Probabilistic Graphical Models

Information lattice learning (ILL) learns interpretable rules of a signal by alternately projecting the signal onto a partition lattice that encodes a hierarchy of abstractions and lifting selected rules back to the signal domain. When the signal is a probability mass function, we show the probabilistic rules learned by ILL admit a natural probabilistic graphical model (PGM) interpretation and develop this interpretation in detail. A partition in ILL induces a deterministic quotient variable, and a rule is the marginal law of that quotient variable. A rule set is therefore a collection of marginal constraints over interpretable abstractions. General lifting is the feasible family of all joint distributions satisfying those constraints, while special lifting chooses a maximum-ignorance reconstruction, implemented in ILL by an L2 uniformity principle closely related to maximum entropy. Under a Shannon-entropy lifting, the same constraints yield a log-linear factor graph whose factors are indexed by learned abstractions. The information lattice itself, however, is not a Bayesian network: its edges encode refinement and coarsening of abstractions, not conditional dependence. Thus ILL is best viewed as structure learning for interpretable constraint-based factor graphs over quotient variables. This view clarifies how ILL relates to graphical models and maximum entropy models, while suggesting new directions for inference, identifiability, and hybrid symbolic-probabilistic learning.

Probabilistic inference over spatially embedded variables requires beliefs that respect $SE(3)$ symmetry, yet existing equivariant networks produce only scalars and vectors -- not the rank-2 precision tensors needed for anisotropic uncertainty, and single-component messages collapse multi-modal energy landscapes to physically meaningless averages. We introduce Equivariant Neural Belief Propagation (ENBP), a factor-graph framework whose messages are equivariant Gaussian mixture models with sufficient statistics that transform exactly under $SE(3)$. Rank-2 precision matrices are synthesised via equivariant outer products, ingested through differentiable spectral decomposition, and kept tractable by a greedy KL-based mixture reduction that provably commutes with $SE(3)$. On GEOM-QM9 and GEOM-Drugs, ENBP achieves 98.9% conformational coverage at 0.090 $\mathring{A}$ error with sub-second latency -- over $100\times$ faster than diffusion baselines at higher accuracy. On multi-body robotic inference, vanilla loopy BP diverges at 15+ agents while ENBP converges with near-zero collision rates and machine-precision equivariance error (${\sim}10^{-7}$ vs.\ $10^{-1}$ for augmented baselines).

Marginal inference in discrete graphical models forces a choice between exactness and scalability: exact algorithms are intractable for high-treewidth graphs, while iterative approximations (Belief Propagation, variational methods) sacrifice convergence guarantees on frustrated topologies. We argue that this dichotomy stems from a mismatched inductive bias: iterative methods abandon the sequential elimination structure that makes exact inference correct. We introduce In-Context Graphical Inference (ICG-I), an autoregressive Graph Transformer that restores this structure by mimicking Variable Elimination with learned, Tensor- Train-compressed intermediate factors, paired with a Dirichlet output layer and Weighted Conformal Prediction for calibrated, distribution-free coverage guarantees under topological shift. We prove that TT compression errors propagate at most lincarly through the autoregressive chain, that the Dirichlet-Multinomial loss is a proper scoring rule, and that WCP maintains coverage with a quantifiable degradation under estimated density ratios. We conducted intensive experiments to evaluate ICG-I and achieved state-of-the-art performance across all benchmarks. ICG-I reduces MAE from 0.041 (best baseline) to 0.020 on standard instances and achieves 0.048 on N=500 frustrated spin glasses where BP diverges entirely.

Rubric-based rewards are increasingly used for open-ended language model post-training, but criterion-level scores are often aggregated as independent utilities. This flat scalarization ignores rubric-specified prerequisite and activation relations among criteria, allowing reward or penalty to be counted even when the condition that licenses it is absent. We call this structural reward-aggregation failure False Credit Propagation (FCP). To address this limitation, we propose \ourname (Graphical Event Aggregation for Rubric rewards), a probabilistic graphical framework for dependency-aware rubric aggregation. \ourname models each criterion outcome as a latent Bernoulli event in a typed rubric graph, propagates soft suppression from unsupported parent events to their children, and aggregates the resulting event probabilities into a normalized expected signed utility. This yields a linear-time reward computation that can be plugged into standard rubric-based RL pipelines without changing the outer optimization algorithm. Experiments on HealthBench, WritingBench, and PLawBench with two policy backbones show that \ourname consistently improves over flat aggregation and deterministic gating, achieving relative gains of up to 15.5% over flat aggregation. FCP diagnostics further show that \ourname reduces leakage by 96.5% relative to flat aggregation while preserving more licensed downstream utility than deterministic gating. Our code is publicly available at https://github.com/LvCan926/GEAR.

