Learning Graphical Models
Environment-Robust Representation Learning with Empirical Bayes
Slavutsky, Yuli, Shen, Matthew, Wu, Bohan, Blei, David M.
We consider multi-environment prediction problems. We assume the environments change the distribution of a latent variable, while the mechanisms generating observed covariates and targets remain stable conditional on that variable. For example, hospitals or clinical cohorts may differ in the prevalence of latent patient states, even though the relationships between those states, physiological measurements, and outcomes remain unchanged. Given a dataset from multiple environments, we formulate a Bayesian model for such problems and derive the corresponding variational objective. We show that this objective decomposes into per-environment terms and an additional cross-environment balancing term induced by the model's structure. We use an empirical Bayes method to set the prior and incorporate it into the objective. Based on this objective, we develop an amortized variational algorithm for posterior approximation, and use the resulting learned latent variables to form predictions in new environments. We study our approach through simulations and real-world studies of astronomical source identification, microbiome-based disease detection, and ICU sepsis prediction. Across these settings, our method outperforms previous approaches for prediction in new environments.
PAC-Bayesian Adversarially Robust Generalization for Message Passing Graph Neural Networks: A Sensitivity Analysis
Liang, Ziling, Yi, Xinping, Wen, Qingsong, Jin, Shi
Whilst the vulnerability of graph neural networks (GNNs) to adversarial attacks poses a critical threat to graph representation learning, the understanding of the robust generalization behavior remains a fundamental challenge in the adversarial setting. Recently, PAC-Bayesian margin-based generalization analysis substantially advances this line of research by providing a flexible and data-dependent analytical framework. However, existing robust analyses often rely on isotropic Gaussian posteriors and control weight perturbations in the full parameter space, which limits the ability to capture heterogeneous parameter sensitivity yet hinges on hidden-width-dependent complexity terms, resulting in not-tight-enough generalization bounds. In this paper, we extend a recently proposed sensitivity-aware PAC-Bayesian framework from deep neural networks to message passing GNNs (MPGNNs) and derive a tighter robust generalization bound in the adversarial setting. Specifically, we first quantify how sensitive the perturbations across different parameter blocks are to the network outputs by deriving the output Jacobians with respect to the weight parameters. Exploiting the fact that these Jacobian matrices have rank at most $K$ in $K$-class graph classification, we then construct Jacobian-aligned sensitivity matrices and use anisotropic Gaussian posteriors with optimized covariances to upper bound the KL divergence in a tight way. Notably, by refining the spectral-norm dependence on the learned weights and reducing the leading dimension factor from hidden-width-dependent terms to the number of classes $K$, our analysis yields much tighter robust generalization guarantees for MPGNNs, thereby guiding their designs to enhance adversarial robustness.
Causal Atlases from Entropic Inference: Bayesian Networks beyond Optimal DAGs
Aliahmadi, Hazhir, Babayan, Irina, van Anders, Greg
Data-driven causal relationship identification is pertinent to advancing understanding of complex systems both within and beyond science. Bayesian networks offer a probabilistic method for modelling generic causal relationships via directed acyclic graphs (DAGs). However, typical techniques for constructing Bayesian networks rely on optimization, which can be ill-suited for learning causal relationships because the underlying data may admit multiple chains of causation. More data-faithful representations of causal relationships would provide frameworks for constructing multiple causal maps that are consistent with the variability that is inherent in underlying data. Here, we show that entropy-based inference generates atlases of plausible causal relationships that are consistent with underlying data. On simulated noisy data of 2- and 20-node linear structural equation models, we sample a maximum-entropy ensemble of graphs that allow us to quantify the inherent structural ambiguity in underlying causal relationships. Our method shows that "optimized" DAGs can contain causal artifacts are not consistent across equivalently accurate topologies.
EML-CD: Causal Mechanism Recovery via EML Symbolic Trees in Structure Learning
Neural network (NN)-based nonlinear causal discovery methods recover DAG structure but leave each causal mechanism as a black box. Waxman et al. argued that extracting causal mechanisms from NN weights is ill-posed. We propose EML-CD, a framework that integrates the EML operator (capable of composing elementary functions from a single binary operator) into causal structure learning, with interpretable mechanism recovery as the primary objective. EML-CD represents each edge mechanism as a gated EML binary tree and automatically discovers closed-form causal equations. Analytical Jacobians can be directly computed from the output equations, enabling quantitative understanding of causal effects. On real data (Sachs protein signaling, d=11), EML-CD achieves SHD=11.2 +/- 0.4 (5-seed mean; baselines are single deterministic runs), on par with PC/GES within seed variance and below CAM, while attaching closed-form equations to each detected edge (precision 0.756, recall 0.365). In a controlled bivariate test with known mechanisms, EML-CD recovers 10 of 11 elementary function families faithfully (held-out shape correlation >= 0.96; only high-frequency sine is partial). On a symbolic synthetic benchmark, EML-CD attains a substantially lower and more stable held-out mechanism f-MSE than a fixed SINDy dictionary (mean 3.67 vs. 7644, the latter inflated by catastrophic extrapolation on one seed), although its structure recovery (SHD 14.0) only matches the dictionary and stays below specialized optimizers; on the Causal Chambers light-tunnel subset, a depth-2 model improves F1 over linear OLS-BIC (0.444 vs. 0.273).
