Bayesian Networks

The Generalized Naive Bayes (GNB) model was introduced for discrete and categorical random variables as an extension of classic Naive Bayes. We now accommodate the GNB framework to continuous explanatory variables. A central result of the paper is that structure learning of the GNB depends only on the pair copulas of the bi-variate marginals. We proved that the GNB structure can be assigned to the basis of a matroid, therefore we give greedy algorithms for finding the optimal GNB structure on the training data, in sense of minimizing Kullback-Leibler divergence. Three cases are considered: joint Gaussian distribution, then a more flexible model where we suppose the dependence structure to be described by a Gaussian copula with arbitrary marginals, and an even more flexible case where the joint continuous probability distribution is arbitrary, i.e. copula and marginal distributions are arbitrary. A method for model reduction, based on the newly introduced concept of GNB forest is given. We close the paper by comparing the newly introduced GNB classification results to other classical "glass-box" algorithms on real datasets.

Large language models are increasingly used as natural-language interfaces to structured data, yet they remain unreliable when answers require consistent evidence conditioning, dependency-aware reasoning, and uncertainty estimation. Bayesian networks provide an explicit probabilistic reasoning layer, but learning useful structures from data remains costly and fragile at scale. We introduce ABSOL, a hybrid LLM-guided Bayesian network structure-learning framework that uses LLMs as bounded semantic guides. Across five discrete BN benchmarks spanning 27 to 1041 nodes, ABSOL is the only evaluated method to produce a viable graph on every benchmark, and achieves the highest Edge F_1 on every benchmark larger than 27 nodes with GPT-5.4. The four LLM augmentations, which contribute complementary semantic evidence to the statistical backbone, improve Edge F_1 over the non-LLM aggregation backbone by +0.23 on average. Complementary post-hoc refinement experiments suggest that these gains depend in part on limiting the LLM's authority over the final structure. Together, these results show that language-derived semantic knowledge can substantially improve scalable probabilistic structure learning when used as bounded guidance within a statistically grounded reasoning pipeline. The code for ABSOL is available at github.com/megagonlabs/absol-bn.

This paper introduces an evolutionary computation approach for consensus in structural Bayesian Network (BN) fusion under the constraint of limited treewidth. The consensus BN aims to reconcile multiple input BNs into a single one that retains key structural features present in the original networks. Treewidth, a graph-based parameter associated with computationally tractable inference, is utilized to restrict the complexity of the resulting network. A genetic algorithm is proposed to look for a BN that codifies as much information about the unrestricted fusion as possible while ensuring the treewidth restriction. Experimental evaluation demonstrates the genetic algorithm's ability to obtain consensus BNs with limited treewidth, providing a valuable tool for aggregating information from diverse sources while returning a computationally actionable model.

Travel survey data are essential for transportation planning and travel behavior analysis, yet collecting large-scale representative samples is costly and time-consuming. A practical alternative is to generate synthetic survey records from a few-shot sample. However, such samples provide incomplete coverage of heterogeneous traveler groups and insufficient evidence for recovering the complex dependencies between demographic characteristics and travel behavior. Existing approaches have complementary limitations. Probabilistic generative models such as Bayesian networks (BNs) offer explicit distributional control, but structures learned from few-shot samples may omit meaningful dependencies or retain spurious ones. Large language models (LLMs) can help address these difficulties in BN structure learning by providing behavioral knowledge that complements the limited statistical evidence. We therefore propose LEBGen, an LLM-enhanced BN framework that uses this knowledge to refine network structure for few-shot travel survey data generation. Specifically, the LLM first identifies traveler personas from demographic attribute and travel behavior statistics, then recovers dependencies missed by the persona-augmented BN structure and prune spurious ones. The refined BN is parameterized exclusively from the observed data to generate synthetic records. Under a 2% few-shot setting on the 2022 Hong Kong Travel Characteristics Survey, LEBGen reduces the mean marginal Jensen-Shannon divergence from 0.0671 to 0.0091 and the mean absolute Cramer's V error by 14.3% over the best-performing baseline, substantially improving both distributional and dependency fidelity.

