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 Learning Graphical Models


Corrected Integrated Laplace Approximation for Bayesian Inference in Latent Gaussian Models

arXiv.org Machine Learning

Latent Gaussian models (LGMs) are a popular class of Bayesian hierarchical models that include Gaussian processes, as well as certain spatial models and mixed-effect models. Efficient Bayesian inference of LGMs often requires marginalizing out the latent variables. For LGMs with a non-Gaussian likelihood, exact marginalization is not possible and a popular approach is to do approximate marginalization with an integrated Laplace approximation (ILA). Using ILA produces an approximate posterior which, in some settings, can differ significantly from the correct posterior, which impacts downstream applications. We propose an importance sampling scheme to correct the error introduced by ILA. By increasing the number of samples in importance sampling, the posterior with ILA converges to the correct posterior. This idea is realized with various techniques, including pseudo-marginalization, quasi-Monte Carlo and randomized quasi-Monte Carlo. We implement our methods in an automatic differentiation framework to support gradient-based algorithms when doing inference on the hyperparameters. For the latter, we specifically consider the use of Hamiltonian Monte Carlo. We demonstrate the benefits of reduced error in various applied models.


Score-Based Causal Discovery of Latent Variable Causal Models

arXiv.org Machine Learning

Identifying latent variables and the causal structure involving them is essential across various scientific fields. While many existing works fall under the category of constraint-based methods (with e.g. conditional independence or rank deficiency tests), they may face empirical challenges such as testing-order dependency, error propagation, and choosing an appropriate significance level. These issues can potentially be mitigated by properly designed score-based methods, such as Greedy Equivalence Search (GES) (Chickering, 2002) in the specific setting without latent variables. Yet, formulating score-based methods with latent variables is highly challenging. In this work, we develop score-based methods that are capable of identifying causal structures containing causally-related latent variables with identifiability guarantees. Specifically, we show that a properly formulated scoring function can achieve score equivalence and consistency for structure learning of latent variable causal models. We further provide a characterization of the degrees of freedom for the marginal over the observed variables under multiple structural assumptions considered in the literature, and accordingly develop both exact and continuous score-based methods. This offers a unified view of several existing constraint-based methods with different structural assumptions. Experimental results validate the effectiveness of the proposed methods.


Understanding Deterioration Random Effects for Causal Discovery in Infrastructure Management

arXiv.org Machine Learning

Infrastructure deterioration poses significant challenges for asset management, yet existing approaches rely on population-averaged models that overlook equipment-specific heterogeneity. We present a novel framework that combines Bayesian hierarchical hazard modeling with causal discovery to identify operational patterns that drive heterogeneous deterioration rates in pump equipment. Our approach first estimates pump-specific random effects $u_i$ using GPU-accelerated No-U-Turn Sampling (NUTS), achieving 3--5$\times$ speedup over CPU implementations. We then employ DirectLiNGAM to discover causal relationships between 22 engineered time-series features and deterioration rates, stratified by positive ($u_i > 0$, faster deterioration) versus negative ($u_i \leq 0$, slower deterioration) random effects. Analyzing 112 pumps with 92,861 observations over 650 days, we uncover striking heterogeneity: the negative group exhibits causal effects 400$\times$ larger than the positive group, with standard deviation (std) showing a strong positive causal effect ($+1.515$) on deterioration rates in low-risk equipment. We validate linearity assumptions through NonlinearLiNGAM comparison and demonstrate practical scalability through GPU acceleration. Our findings enable targeted maintenance strategies by revealing that different operational regimes require fundamentally distinct management approaches, advancing predictive maintenance from population-averaged to heterogeneity-aware decision making.


Divide et Calibra: Multiclass Local Calibration via Vector Quantization

arXiv.org Machine Learning

Accurate and well-calibrated Machine Learning (ML) models are mandatory in high-stakes settings, yet effective multiclass calibration remains challenging: global approaches assume calibration errors are homogeneous across the latent space, while local methods often rely on latent-space dimensionality reduction, which leads to information loss. To address these issues, we propose a compositional approach to multiclass calibration, where region-specific calibration maps are constructed from shared codeword-dependent factors. We instantiate this idea via Vector Quantization (VQ), which induces a structured partition of the representation space, and an indexed parameterization of Dirichlet concentrations that enables parameter sharing across regions. Our approach learns heterogeneous calibration maps that generalize well even to sparse regions of the latent space. Experiments on benchmark datasets show significant improvements in local calibration while maintaining competitive global calibration and predictive performance.