Stacking probabilistic building blocks into deeper architectures typically breaks closed-form inference. We show that closed-form inference can be preserved. We identify five factor-graph primitives: a bilinear factor, an exponential link, a Gamma prior, a Gaussian likelihood, and an equality node, and prove that any model composed from them admits closed-form variational message passing. The construction works because each primitive preserves a small set of message families: under mean-field factorization, messages on Gaussian variables remain Gaussian and messages on precision variables remain Gamma, while the only non-conjugate interface, the exponential link, remains tractable through the Gaussian moment-generating function and the sufficient statistics of the Gamma family. We demonstrate composition at increasing depth, from static ensembles through input-dependent gating to split-branch routing, and show that stacking routing layers encodes arbitrary decision trees, establishing universal function approximation with closed-form inference. Applied to ensemble time-series forecasting, the framework yields a Bayesian mixture of experts in which gating functions are inferred rather than learned, providing calibrated uncertainty over expert selection across five benchmark datasets.

We consider the problem of testing properties of graphs underlying high-dimensional graphical models. We adopt the model of covariance queries introduced by Lugosi, Truszkowski, Velona, and Zwiernik (2021). We study the case when the underlying graph is a tree. The main results of the paper show that, while reconstructing the entire tree may be costly, certain global structural properties can be tested efficiently. In particular, we design randomized tests for global structural properties that use a sub-quadratic number of queries. We develop testing procedures for several fundamental properties, including the number of leaves, the maximum degree, the typical distance, and the diameter of the tree. For each property, we obtain explicit query complexity bounds that depend on the target threshold and tolerance parameters.

A central challenge in large-scale decision-making under incomplete information is estimating reliable probabilities. Recent approaches use Large Language Models (LLMs) to generate explanatory factors and coarse-grained probability estimates, which are then refined by a Naïve Bayes model over factor combinations. However, sparse factor spaces often yield unknown'' predictions, while expanding factors increases noise and spurious correlations, weakening conditional independence and degrading reliability. To address these limitations, we propose Anchor, an aggregated Bayesian inference framework over a hierarchical factor space. It constructs dense factor hierarchies through iterative generation and clustering, maps contexts via hierarchical retrieval and refinement, and augments Naïve Bayes with a Causal Bayesian Network to model latent factor dependencies. Experiments show that Anchor markedly reduces unknown'' predictions and produces more reliable probability estimates than direct LLM baselines, achieving state-of-the-art performance while significantly reducing time and token overhead.

Polytrees are a subclass of Bayesian networks that seek to capture the conditional dependencies between a set of $n$ variables as a directed forest and are motivated by their more efficient inference and improved interpretability. Since the problem of learning the best polytree is NP-hard, we study which restrictions make it more tractable by considering for example in-degree bounds, properties of score functions measuring the quality of a polytree, and approximation algorithms. We devise an algorithm that finds the optimal polytree in time $O((2+ε)^n)$ for arbitrarily small $ε> 0$ and any constant in-degree bound $k$, improving over the fastest previously known algorithm of time complexity $O(3^n)$. We further give polynomial-time algorithms for finding a polytree whose score is within a factor of $k$ from the optimal one for arbitrary scores and a factor of $2$ for additive ones. Many of the results are complemented by (nearly) tight lower bounds for either the time complexity or the approximation factors.