We present tensor network representations for discrete maximum entropy distributions under expectation constraints. To this end, we introduce Computation-Activation Networks (CompActNets), a tensor network architecture that subsumes exponential families. By leveraging the geometry of the convex polytope of realizable expectation vectors, we represent any maximum entropy distribution in the same architecture. We exploit the fact that proper faces of this polytope correspond to the boundary closure of exponential families, which restricts the distribution's support. We then derive explicit representations for the support within the CompActNet architecture. The proposed framework suggests tensor network ranks as complexity measures for faces. Finally, a case study on Boolean statistics links the geometry of 0/1-polytopes directly to propositional formulas.

Bayesian Network (BN) fusion combines multiple input networks into a single structure, balancing dependency preservation with computational tractability. While unrestricted fusion retains all dependencies, it often results in overly complex networks with high treewidth, which affects inference scalability. Limited fusion mitigates this by pruning edges to control treewidth but risks overfitting to input-specific noise and omitting dependencies from the original BNs. This paper introduces a consensus framework that prioritizes shared structures among input networks while enforcing treewidth constraints, ensuring a good consensus. We propose genetic algorithms with advanced initialization, specialized operators, and a tailored fitness function. Additionally, we adapt existing methods to this problem and implement greedy baselines for benchmarking and further optimization. Experiments on synthetic and real-world BNs show the superiority of the proposed genetic algorithms over the adapted methods and greedy baselines.

Probabilistic logic programming is a formalism of statistical relational artificial intelligence that supports causal queries, including interventions from outside the system. When the structure of a probabilistic logic program is learned from data, however, only probabilistic information is used, and a single probability distribution may be compatible with several causal orders. This leads to ambiguity in interventional reasoning, raising the question of when the causal order is uniquely determined by the distribution. Exploiting the relationship between acyclic probabilistic logic programs and Bayesian networks, we derive conditions under which the probabilistic information encoded in a program determines a unique causal order. We also incorporate constraints arising from relational structure by taking into account prescribed sets of causal symmetries induced by the underlying relational vocabulary. The result is a method for verifying when a learned probabilistic logic program supports well-defined intervention semantics.

Bayesian causal discovery seeks to determine the posterior distribution of causal theories, which are interpreted as directed acyclic graphs (DAGs) that explain the observed data. The resulting posterior allows systematic reasoning regarding epistemic uncertainty within these theories. Nonetheless, finding such graphs is difficult due to identifiability problems and limited observational data. Furthermore, precisely approximating posterior over graphs is challenging given vast range of potential DAGs. Recent Bayesian approaches have addressed some of these challenges, yet they remain limited as they fail to encode dependencies between edges, and lack principled ways to incorporate domain knowledge as inductive biases during the search process. To overcome these limitations, we propose SVI-DAG, a structured variational inference approach to Bayesian causal discovery using observational data and prior beliefs that uses normalizing flows to model dependencies between edges, supporting expressive and multimodal posterior learning over DAGs. To mitigate mode seeking behaviour in evidence lower bound optimization and promote mode coverage, we use stein variational gradient descent to update the node potentials using a kernel in acyclicity space. We evaluate SVI-DAG against 5 state-of-the-art Bayesian DAG learning methods and demonstrate superior performance in uncertainty quantification while remaining competitive in terms of structural accuracy.

Survival analysis is an established framework for analyzing time-to-event data, yet many clinical machine learning studies still binarize the outcome before model training. This practice excludes censored patients, collapses temporal information into a single threshold, and can affect which features are selected as prognostically relevant. We examine the cost of this binarization in the context of Bayesian network (BN) feature selection, using two recent publications as case studies: one that applies BN-based feature selection to a head-and-neck cancer cohort and a second surgical cohort study that, while not BN-based, likewise binarizes its survival endpoint. We replace the binary scoring function with the Cox partial log-likelihood for feature-to-outcome edges, a modification we call the Survival-Aware Bayesian network, and recover prognostic features that binarization misses. Our ablation experiment confirms that the improvement is driven by the time-to-event scoring formulation rather than by retaining more patients. The results generalize across five endpoint-cohort combinations in head-and-neck cancer and extend to three further cancer types (breast, colorectal, and kidney). We propose that clinical studies with survival outcomes should use time-to-event methods by default, as binarization discards the prognostic signal retained by survival analysis.