$L^2$ over Wasserstein: Statistical Analysis for Optimal Transport

arXiv.org Machine Learning

Optimal transport provides an inherently geometric and highly structured framework for studying spaces of probability measures, supplying a rich theoretical toolkit for contemporary statistics, machine learning, and generative modelling. In applications, however, the measures of interest are almost never known precisely, calling for a theory of optimal transport that accounts for statistical uncertainty. We construct such a framework, lifting the classical theory to the setting of random probability measures. We introduce the $L^2$ over Wasserstein space establishing that it inherits the formal Riemannian structure of the Wasserstein space by characterising distances and geodesic geometry. The structure induces random flows with Wasserstein gradient flow sample paths, making it the natural extension of the Wasserstein space which allows for random gradient flow dynamics. We ensemble statistical convergence results of the optimal transport machinery using the empirical measure within the $L^2$ over Wasserstein framework. Moreover, in the setting of Bayesian non-parametrics, we refine Schwartz's consistency theorem to the Wasserstein topology and deduce posterior convergence of the same machinery in the $L^2$ over Wasserstein space. We demonstrate that the growing theory of random token sampling for transformer models using self-attention flow paths can be embedded into the our framework. The results provide a unified treatment of random optimal transport and its consequences for principled inference and generative modelling under the statistical uncertainty of random sampling.


When Individually Calibrated Models Become Collectively Miscalibrated

arXiv.org Machine Learning

A natural assumption is that if each model is individually calibrated, the aggregate prediction will also be well calibrated. We show that this assumption fails in multi-agent settings: individually calibrated predictors can become collectively miscalibrated when their predictions interact strategically--where "strategically" refers to the game-theoretic sense of Brier-optimal local response, not deliberate gaming or collusion, and arises naturally whenever agents are independently trained on overlapping data. This phenomenon affects multiple independent agents in federated healthcare, multi-vendor intrusion detection, and crowdsourced forecasting, where agents optimize their own objectives. Specifically, we prove that under Brier-score-based aggregation with positively correlated beliefs each agent's individually optimal report systematically underestimates the positive-class probability, yielding a Price of Anarchy strictly greater than one whenever Cov(bi,bj) > 0. At our canonical setting (n=5 agents, pairwise correlation ρ=0.5, base rate µ=0.3, threshold τ=0.3) the empirically measured PoA in false-negative rate is 7.25 (mean aggregate bias 0.375). In contrast, VCG-based aggregation, which rewards each agent's marginal contribution to aggregate accuracy, achieves dominant-strategy incentive compatibility and the lowest empirical PoA among all mechanisms studied (PoA 1.0). On three real-world datasets (NSL-KDD, UNSW-NB15, Credit Card Fraud) with featurepartitioned agents, VCG provides the strongest robustness guarantees among the aggregation methods we evaluate, while maintaining comparable accuracy. In data-sparse regimes (n 500), VCG consistently outperforms stacking and majority voting; under adversarial agents, VCG maintains substantially lower false-negative rates than robust aggregation baselines. Adaptive weight updates further reduce false negatives by 20-22% under distribution shift, with O( T) online regret guarantees. These results establish that how probabilistic predictions are aggregated matters as much as how well individual models are calibrated.


Bayesian Latent Space Models for Graphs Are Misspecified: Toward Robust Inference via Generalized Posteriors

arXiv.org Machine Learning

Bayesian latent space models offer a principled approach to network representation, but rely on correct specification of both geometry and link function. Real-world networks often violate these assumptions, exhibiting geometric mismatch and structural anomalies that break standard metric properties. We show that such misspecification pushes the data-generating distribution outside the model class, causing Bayesian inference to become overconfident and poorly calibrated. To address this, we propose a generalized posterior framework for random geometric graphs. We introduce Link-Sequential R-SafeBayes, a method that exploits dyadic conditional independence to estimate prequential risk and adaptively tune posterior regularization. Experiments on synthetic and real-world networks demonstrate improved calibration, better link prediction performance, and a reliable criterion for selecting latent geometries across Euclidean, spherical, and hyperbolic spaces.