The health condition of components in civil infrastructures can be described by various discrete states according to their performance degradation. Inferring these states from measurable responses is typically an ill-posed inverse problem. Although Bayesian methods are well-suited to tackle such problems, computing the posterior probability density function (PDF) presents challenges. The likelihood function cannot be analytically formulated due to the unclear relationship between discrete states and structural responses, and the high-dimensional state parameters resulting from numerous components severely complicates the computation of the marginal likelihood function. To address these challenges, this study proposes a novel Bayesian inversion paradigm for discrete variables based on Probabilistic Graphical Models (PGMs). The Markov networks are employed as modeling tools, with model parameters learned from data and structural topology prior. It has been proved that inferring this PGM produces the same probabilistic estimation as the posterior PDF derived from Bayesian inference, which effectively solves the above challenges. The inference is accomplished by Graph Neural Networks (GNNs), and a graph property-based GNN training strategy is developed to enable accurate inference across varying graph scales, thereby significantly reducing the computational overhead in high-dimensional problems. Both synthetic and experimental data are used to validate the proposed framework

We present a generic algorithm for learning and approximate inference with an intuitive epistemic interpretation: iteratively focus on a subset of the model and resolve inconsistencies using the parameters under control. This framework, which we call Local Inconsistency Resolution (LIR) is built upon Probabilistic Dependency Graphs (PDGs), which provide a flexible representational foundation capable of capturing inconsistent beliefs. We show how LIR unifies and generalizes a wide variety of important algorithms in the literature, including the Expectation-Maximization (EM) algorithm, belief propagation, adversarial training, GANs, and GFlowNets. In the last case, LIR actually suggests a more natural loss, which we demonstrate improves GFlowNet convergence. Each method can be recovered as a specific instance of LIR by choosing a procedure to direct focus (attention and control). We implement this algorithm for discrete PDGs and study its properties on synthetically generated PDGs, comparing its behavior to the global optimization semantics of the full PDG.

In this paper, the relationship between probabilistic graphical models, in particular Bayesian networks, and causal diagrams, also called structural causal models, is studied. Structural causal models are deterministic models, based on structural equations or functions, that can be provided with uncertainty by adding independent, unobserved random variables to the models, equipped with probability distributions. One question that arises is whether a Bayesian network that has obtained from expert knowledge or learnt from data can be mapped to a probabilistic structural causal model, and whether or not this has consequences for the network structure and probability distribution. We show that linear algebra and linear programming offer key methods for the transformation, and examine properties for the existence and uniqueness of solutions based on dimensions of the probabilistic structural model. Finally, we examine in what way the semantics of the models is affected by this transformation. Keywords: Causality, probabilistic structural causal models, Bayesian networks, linear algebra, experimental software.

To generate synthetic datasets, e.g., in domains such as healthcare, the literature proposes approaches of two main types: Probabilistic Graphical Models (PGMs) and Deep Learning models, such as LLMs. While PGMs produce synthetic data that can be used for advanced analytics, they do not support complex schemas and datasets. LLMs on the other hand, support complex schemas but produce skewed dataset distributions, which are less useful for advanced analytics. In this paper, we therefore present Amalgam, a hybrid LLM-PGM data synthesis algorithm supporting both advanced analytics, realism, and tangible privacy properties. We show that Amalgam synthesizes data with an average 91 % $χ^2 P$ value and scores 3.8/5 for realism using our proposed metric, where state-of-the-art is 3.3 and real data is 4.7.

Conditional independence is central to modern statistics, but beyond special parametric families it rarely admits an exact covariance characterization. We introduce the binary expansion group intersection network (BEGIN), a distribution-free graphical representation for multivariate binary data and bit-encoded multinomial variables. For arbitrary binary random vectors and bit representations of multinomial variables, we prove that conditional independence is equivalent to a sparse linear representation of conditional expectations, to a block factorization of the corresponding interaction covariance matrix, and to block diagonality of an associated generalized Schur complement. The resulting graph is indexed by the intersection of multiplicative groups of binary interactions, yielding an analogue of Gaussian graphical modeling beyond the Gaussian setting. This viewpoint treats data bits as atoms and local BEGIN molecules as building blocks for large Markov random fields. We also show how dyadic bit representations allow BEGIN to approximate conditional independence for general random vectors under mild regularity conditions. A key technical device is the Hadamard prism, a linear map that links interaction covariances to group structure.