Tabular data generation supports analysis and decision-making when target-domain data are scarce, yet collecting complete target samples is often costly. A practical but underexplored setting provides only a few target records together with richer source data from a related domain. Existing few-shot tabular generators often either fit sparse target statistics directly, which can overfit incidental patterns, or reuse source-domain generators, which may preserve dependencies that no longer hold in the target domain. To address this problem, we propose LAB-Tab, an LLM-augmented Bayesian network (BN) adaptation framework for source-aware few-shot tabular generation. LAB-Tab first fits a BN from source data and then uses an LLM to propose plausible target-domain BN edges that are absent from the source BN graph. This step converts semantic and weak statistical evidence into explicit structural hypotheses, thereby expanding the editable edge space beyond the source-fitted graph. Because the proposed edges may be noisy and interact with existing dependencies, a PPO policy calibrates edges in the augmented BN through edge-level actions, including keep, weaken, strengthen, flip, and deactivate. The PPO policy is trained with a reward that combines distributional alignment, downstream utility, and preservation of target-relevant dependencies. The adapted BN is then sampled to synthesize target-domain tables. Across six source--target distribution-shift scenarios built from three US Census (ACS) prediction tasks, LAB-Tab achieves the best performance at the 10% target-data budget, leads four of the six individual scenarios, and reduces the macro Overall score by 33.8% relative to the strongest baseline. It also obtains the best macro JSD, WAPE, and UtilityGap while maintaining competitive feature--label preservation.

Identifying reliable Alzheimer's disease (AD) markers typically requires manual, labor-intensive transcription and expert analysis, limiting its scale. We introduce an automated pipeline that extracts qualitative knowledge about potential AD progression indicators directly from audio recordings of verbal fluency tests. Our method uses pretrained foundation models to process raw audio and extract clinically relevant variables to construct a Bayesian Network (BN); this BN is used to reason about the AD progression markers and infer their qualitative relationships. Our system successfully recovers known clinical knowledge and identifies novel relationships between linguistic markers.

Minimax-optimal rates for multivariate distribution estimation are known to suffer from the curse of dimensionality. We propose a sparse Bayesian network approach in which each conditional probability is estimated using sparsity-aware conditional mean methods. The resulting estimator, \textit{BAyesian Network Distribution regression} (BAND), handles mixed data types in high-dimensional time series and achieves polynomial total variation convergence rates while allowing the feature dimension to grow polynomially with the sample size. These rates are substantially faster than the classical optimal rates for multivariate histogram density estimators that lack sparsity. Empirical evaluations show that BAND performs competitively for data sampling and confidence region forecasting against a range of state-of-the-art benchmarks.

The problem of learning the graphical Markov blanket (MB) of a variable from data has applications in many areas such as structure learning for Bayesian networks and Markov random fields, causal discovery, and feature selection. However, a common assumption most methods make is that the conditional independencies in the distribution imply the same separation in the graphical structure -- also known as the faithfulness assumption. Unfortunately, this assumption can be violated by higher-order dependencies such as XOR and parity-type relations, and -- on finite samples -- by empirical violations that, in extreme cases, even induce spurious dependencies absent from the true distribution. Therefore, in this paper we propose a "k-order" relaxation of the faithfulness assumption that captures parity type relationships between k+2 variables. We then propose a proof of concept algorithm called k-order Markov blanket (kOMB) that uses this relaxation for MB discovery. Finally, we empirically show how kOMB can recover the MB of a variable under both true and empirical violations of faithfulness. Code available at: https://github.com/lklee9/k-order-Markov-blanket

This paper investigates how multi-agent systems (MAS)-based on large language models (LLMs) can support actuarial risk modelling, with a particular focus on uncertainty quantification. Actuarial workflows represent a high-stakes decision-support setting where unreliable outputs may lead to incorrect risk assessment, unfair pricing, and regulatory non-compliance. To address uncertainty introduced by the probabilistic nature of LLMs and dependencies between agents, a multi-agent framework is proposed in which specialised agents perform data preparation, modelling, review, and explanation tasks under a central hub. The main contribution is a novel approach to uncertainty propagation using token-level log-probabilities and a Bayesian Network. Importantly, log probabilities are not treated as direct probabilities of correctness or task success. Instead, length-normalised log-probability summaries are transformed into calibrated task-level confidence estimates before incorporation into the Bayesian Network. Results show that the framework reproduces baseline actuarial performance while providing additional insight into workflow stability and runtime uncertainty propagation.