Causal Inference with Categorical Unobserved Confounder via Mixture Learning

arXiv.org Machine Learning

Unobserved confounding is a fundamental challenge for estimating causal effects. To address unobserved confounding, recent literature has turned to two different approaches -- proxy variables and the use of multiple treatments. The first approach, commonly referred to as proximal causal inference, requires proxies to be assigned to specific asymmetric roles: treatment-inducing proxies (negative control exposures), variables that act as common causes of the treatment and outcome, and outcome-inducing proxies (negative control outcomes). In practice, however, identifying variables that satisfy these asymmetric roles can be difficult depending on the application domain. The second approach, commonly referred to as the ``Deconfounder," deals with multiple conditionally independent treatments. There has been limited progress towards developing a consistent estimation method for this setting. As the primary contribution of this work, we establish that causal effects are identifiable in both settings when the unobserved confounder is categorical under suitable conditions. Our approach builds on a mixture learning perspective: we show that the underlying confounding structure can be recovered by identifying the corresponding mixture distribution. We propose an estimation procedure based on tensor decomposition, which allows consistent recovery of the latent structure and comes with non-asymptotic guarantees. Simulation studies and real data experiments demonstrate that the proposed method performs well even with limited data.


A Unified Framework for Structure-Aware Clustering and Heterogeneous Causal Graph Learning

arXiv.org Machine Learning

In complex multivariate systems, interactions among variables are defined by dependency structures, often encoded as directed acyclic graphs ($\text{DAGs}$). However, dependency structures can vary across subjects, and ignoring this structural heterogeneity introduces bias and obscures subpopulation-specific dependencies. To address this, we propose Directed Acyclic Graph-based Dependency Clustering via Alternating Direction Method of Multipliers (DAG-DC-ADMM), a unified framework built upon Structural Equation Modeling (SEM) that jointly learns cluster assignments and cluster-specific dependency structures. We encode acyclicity via a smooth constraint and integrate a groupwise truncated Lasso fusion penalty (gTLP) to cluster subjects based on their structural similarity. This yields a nonconvex optimization problem that incorporates sparsity, acyclicity, and structural consensus constraints. We address the nonconvexity by using the augmented Lagrangian method and solve it with an adapted version of the Alternating Direction Method of Multipliers (ADMM) for difference-of-convex programs. For certain graph structures, such as upper triangular adjacency matrices, our algorithm is guaranteed to converge to a Karush-Kuhn-Tucker (KKT) point. Experiments demonstrate that our method recovers cluster-specific causal dependency structures with a high true positive rate and a low false discovery rate. This capability enables the robust discovery of heterogeneous dependencies across subjects where the subpopulation label is unknown.


Posterior Contraction of Lévy Adaptive B-spline Regression in Besov Spaces

arXiv.org Machine Learning

We investigate the asymptotic properties of the Lévy Adaptive B-spline (LABS) regression model, a Bayesian nonparametric method that incorporates B-spline kernels into the Lévy Adaptive Regression Kernel (LARK) model. LABS applies splines of varying degrees with independently defined knots, yielding a flexible model class capable of adapting to irregular and locally structured features of the true function. Within the nonparametric regression framework with univariate random design and Gaussian errors, we establish that the LABS posterior contracts around the true function in Besov classes at nearly minimax-optimal rates, up to a logarithmic factor, while adapting automatically to unknown smoothness. This study contributes to filling a gap in the literature, where theoretical results on posterior contraction of the LARK model in Besov spaces remain scarce. Simulation experiments on standard test functions in Besov spaces, including Blocks, Bumps, HeaviSine, and Doppler, complement the theoretical results and demonstrate the practical utility of LABS.