Theory of Mind (ToM) reasoning with Large Language Models (LLMs) requires inferring how people's implicit, evolving beliefs shape what they seek and how they act under uncertainty -- especially in high-stakes settings such as disaster response, emergency medicine, and human-in-the-loop autonomy. Prior approaches either prompt LLMs directly or use latent-state models that treat beliefs as static and independent, often producing incoherent mental models over time and weak reasoning in dynamic contexts. We introduce a structured cognitive trajectory model for LLM-based ToM that represents mental state as a dynamic belief graph, jointly inferring latent beliefs, learning their time-varying dependencies, and linking belief evolution to information seeking and decisions. Our model contributes (i) a novel projection from textualized probabilistic statements to consistent probabilistic graphical model updates, (ii) an energy-based factor graph representation of belief interdependencies, and (iii) an ELBO-based objective that captures belief accumulation and delayed decisions. Across multiple real-world disaster evacuation datasets, our model significantly improves action prediction and recovers interpretable belief trajectories consistent with human reasoning, providing a principled module for augmenting LLMs with ToM in high-uncertainty environment. https://anonymous.4open.science/r/ICML_submission-6373/

We study constraint-based structure learning of Markov networks and Bayesian networks in the presence of an unreliable conditional independence oracle that makes at most a bounded number of errors. For Markov networks, we observe that a low maximum number of vertex-wise disjoint paths implies that the structure is uniquely identifiable even if the number of errors is (moderately) exponential in the number of vertices. For Bayesian networks, however, we prove that one cannot tolerate any errors to always identify the structure even when many commonly used graph parameters like treewidth are bounded. Finally, we give algorithms for structure learning when the structure is uniquely identifiable.

Machine Learning often involves various imprecise labels, leading to diverse weakly supervised settings. While recent methods aim for universal handling, they usually suffer from complex manual pre-work, ignore the relationships between associated labels, or are unable to batch process due to computational design flaws, resulting in long running times. To address these limitations, we propose a novel general framework that efficiently infers latent true label distributions across various weak supervisions. Our key idea is to express the label brute-force search process as a probabilistic transition of label variables, compressing diverse weakly supervised DFS tree structures into a shared Bayesian network. From this, we derived a latent probability calculation algorithm based on generalized belief propagation and proposed two joint acceleration strategies: 1) introducing a low-rank assumption to approximate the transition matrix, reducing time complexity; 2) designing an end-to-end state evolution module to learn batch-scale transition matrices, facilitating multi-category batch processing. In addition, the equivalence of our method with the EM algorithm in most scenarios is further demonstrated. Extensive experiments show that our method achieves SOTA results under most weakly supervised settings, and achieves up to hundreds of times faster acceleration in running time compared to other general methods.

This paper addresses graph learning in Gaussian Graphical Models (GGMs). In this context, data matrices often come with auxiliary metadata (e.g., textual descriptions associated with each node) that is usually ignored in traditional graph estimation processes. To fill this gap, we propose a graph learning approach based on Laplacian-constrained GGMs that jointly leverages the node signals and such metadata. The resulting formulation yields an optimization problem, for which we develop an efficient majorization-minimization (MM) algorithm with closed-form updates at each iteration. Experimental results on a real-world financial dataset demonstrate that the proposed method significantly improves graph clustering performance compared to state-of-the-art approaches that use either signals or metadata alone, thus illustrating the interest of fusing both sources of information.

Depth completion aims to predict a dense depth map from a color image with sparse depth measurements. Although deep learning methods have achieved state-of-the-art (SOTA), effectively handling the sparse and irregular nature of input depth data in deep networks remains a significant challenge, often limiting performance, especially under high sparsity. To overcome this limitation, we introduce the Gaussian Belief Propagation Network (GBPN), a novel hybrid framework synergistically integrating deep learning with probabilistic graphical models for end-to-end depth completion. Specifically, a scene-specific Markov Random Field (MRF) is dynamically constructed by the Graphical Model Construction Network (GMCN), and then inferred via Gaussian Belief Propagation (GBP) to yield the dense depth distribution. Crucially, the GMCN learns to construct not only the data-dependent potentials of MRF but also its structure by predicting adaptive non-local edges, enabling the capture of complex, long-range spatial dependencies. Furthermore, we enhance GBP with a serial & parallel message passing scheme, designed for effective information propagation, particularly from sparse measurements. Extensive experiments demonstrate that GBPN achieves SOTA performance on the NYUv2 and KITTI benchmarks. Evaluations across varying sparsity levels, sparsity patterns, and datasets highlight GBPN's superior performance, notable robustness, and generalizable capability.