Pearl famously argues that causal knowledge enables the prediction of intervention effects. By contrast, purely descriptive knowledge supports only conclusions drawn from observations. His theory of causality, however, is developed exclusively within Bayesian networks and causal models. Consequently, it is largely restricted to acyclic causal relationships, and transferring its ideas to other formalisms risks misinterpretation or inconsistency. This paper brings Pearl's approach to causality into probabilistic logic programming (PLP). To this end, such programs are aligned with philosophical foundations established in prior work that do not rely on temporal notions; that is, all relevant events are assumed to occur simultaneously. A formal causal semantics for these programs, together with a notion of intervention and an implementation, is proposed. It is shown that this semantics coincides with the P-log semantics for stratified ProbLog programs, while the two may differ in the non-stratified case and for other PLP formalisms.

Probabilistic inference in high-dimensional Bayesian networks is difficult because exact manipulation of the joint distribution scales exponentially with network size. We propose a decomposition framework based on directed convex subgraphs and introduce a minimal d-decomposition tree. Together, they provide a principled alternative to classical junction-tree constructions. The proposed framework represents the joint distribution by lower-dimensional sub-models that can be learned and stored separately. This decomposition reduces computational cost and naturally enables parallel computation. Based on a minimal d-decomposition tree, we further develop two parallel algorithms for parameter estimation and probabilistic inference. Experiments show that the proposed method substantially improves computational efficiency over junction-tree methods while maintaining inference accuracy, especially for low-dimensional queries.

Machine Learning (ML) algorithms have been widely used to estimate agricultural variables across diverse contexts. However, because the quantity and quality of training data strongly influence performance of ML algorithms, their use can be constrained by limited or incomplete reference data. Synthetic Data Generation (SDG) offers a practical approach to address this issue by producing artificial but realistic samples that preserve key characteristics of the original data. Building on teacher-student knowledge transfer and in-context learning for tabular data, this study proposes a Task-Conditioned SDG (TCSDG) algorithm that pairs a Bayesian Network generator with a transformer-based tabular foundation model (TabICL). The proposed algorithm was evaluated on two agricultural prediction tasks: crop yield prediction and crop type classification. Six benchmark SDG algorithms were also utilized to compare their performance with that of TCSDG. Across twelve study sites, two training-data fractions, four multiplication ratios, and three predictive ML algorithms, augmenting the original data with TCSDG-generated synthetic data improved ML performance in 89% of the crop type classification experiments and 74% of the crop yield prediction experiments. TCSDG also substantially outperformed benchmark SDG algorithms and was the only method to consistently improve ML performance across both tasks at the aggregate level. The study demonstrates that carefully designed and processed synthetic data can improve ML performance in precision-agriculture applications. TCSDG offers a practical and extensible framework for generating synthetic data that supports downstream ML agricultural prediction. The full implementation of TCSDG is publicly available as open source at https://github.com/HamidEbrahimy/TCSDG.

Programming adaptive behaviors at the cellular level is a long-standing goal that raises the question of how probabilistic computation can be implemented in biochemical systems. Chemical reaction networks (CRNs) provide such a substrate and have been shown to realize probabilistic models, including hidden Markov models and factor graphs, with dynamics reproducing Bayesian inference and belief propagation. However, encoding these algorithms typically requires prohibitively large reaction networks, and classical CRN reduction techniques do not directly apply. By recovering the factor graph structure encoded in Napp--Adams-compiled CRNs, we transport recent factor-graph reduction results to their chemical implementations, obtaining significantly smaller CRNs while preserving the belief-propagation fixed points on surviving variables.

Alzheimer's disease (AD) progression is often described through the amyloid-tau-neurodegeneration, or AT(N), cascade. However, most longitudinal models represent this cascade either as a fixed sequence of biomarkers or as a black-box forecasting task. This makes it difficult to determine when biologically guided biomarker relationships influence future regional pathology. In this study, we introduce Bayesian Networks with Latent Time Embedding (BN-LTE), a Bayesian structural framework for stage-aware modeling of AD progression. BN-LTE estimates disease pseudotime from baseline biomarker profiles and constrains directed dependencies according to biologically plausible AT(N) ordering. Posterior spline-varying structural equations are then used to link initial multimodal measurements with future annualized regional tau-PET change. Across repeated subject-disjoint evaluations using ADNI data, BN-LTE shows strong spatial reconstruction of tau progression compared with the included forecasting baselines. Beyond spatial reconstruction, BN-LTE recovers posterior stage-varying AT(N)-constrained effects and identifies a mid-pseudotime window of amyloid sensitivity. This window is supported by model-implied g-formula contrasts, root-adjusted AIPW, mechanism-sensitive ablations, and robustness analyses across spline and prior specifications. Overall, these findings position BN-LTE as a Bayesian structural framework for forecasting tau progression while examining stage-dependent AT(N)-cascade mechanisms in observational longitudinal neuroimaging data. Our code is available at https://github.com/danleneurocom/BN-LTE.

