In this paper, we consider the problem of learning a sparse graph from the Laplacian constrained Gaussian graphical model. This problem can be formulated as a penalized maximum likelihood estimation of the precision matrix under Laplacian structural constraints. Like in the classical graphical lasso problem, recent works made use of the $\ell_1$-norm with the goal of promoting sparsity in the Laplacian constrained precision matrix estimation. However, through empirical evidence, we observe that the $\ell_1$-norm is not effective in imposing a sparse solution in this problem. From a theoretical perspective, we prove that a large regularization parameter will surprisingly lead to a solution representing a fully connected graph instead of a sparse graph. To address this issue, we propose a nonconvex penalized maximum likelihood estimation method, and establish the order of the statistical error. Numerical experiments involving synthetic and real-world data sets demonstrate the effectiveness of the proposed method.

We give methods for Bayesian inference of directed acyclic graphs, DAGs, and the induced causal effects from passively observed complete data. Our methods build on a recent Markov chain Monte Carlo scheme for learning Bayesian networks, which enables efficient approximate sampling from the graph posterior, provided that each node is assigned a small number K of candidate parents. We present algorithmic techniques to significantly reduce the space and time requirements, which make the use of substantially larger values of K feasible. Furthermore, we investigate the problem of selecting the candidate parents per node so as to maximize the covered posterior mass. Finally, we combine our sampling method with a novel Bayesian approach for estimating causal effects in linear Gaussian DAG models. Numerical experiments demonstrate the performance of our methods in detecting ancestor-descendant relations, and in causal effect estimation our Bayesian method is shown to outperform previous approaches.

We show that the matrix perspective function, which is jointly convex in the Cartesian product of a standard Euclidean vector space and a conformal space of symmetric matrices, has a proximity operator in an almost closed form. The only implicit part is to solve a semismooth, univariate root finding problem. We uncover the connection between our problem of study and the matrix nearness problem. Through this connection, we propose a quadratically convergent Newton algorithm for the root finding problem.Experiments verify that the evaluation of the proximity operator requires at most 8 Newton steps, taking less than 5s for 2000 by 2000 matrices on a standard laptop. Using this routine as a building block, we demonstrate the usefulness of the studied proximity operator in constrained maximum likelihood estimation of Gaussian mean and covariance, peudolikelihood-based graphical model selection, and a matrix variant of the scaled lasso problem.

Analyzing causality in multivariate systems involves establishing how information is generated, distributed and combined, and thus requires tools that capture interactions beyond pairwise relations. Higher-order information theory provides such tools. In particular, Partial Information Decomposition (PID) allows the decomposition of the information that a set of sources provides about a target into redundant, unique, and synergistic components. Yet the mathematical connection between such higher-order information-theoretic measures and causal structure remains undeveloped. Here we establish the first theoretical correspondence between PID components and causal structure in both Bayesian networks and hypergraphs. We first show that in Bayesian networks unique information precisely characterizes direct causal neighbors, while synergy identifies collider relationships. This establishes a localist causal discovery paradigm in which the structure surrounding each variable can be recovered from its immediate informational footprint, eliminating the need for global search over graph space. Extending these results to higher-order systems, we prove that PID signatures in Bayesian hypergraphs differentiate parents, children, co-heads, and co-tails, revealing a higher-order collider effect unique to multi-tail hyperedges. We also present procedures by which our results can be used to characterize systematically the causal structure of Bayesian networks and hypergraphs. Our results position PID as a rigorous, model-agnostic foundation for inferring both pairwise and higher-order causal structure, and introduce a fundamentally local information-theoretic viewpoint on causal discovery.

Goodness-of-fit (GoF) tests are fundamental for assessing model adequacy. Score-based tests are appealing because they require fitting the model only once under the null. However, extending them to powerful nonparametric alternatives is difficult due to the lack of suitable score functions. Through a class of exponentially tilted models, we show that the resulting score-based GoF tests are equivalent to the tests based on integral probability metrics (IPMs) indexed by a function class. When the class is rich, the test is universally consistent. This simple yet insightful perspective enables reinterpretation of classical distance-based testing procedures-including those based on Kolmogorov-Smirnov distance, Wasserstein-1 distance, and maximum mean discrepancy-as arising from score-based constructions. Building on this insight, we propose a new nonparametric score-based GoF test through a special class of IPM induced by kernelized Stein's function class, called semiparametric kernelized Stein discrepancy (SKSD) test. Compared with other nonparametric score-based tests, the SKSD test is computationally efficient and accommodates general nuisance-parameter estimators, supported by a generic parametric bootstrap procedure. The SKSD test is universally consistent and attains Pitman efficiency. Moreover, SKSD test provides simple GoF tests for models with intractable likelihoods but tractable scores with the help of Stein's identity and we use two popular models, kernel exponential family and conditional Gaussian models, to illustrate the power of our method. Our method achieves power comparable to task-specific normality tests such as Anderson-Darling and Lilliefors, despite being designed for general nonparametric alternatives.

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.

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.

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.