Supervised fine-tuning performance for large language models depends strongly on how training budget is distributed across a heterogeneous set of tasks. In practice, mixtures are often fixed using simple heuristics (e.g., uniform or size-proportional sampling) that ignore task interactions, which can hurt transfer and waste budget on redundant sources. We introduce TaskPGM, a framework for learning continuous task mixtures via an energy-based model over tasks. Tasks form the nodes of a Markov random field: unary potentials capture per-task utility, and pairwise potentials encode inter-task relationships using behavioral divergences computed from predictive distributions of single-task fine-tuned models (e.g., Jensen--Shannon divergence and pointwise mutual information). Optimizing this objective yields mixtures that balance coverage against redundancy. We show that the resulting set function is weakly submodular under budget constraints, enabling approximation guarantees for discrete selection variants. Across multiple model families (LLaMA-7B, Qwen2-7B) and evaluation suites (BIG-Bench Hard), TaskPGM improves over standard mixing strategies and provides interpretable structure over task interactions.

In this work, we evaluate the potential of Large Language Models (LLMs) in building Bayesian Networks (BNs) by approximating domain expert priors. LLMs have demonstrated potential as factual knowledge bases; however, their capability to generate probabilistic knowledge about real-world events remains understudied. We explore utilizing the probabilistic knowledge inherent in LLMs to derive probability estimates for statements regarding events and their relationships within a BN. Using LLMs in this context allows for the parameterization of BNs, enabling probabilistic modeling within specific domains. Our experiments on eighty publicly available Bayesian Networks, from healthcare to finance, demonstrate that querying LLMs about the conditional probabilities of events provides meaningful results when compared to baselines, including random and uniform distributions, as well as approaches based on next-token generation probabilities. We explore how these LLM-derived distributions can serve as expert priors to refine distributions extracted from data, especially when data is scarce. Overall, this work introduces a promising strategy for automatically constructing Bayesian Networks by combining probabilistic knowledge extracted from LLMs with real-world data. Additionally, we establish the first comprehensive baseline for assessing LLM performance in extracting probabilistic knowledge.

We present a new algorithm for amortized inference in sparse probabilistic graphical models (PGMs), which we call $Δ$-amortized inference ($Δ$-AI). Our approach is based on the observation that when the sampling of variables in a PGM is seen as a sequence of actions taken by an agent, sparsity of the PGM enables local credit assignment in the agent's policy learning objective. This yields a local constraint that can be turned into a local loss in the style of generative flow networks (GFlowNets) that enables off-policy training but avoids the need to instantiate all the random variables for each parameter update, thus speeding up training considerably. The $Δ$-AI objective matches the conditional distribution of a variable given its Markov blanket in a tractable learned sampler, which has the structure of a Bayesian network, with the same conditional distribution under the target PGM. As such, the trained sampler recovers marginals and conditional distributions of interest and enables inference of partial subsets of variables. We illustrate $Δ$-AI's effectiveness for sampling from synthetic PGMs and training latent variable models with sparse factor structure.

This paper develops on algebraic grounds a polynomial time exact linear solution to the hard combinatorial problem of marginal inference in Markov random field (MRF) models under general assumptions. To prove our claim, we first implicitly remodel a MRF joint distribution as the unique solution of some linear identity assuming its clique potential functions (equivalently, its individual conditional distributions) to be specified. Then, by assuming an arbitrary point subset, we relax accordingly such a (global) linear identity for deriving a second linear identity, solely, acting on a polynomial time number of entries (e.g.; local marginals or Fourier frequencies) of a solution. Then, we show, only using linear algebraic techniques, that such an identity enables to capture all the entries necessary for the exact reconstruction of an MRF marginal distribution, thus, allowing to solve for the latter, exactly and in polynomial time, using a standard linear solver. Last, but not least, this paper probably solves, once and for all, the P = NP conjecture.