The adoption and integration of heterogeneous stacks in most of today's open-source based networks brings clear benefits like interoperability and availability of advanced features. Yet, on the other hand the increasing number of interconnecting components and moving parts requires maintaining an ever increasing base of interdisciplinary knowledge of different tools in different domains to ensure proper operation. To alleviate such efforts, this work proposes a Decision Support System (DSS) to guide infrastructure operators through the selection of security approaches (e.g. tools) to adopt in their environments. This framework easily captures the end-user high-level requirements on the security triad for different domains and runs inference on the designated models to provide the identified tools (security mechanisms) that better serve such needs. The presented DSS aims at delivering an understandable and extensible framework to accommodate varying requirements and Bayesian Network (BN) models. The architecture and modelling of the system are proposed, aligned with its theoretical framework. Its performance is evaluated in terms of time and prediction accuracy.

Learning Bayesian network (BN) structure from sparse discrete data is hard: when each instance records only a few variables, most variable pairs lack the joint observations needed for reliable scoring, and data-only methods recover little structure. Imperfect domain knowledge, expressible as a weighted directed knowledge graph (KG), is often available. KG-SoftMAP encodes such a KG as a finite-strength, confidence-weighted edge prior and maximizes a MAP objective that adds this logit-form prior to the BDeu score. With an informative but imperfect KG, KG-SoftMAP recovers partial directed structure even at observation rate rho=0.05, with directed F1 (DF1) of 0.19-0.32 across benchmarks. At higher observation rates within this sparse grid, DF1 reaches 0.44-0.66 at rho=0.20 and 0.46-0.64 at rho=0.40. Across the same three rates, KG-SoftMAP without the KG prior averages DF1 0.00, 0.19, and 0.21. Stress tests that corrupt, remove, or blur the KG signal, together with checks on LLM-extracted graphs beyond canonical benchmarks, show that recovery rises and falls with KG quality. On three real sparse educational datasets without ground-truth DAGs, we evaluate prediction, calibration, and KG-consistency. On Short Answer Feedback (SAF), KG-SoftMAP+VE reaches Fail-class F1 0.75 versus 0.78 for logistic regression while also providing an inspectable concept graph, calibrated Fail probabilities, and posterior queries from partially observed concept evidence. The remaining datasets sharpen the operating picture: weak heuristic KG signal leaves prediction unchanged, while an independent expert ontology moves the learned graph toward expert relatedness.

Large language models are rapidly becoming infrastructural components in high-stakes institutional settings, including public administration, legal reasoning, and healthcare, where opacity is not merely inconvenient but institutionally and legally untenable. Existing approaches to explainability are predominantly post-hoc, offering unstable, non-contestable accounts that have no formal relationship to the reasoning process that produced the output. We argue that the problem is not the absence of explanation but the absence of structured reasoning in the first place. This paper makes the case for a fundamentally different architecture, which we call the Glassbox Framework, in which Bayesian networks serve as transparent, ante-hoc mediation layers for generative models. Bayesian networks encode domain knowledge, causal assumptions, and probabilistic dependencies before inference occurs, enabling auditable reasoning traces, uncertainty quantification, and contestable outputs. We characterise the architecture of this framework and ground it in a benefit eligibility scenario, identifying the foundational challenges spanning semantic alignment, dynamic model construction, probabilistic grounding, and human governance that must be solved to realise it at scale. By shifting from post-hoc explanation to ante-hoc probabilistic mediation, this work outlines a principled path toward AI systems that are not only powerful but fundamentally accountable.