On-line Bayesian System Identification
Romeres, Diego, Prando, Giulia, Pillonetto, Gianluigi, Chiuso, Alessandro
We consider an on-line system identification setting, in which new data become available at given time steps. In order to meet real-time estimation requirements, we propose a tailored Bayesian system identification procedure, in which the hyper-parameters are still updated through Marginal Likelihood maximization, but after only one iteration of a suitable iterative optimization algorithm. Both gradient methods and the EM algorithm are considered for the Marginal Likelihood optimization. We compare this "1-step" procedure with the standard one, in which the optimization method is run until convergence to a local minimum. The experiments we perform confirm the effectiveness of the approach we propose.
Tensor decompositions for learning latent variable models
Anandkumar, Anima, Ge, Rong, Hsu, Daniel, Kakade, Sham M., Telgarsky, Matus
This work considers a computationally and statistically efficient parameter estimation method for a wide class of latent variable models---including Gaussian mixture models, hidden Markov models, and latent Dirichlet allocation---which exploits a certain tensor structure in their low-order observable moments (typically, of second- and third-order). Specifically, parameter estimation is reduced to the problem of extracting a certain (orthogonal) decomposition of a symmetric tensor derived from the moments; this decomposition can be viewed as a natural generalization of the singular value decomposition for matrices. Although tensor decompositions are generally intractable to compute, the decomposition of these specially structured tensors can be efficiently obtained by a variety of approaches, including power iterations and maximization approaches (similar to the case of matrices). A detailed analysis of a robust tensor power method is provided, establishing an analogue of Wedin's perturbation theorem for the singular vectors of matrices. This implies a robust and computationally tractable estimation approach for several popular latent variable models.
Sample Complexity and Decision-Theoretic Guarantees for Bayesian Model Averaging over Decision Trees with Catalan-Exponential Priors
Jakaite, Livija, Schetinin, Vitaly
We ask: when do Bayesian model averaging (BMA) weights over decision trees carry sufficient epistemic information to justify committed exploitation of the averaging distribution? We answer this question in closed form for Bayesian decision trees (BDTs) with Dirichlet-Multinomial leaf models and a Catalan-exponential tree-size prior (Schetinin&Jakaite, 2025), establishing a complete non-asymptotic theory of rational commitment thresholds.
Large-scale Uncertainty Quantification for Latent Variable Models Using Subsampling Markov Chain Monte Carlo
Wang, Xiaoyu, Huggins, Jonathan H.
Stochastic gradient Langevin dynamics combined with Gibbs updates (SGLD--Gibbs) provides a highly scalable approach to approximate Bayesian inference in latent variable models. However, it remains unclear how to tune the algorithm's hyperparameters in a principled manner to ensure the uncertainty estimates are statistically meaningful. In this work, we address this gap in tuning guidance by developing a statistical scaling limit theory for SGLD--Gibbs. We derive a joint asymptotic limit for the global parameters and latent variables under appropriate space-time rescaling. We show that global parameters converge to a diffusion-type limit, while each latent variable converges to a jump process, reflecting the use of intermittent Gibbs updates. This joint jump-diffusion structure reveals how latent-variable randomness contributes to the stationary distribution of the global parameters. We leverage our results to propose explicit guidance on hyperparameter tuning for SGLD--Gibbs that ensures meaningful uncertainty quantification. Numerical experiments show that SGLD--Gibbs with our tuning guidance leads to better parameter estimates, uncertainty quantification, and predictive performance than stochastic variational inference.
MINTS: Minimalist Thompson Sampling
The Bayesian paradigm offers principled tools for sequential decision-making under uncertainty, but its reliance on a probabilistic model for all parameters can hinder the incorporation of complex structural constraints. We introduce a minimalist Bayesian framework that places a prior only on the location of the optimum, while eliminating nuisance parameters through profile likelihood. This yields a generalized posterior that naturally accommodates structural constraints. As a direct instantiation, we develop MINimalist Thompson Sampling (MINTS). For multi-armed bandits with mean constraints, we establish near-optimal non-asymptotic regret guarantees and sharp almost-sure asymptotic regret characterizations. In particular, MINTS attains the classical Lai--Robbins constant in the unstructured setting and automatically adapts to unimodal structure, achieving the sharp constant determined only by the immediate neighbors of the optimal arm.
True Self-Avoiding Walk for Accelerating Markov-Chain Monte Carlo Integration
Qinghua, null, Ding, null, Anantharam, Venkat
We study true self-avoiding walk (TSAW) as a mechanism for improving empirical integral estimation via Markov chain Monte Carlo (MCMC). We consider finite-state adaptive sampling dynamics associated with an irreducible Markov kernel $P$ on a finite set, with stationary distribution $π$, in which the transition probabilities are penalized according to empirical overuse. Our main result is that the empirical occupation counts $L_t(i)$ and transition counts $N_t(i,j)$ of the resulting TSAW-based walk satisfy \[ L_t(i)-tπ_i = O(\sqrt{\log t}) \quad\text{and}\quad N_t(i,j)-tπ_iP_{ij}=O(\sqrt{\log t}) \qquad\text{almost surely} \] for every state $i$ and every edge $(i,j)$ with $P_{ij}>0$. Consequently, for every bounded function $f:V\to\mathbb R$, the error of our integral estimator converges as \[ \left|\frac1t\sum_{s=0}^{t-1} f(X_s)-\sum_{i\in V}π_i f(i)\right| = O\left(\frac{\sqrt{\log t}}{t}\right) \qquad\text{almost surely}. \] These results show that, in contrast with the usual $t^{-1/2}$ error scaling for empirical averages under standard random-walk-based methods, TSAW-based estimator yields empirical integral errors of order $O(\sqrt{\log t}/t)$ almost surely, thereby achieving a substantially sharper dependence on the sample size $t$.