then use it to extend EB to other probabilistic symmetries: (i) EB matrix recovery for arrays and graphs; (ii) covariate-assisted EB for conditional data; (iii) EB spatial regression under shift invariance. We develop scalable algorithms based on variational inference and neural networks. In simulations, BEB outperforms existing approaches to denoising arrays and spatial data. On real data, we demonstrate BEB by denoising a cancer gene-expression matrix and analyzing spatial air-quality data from New York City.

Multivariate zero-inflated count data arise in a wide range of areas such as economics, social sciences, and biology. To infer causal relationships in zero-inflated count data, we propose a new zero-inflated Poisson Bayesian network (ZIPBN) model. We show that the proposed ZIPBN is identifiable with cross-sectional data. The proof is based on the well-known characterization of Markov equivalence class which is applicable to other distribution families. For causal structural learning, we introduce a fully Bayesian inference approach which exploits the parallel tempering Markov chain Monte Carlo algorithm to efficiently explore the multi-modal network space. We demonstrate the utility of the proposed ZIPBN in causal discoveries for zero-inflated count data by simulation studies with comparison to alternative Bayesian network methods. Additionally, real single-cell RNA-sequencing data with known causal relationships will be used to assess the capability of ZIPBN for discovering causal relationships in real-world problems.

We study the problem of inferring time-varying Gaussian Markov random fields, where the underlying graphical model is both sparse and changes {sparsely} over time. Most of the existing methods for the inference of time-varying Markov random fields (MRFs) rely on the \textit{regularized maximum likelihood estimation} (MLE), that typically suffer from weak statistical guarantees and high computational time. Instead, we introduce a new class of constrained optimization problems for the inference of sparsely-changing Gaussian MRFs (GMRFs). The proposed optimization problem is formulated based on the exact $\ell_0$ regularization, and can be solved in near-linear time and memory. Moreover, we show that the proposed estimator enjoys a provably small estimation error. We derive sharp statistical guarantees in the high-dimensional regime, showing that such problems can be learned with as few as one sample per time period. Our proposed method is extremely efficient in practice: it can accurately estimate sparsely-changing GMRFs with more than 500 million variables in less than one hour.

Virtually any model we use in machine learning to make predictions does not perfectly represent reality. So, most of the learning happens under model misspecification. In this work, we present a novel analysis of the generalization performance of Bayesian model averaging under model misspecification and i.i.d.

The key distinguishing property of a Bayesian approach is marginalization, rather than using a single setting of weights. Bayesian marginalization can particularly improve the accuracy and calibration of modern deep neural networks, which are typically underspecified by the data, and can represent many compelling but different solutions. We show that deep ensembles provide an effective mechanism for approximate Bayesian marginalization, and propose a related approach that further improves the predictive distribution by marginalizing within basins of attraction, without significant overhead. We also investigate the prior over functions implied by a vague distribution over neural network weights, explaining the generalization properties of such models from a probabilistic perspective. From this perspective, we explain results that have been presented as mysterious and distinct to neural network generalization, such as the ability to fit images with random labels, and show that these results can be reproduced with Gaussian processes. We also show that Bayesian model averaging alleviates double descent, resulting in monotonic performance improvements with increased flexibility.

We study a multi-armed bandit problem where the rewards exhibit regime switching. Specifically, the distributions of the random rewards generated from all arms are modulated by a common underlying state modeled as a finite-state Markov chain. The agent does not observe the underlying state and has to learn the transition matrix and the reward distributions. We propose a learning algorithm for this problem, building on spectral method-of-moments estimations for hidden Markov models, belief error control in partially observable Markov decision processes and upper-confidence-bound methods for online learning. We also establish an upper bound $O(T^{2/3}\sqrt{\log T})$ for the proposed learning algorithm where $T$ is the learning horizon. Finally, we conduct proof-of-concept experiments to illustrate the performance of the learning algorithm.

This paper re-examines a continuous optimization framework dubbed NOTEARS for learning Bayesian networks. We first generalize existing algebraic characterizations of acyclicity to a class of matrix polynomials. Next, focusing on a one-parameter-per-edge setting, it is shown that the Karush-Kuhn-Tucker (KKT) optimality conditions for the NOTEARS formulation cannot be satisfied except in a trivial case, which explains a behavior of the associated algorithm. We then derive the KKT conditions for an equivalent reformulation, show that they are indeed necessary, and relate them to explicit constraints that certain edges be absent from the graph. If the score function is convex, these KKT conditions are also sufficient for local minimality despite the non-convexity of the constraint. Informed by the KKT conditions, a local search post-processing algorithm is proposed and shown to substantially and universally improve the structural Hamming distance of all tested algorithms, typically by a factor of 2 or more. Some combinations with local search are both more accurate and more efficient than the original NOTEARS.

Probabilistic context-free grammars (PCFGs) and dynamic Bayesian networks (DBNs) are widely used sequence models with complementary strengths and limitations. While PCFGs allow for nested hierarchical dependencies (tree structures), their latent variables (non-terminal symbols) have to be discrete. In contrast, DBNs allow for continuous latent variables, but the dependencies are strictly sequential (chain structure). Therefore, neither can be applied if the latent variables are assumed to be continuous and also to have a nested hierarchical dependency structure. In this paper, we present Recursive Bayesian Networks (RBNs), which generalise and unify PCFGs and DBNs, combining their strengths and containing both as special cases. RBNs define a joint distribution over tree-structured Bayesian networks with discrete or continuous latent variables. The main challenge lies in performing joint inference over the exponential number of possible structures and the continuous variables. We provide two solutions: 1) For arbitrary RBNs, we generalise inside and outside probabilities from PCFGs to the mixed discrete-continuous case, which allows for maximum posterior estimates of the continuous latent variables via gradient descent, while marginalising over network structures.

We analyze the complexity of learning directed acyclic graphical models from observational data in general settings without specific distributional assumptions. Our approach is information-theoretic and uses a local Markov boundary search procedure in order to recursively construct ancestral sets in the underlying graphical model. Perhaps surprisingly, we show that for certain graph ensembles, a simple forward greedy search algorithm (i.e.

Models of many real-life applications, such as queueing models of communication networks or computing systems, have a countably infinite state-space. Algorithmic and learning procedures that have been developed to produce optimal policies mainly focus on finite state settings, and do not directly apply to these models. To overcome this lacuna, in this work we study the problem of optimal control of a family of discrete-time countable state-space Markov Decision Processes (MDPs) governed by an unknown parameter $\theta\in\Theta$, and defined on a countably-infinite state-space $\mathcal X=\mathbb{Z}_+^d$, with finite action space $\mathcal A$, and an unbounded cost function. We take a Bayesian perspective with the random unknown parameter $\boldsymbol{\theta}^*$ generated via a given fixed prior distribution on $\Theta$. To optimally control the unknown MDP, we propose an algorithm based on Thompson sampling with dynamically-sized episodes: at the beginning of each episode, the posterior distribution formed via Bayes' rule is used to produce a parameter estimate, which then decides the policy applied during the episode. To ensure the stability of the Markov chain obtained by following the policy chosen for each parameter, we impose ergodicity assumptions. From this condition and using the solution of the average cost Bellman equation, we establish an $\tilde O(dh^d\sqrt{|\mathcal A|T})$ upper bound on the Bayesian regret of our algorithm, where $T$ is the time-horizon. Finally, to elucidate the applicability of our algorithm, we consider two different queueing models with unknown dynamics, and show that our algorithm can be applied to develop approximately optimal control algorithms.