Electronic health records (EHR) pose large-scale multi-disease modeling problems in which many outcomes are rare and strongly influenced by shared risk factors. While modern approaches achieve strong predictive performance, they often treat diseases independently or rely on black-box architectures, offering limited insight into how risk factors organize disease risk and little principled uncertainty quantification. We introduce a Bayesian hypergraph inference framework that reframes multi-disease modeling around latent, risk-factor-modulated disease pathways. Risk factors act on hyperedges, latent disease subsets with shared risk patterns, allowing diseases to participate in multiple distinct pathways and enabling interpretable, higher-order structure beyond pairwise associations. A repulsion prior encourages parsimonious and identifiable structure, while posterior inference provides calibrated uncertainty over both disease groupings and risk-factor influence. To enable scalable inference on large EHR datasets, we develop a structured variational inference algorithm that preserves logical dependencies among hyperedge existence, disease membership, and pathway-level effects. Experiments on simulated data and UK Biobank demonstrate stable and interpretable disease pathway structure, well-calibrated uncertainty, improved estimation for rare diseases, and competitive predictive performance.

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.

Metamodels for discrete-event simulations approximate the behavior of simulation models without running expensive simulations. Prior work introduced modular dynamic Bayesian networks (MDBNs) -- a class of metamodels that can estimate a range of probabilistic and causal queries (PCQs) using a single, trained model -- but the method was limited to Markovian systems. In this paper, we initiate an extension of MDBNs to non-Markovian queues by approximating non-exponential distributions using phase-type distributions. This approach raises novel challenges, including balancing metamodeling accuracy and tractability when choosing the number of phases, efficiently learning metamodel parameters, and choosing the sampling interval that is used to approximate a continuous-time simulation by a discrete-time MDBN. We provide preliminary solutions to these challenges, yielding the first causal metamodeling technique for non-Markovian systems. Experiments on a G/M/1 queue demonstrate that the MDBN can produce accurate answers to PCQs with orders-of-magnitude speedup of inference times relative to direct simulation.

Bayesian Networks (BNs) are of interest from an explainable AI viewpoint, offering transparent probabilistic models for decision support. Baymex is a recently introduced multi-objective evolutionary algorithm for learning discretized BNs, enabling experts to trade-off different objectives of interest, such as likelihood, model complexity, and prior beliefs. While Baymex has been shown to outperform state-of-the-art BN learning approaches, Baymex still 1) requires a lot of computation time and 2) has only been evaluated on synthetic data. To improve scalability, we introduce a parallelization strategy as well as a mechanism that enables adaptively steering optimization toward networks that overfit less. We furthermore reconfigure Baymex to train a BN classifier through multi-objective optimization of cross-entropy loss and the BIC complexity term so as to evaluate its performance on real-world clinical classification tasks. Besides observing speedups up to over 54 times on a 16-core CPU, comparisons against clinically familiar baselines (decision trees, logistic regression, naive Bayes, and random forests) on two open-source (RADCURE and SUPPORT) and one in-house dataset, show that Baymex obtains statistically similar or better predictive performance while producing compact, clinically inspectable BNs. Importantly, Baymex finds multiple plausible BN classifiers that contain predictors consistent with established clinical factors.

Tabular data in knowledge-rich domains often carries a latent prior in the form of Boolean implication relationships (BIRs) between pairs of features. We mine such relationships with a sparse-exception binomial test. The mined implications form a typed directed graph, equivalent to a propositional rule base of 2-literal clauses. We encode this graph as the connectivity of a layered neural network, called BIRDNet, in which each hidden unit corresponds to one mined rule and binds only to its two features. We show two consequences of this design: First, the architecture is sparse by construction: at most $2/d$ of the weights in each BIR layer are active, where $d$ is the input dimension. Second, the model is interpretable: every trained unit keeps a stable symbolic identity, so rules can be read off the network without surrogate models. Unlike most neurosymbolic models, BIRDNet does not consume an external rule base; its structural prior is mined from the data. We evaluate BIRDNet on six transcriptomic and proteomic benchmarks. Our results show that BIRDNet stays within 0.02 AUROC of the strongest dense baseline, at a small accuracy cost, while using up to $96\times$ fewer active parameters than an architecture-matched dense MLP. First-layer rules recover known biological signatures across multiple cancer subtypes and tissue types, including canonical amplicons, lineage-defining co-expression modules, and immune-infiltration markers. Data and code are available at: https://github.com/MAHI-Group/BIRDNet.

We introduce the problem of \emph{entropy equivalence testing} for probability distributions, a relaxation of the well-studied closeness testing problem, where the distribution testing algorithm is now only required to distinguish, given samples from two unknown distributions $p,q$ and a parameter $\varepsilon \in(0,1/2]$, between $p=q$ and $|H(p)-H(q)| \geq \varepsilon$ (where $H$ denotes the Shannon entropy). We provide a time- and sample-efficient algorithm for this task, showing that the optimal sample complexity for this task can be significantly lower than that of closeness testing. As an application, we leverage this result to provide the first non-trivial testing algorithm for (standard) closeness of low-degree \emph{Bayesian networks}, which significantly improves on either the sample or time complexity of a baseline based on full learning.

A "path-based sensor" produces a single observation along a continuous path. For example, a boolean path-based sensor returns a single "1" if an event of interest is detected at any point along the path and a "0" otherwise. Notably, a "1" provides no direct information about where along the path the event(s) may have occurred. Previous work has demonstrated that observations from multiple path-based sensors can be fused to create a Bayesian belief map over the spatial locations of the underlying event or phenomenon. Moreover, path planning can employ Shannon information theory to accelerate the rate of convergence of the belief map. In this paper, we present a new method to update the belief map based on a path-based sensor observation, and then plan paths to increase information gain. In contrast to prior work that approximates the posterior by averaging over the alternative event histories, we introduce a Bayesian Network (BN) formulation that models the probabilistic relationships between the latent variables and path-based sensor measurements, enabling a more principled Bayesian belief update. We consider static hazard detection in a communication-denied environment as a representative problem setting. The event of a robot returning from its path corresponds to a path-based hazard sensor reading of "0" (hazard not detected), while a robot failing to return corresponds to a reading of "1" (hazard detected). We consider false positives and false negatives. We find that the new method leads to quicker convergence of the belief map than prior work in both single- and multi-robot cases.

We introduce the Free Energy Manifold (FEM), a score-trained conditional energy model specialized for inference in hybrid Bayesian networks with discrete and continuous variables. FEM represents each conditional factor as an energy landscape over learned discrete-parent embeddings and continuous observations, enabling posterior evaluation, generative sampling, and compositional inference across multiple continuous leaves by energy addition under conditional independence. A central finding is the mode-bridge artifact: standard conditional energy models can create low-energy ridges between separated modes of the same class, producing overconfident posteriors at off-data interior points. We analyze this failure and propose valley regularization, an off-data calibration term that restores near-uniform posteriors in such regions while preserving in-data fit. Across synthetic multimodal hybrid-BN benchmarks, FEM substantially reduces KL divergence relative to classical baselines and a vanilla conditional EBM, including large gains at mode-bridge midpoint queries and in multi-leaf evidence composition. We also evaluate high-cardinality discrete-parent settings and a UCI Breast Cancer sanity check, showing that FEM is most useful when multimodal or compositional Bayesian-network inference is required, while discriminative classifiers remain preferable for closed-world classification tasks.

Anomaly detection methods can be very useful in identifying interesting or concerning events. In this work, we develop and examine new probabilistic anomaly detection methods that let us evaluate management decisions for a specific patient and identify those decisions that are highly unusual with respect to patients with the same or similar condition. The statistics used in this detection are derived from probabilistic models such as Bayesian networks that are learned from a database of past patient cases. We apply our methods to the problem of identifying unusual patient-management decisions in post-surgical cardiac patients.

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.

Dialogue models are inherently reactive, responding to the current user turn without anticipating upcoming intents, which leads to redundant interactions in multi-intent settings. We address this limitation by introducing a lightweight intent-transition prior derived from dialogue data and injected into the system prompt at inference time. We instantiate this prior using a Temporal Bayesian Network (T-BN) trained on per-turn intent annotations in MultiWOZ 2.2. The T-BN achieves Recall@5 = 0.787 and MRR = 0.576 on 1,071 held-out USER-turn pairs. In a ground-truth replay over 200 dialogues, BN-guided generation improves Coverage AUC from 0.742 to 0.856 and reduces the number of turns required to reach 75% intent coverage from 3.95 to 2.73. These results show that lightweight intent-transition guidance enables more proactive and efficient dialogue behavior without modifying the underlying language model.

Constraint-based causal discovery is brittle in finite-sample regimes because erroneous conditional-independence (CI) decisions can cascade into substantial structural errors. We propose Quantitative Argumentation for Causal Discovery (QACD), a semantics-driven framework that represents CI outcomes as graded, defeasible arguments rather than irreversible constraints. QACD maps statistical test outcomes to argument strengths and aggregates conflicting evidence through connectivity-mediated witness propagation, producing a fixed-point acceptability labeling over candidate adjacencies. Experiments on standard benchmark Bayesian networks suggest that QACD improves structural coherence and interventional reliability in several noisy or inconsistent CI regimes, while remaining competitive with classical constraint-based, hybrid, and prior argumentation-based baselines.

Autonomous robots deployed in mass casualty incidents (MCI) face the challenge of making critical decisions based on incomplete and noisy perceptual data. We present an autonomous robotic system for casualty assessment that fuses outputs from multiple vision-based algorithms, estimating signs of severe hemorrhage, visible trauma, or physical alertness, into a coherent triage assessment. At the core of our system is a Bayesian network, constructed from expert-defined rules, which enables probabilistic reasoning about a casualty's condition even with missing or conflicting sensory inputs. The system, evaluated during the DARPA Triage Challenge (DTC) in realistic MCI scenarios involving 11 and 9 casualties, demonstrated a nearly three-fold improvement in physiological assessment accuracy (from 15% to 42% and 19% to 46%) compared to a vision-only baseline. More importantly, overall triage accuracy increased from 14% to 53%, while the diagnostic coverage of the system expanded from 31% to 95% of cases. These results demonstrate that integrating expert-guided probabilistic reasoning with advanced vision-based sensing can significantly enhance the reliability and decision-making capabilities of autonomous systems in critical real-world applications.

This work shows how adaptivity can enhance value realization of digital twins in civil engineering. We focus on adapting the state transition models within digital twins represented through probabilistic graphical models. The bi-directional interaction between the physical and virtual domains is modeled using dynamic Bayesian networks. By treating state transition probabilities as random variables endowed with conjugate priors, we enable hierarchical online learning of transition dynamics from a state to another through effortless Bayesian updates. We provide the mathematical framework to account for a larger class of distributions with respect to the current literature on digital twins. To compute dynamic policies with precision updates we solve parametric Markov decision processes through reinforcement learning. The proposed adaptive digital twin framework enjoys enhanced personalization, increased robustness, and improved cost-effectiveness. We assess our approach on a case study involving structural health monitoring and maintenance planning of a railway bridge.

Generative networks are perfect tools to enhance the speed and precision of LHC simulations. Especially when generating events beyond the size of the training dataset, it is important to understand their statistical precision. We present two complementary methods to estimate the amplification factor without large holdout datasets. Averaging amplification uses Bayesian networks or ensembling to estimate amplification from the precision of integrals over given phase-space volumes. Differential amplification uses hypothesis testing to quantify amplification without any resolution loss. Applied to state-of-the-art event generators, both methods indicate that amplification is already possible in specific regions of phase space.

Reinforcement learning (RL) provides a principled framework for decision-making in partially observable environments, which can be modeled as Markov decision processes and compactly represented through dynamic decision Bayesian networks. Recent advances demonstrate that inference on sparse Bayesian networks can be accelerated using quantum rejection sampling combined with amplitude amplification, leading to a computational speedup in estimating acceptance probabilities. Building on this result, we introduce Quantum Bayesian Reinforcement Learning (QBRL), a hybrid quantum-classical look-ahead algorithm for model-based RL in partially observable environments. We present a rigorous, oracle-free time complexity analysis under fault-tolerant assumptions for the quantum device. Unlike standard treatments that assume a black-box oracle, we explicitly specify the inference process, allowing our bounds to more accurately reflect the true computational cost. We show that, for environments whose dynamics form a sparse Bayesian network, horizon-based near-optimal planning can be achieved sub-quadratically faster through quantum-enhanced belief updates. On the other hand, we show that there is no quantum speed-up for environments that are either fully observable, or characterized by Bayesian networks whose maximum in-degree is not small. Furthermore, we present numerical experiments benchmarking QBRL against its classical counterpart on simple yet illustrative decision-making tasks. Our results offer a detailed analysis of how the quantum computational advantage translates into decision-making performance, highlighting that the magnitude of the advantage can vary significantly across different deployment settings.

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.

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.