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 Learning Graphical Models


Horseshoe Forests for High-Dimensional Causal Survival Analysis

arXiv.org Machine Learning

We develop a Bayesian tree ensemble model to estimate heterogeneous treatment effects in censored survival data with high-dimensional covariates. Instead of imposing sparsity through the tree structure, we place a horseshoe prior directly on the step heights to achieve adaptive global-local shrinkage. This strategy allows flexible regularisation and reduces noise. We develop a reversible jump Gibbs sampler to accommodate the non-conjugate horseshoe prior within the tree ensemble framework. We show through extensive simulations that the method accurately estimates treatment effects in high-dimensional covariate spaces, at various sparsity levels, and under non-linear treatment effect functions. We further illustrate the practical utility of the proposed approach by a re-analysis of pancreatic ductal adenocarcinoma (PDAC) survival data from The Cancer Genome Atlas.


Position: agentic AI orchestration should be Bayes-consistent

arXiv.org Machine Learning

LLMs excel at predictive tasks and complex reasoning tasks, but many high-value deployments rely on decisions under uncertainty, for example, which tool to call, which expert to consult, or how many resources to invest. While the usefulness and feasibility of Bayesian approaches remain unclear for LLM inference, this position paper argues that the control layer of an agentic AI system (that orchestrates LLMs and tools) is a clear case where Bayesian principles should shine. Bayesian decision theory provides a framework for agentic systems that can help to maintain beliefs over task-relevant latent quantities, to update these beliefs from observed agentic and human-AI interactions, and to choose actions. Making LLMs themselves explicitly Bayesian belief-updating engines remains computationally intensive and conceptually nontrivial as a general modeling target. In contrast, this paper argues that coherent decision-making requires Bayesian principles at the orchestration level of the agentic system, not necessarily the LLM agent parameters. This paper articulates practical properties for Bayesian control that fit modern agentic AI systems and human-AI collaboration, and provides concrete examples and design patterns to illustrate how calibrated beliefs and utility-aware policies can improve agentic AI orchestration.


PRCD-MAP: Learning How Much to Trust Imperfect Priors in Causal Discovery

arXiv.org Machine Learning

External priors of unknown reliability create a brittle trade-off in causal discovery: blind trust amplifies errors, blind rejection wastes signal. Real priors are also heterogeneously reliable -- physical laws are trustworthy, LLM-suggested edges are speculative -- yet existing methods either ignore priors or impose them through globally uniform trust. We propose PRCD-MAP, a soft prior-consumption layer that assigns per-edge trust to an imperfect prior and uses it to modulate a prior-aware $\ell_1$ and prior-weighted $\ell_2$ regularizer in a MAP objective. Trust is calibrated by empirical Bayes on a Laplace-approximated marginal likelihood and propagated along the prior graph by an MLP, so data-confirmed neighborhoods boost trust and contradictions suppress it. PRCD-MAP enjoys a population-level safety guarantee: it is $\varepsilon$-safe in expectation over the prior-generation distribution, with $\varepsilon\leq C\cdot\mathrm{acc}(1{-}\mathrm{acc})\cdot d^2/T$ at the parametric $T^{-1}$ rate and vanishing at the prior-quality endpoints. When the prior is uninformative, learned trust provably collapses to its floor and the method recovers a no-prior baseline. Empirically, on real CausalTime data PRCD-MAP exploits informative LLM priors (LLM-prior gain $+0.067/+0.089$ AUROC on AQI/Medical over a no-prior PRCD-MAP backbone; combined backbone+prior lead $+0.123/+0.043$ over PCMCI+), auto-attenuates on the anonymous-variable Traffic stress test, and retains a lead at $d{=}300$; against BayesDAG, the closest soft-Bayesian baseline, PRCD-MAP wins on every CausalTime dataset under a matched $W_0$-only protocol. A four-way ablation isolates each component: EB calibration and MLP trust propagation jointly carry the plurality of the gain, with positive sign on every dataset. Extensions to nonlinear (NAM) and cross-sectional settings show the calibrated-trust principle is setting-agnostic.


Forecasting Oncology Demand Trends with Boosting-Based Bayesian Conjugate Models

arXiv.org Machine Learning

Accurate trend forecasting in healthcare time series is essential for planning and resource allocation. This paper proposes a Bayesian framework for predicting oncology demand trends, modeling weekly appointments as a Poisson process with a Gamma prior to the demand rate. To enhance adaptability and capture persistent directional patterns, we incorporate a residual-based boosting mechanism grounded in a Gamma-Log-Normal conjugate structure. This boosting approach allows the model to track both short- and long-term trend shifts while maintaining the analytical tractability of conjugate Bayesian updating. The methodology was evaluated on real oncology service data from Cariri, Ceara, Brazil, and compared against established baselines, including linear regression, ARIMA, naive forecasting, LSTM neural networks, and XGBoost. Results showed that the proposed model outperforms competing methods in trend detection accuracy, with gains in terms of percentage of correct direction of 38.25% in relation to the second best approach in some cases.


Estimating Implicit Regularization in Deep Learning

arXiv.org Machine Learning

Deep learning systems are known to exhibit implicit regularization (alt. implicit bias), favoring simple solutions instead of merely minimizing the loss function. In some cases, we can analytically derive the implicit regularization -- connecting it to an equivalent penalty that augments the learning objective. However, modern deep learning systems are complex, carrying modifications to the training procedure and architecture (e.g. early stopping, minibatching, dropout) whose effects are not always directly interpretable. Although estimating the resulting implicit regularization could aid theorists in algorithm design and practitioners in interpreting their hyperparameter choices, this problem has received little direct attention. It is also tractable: regularization makes weight updates deviate from loss gradients, promising a signal for identifying implicit bias. Here we provide gradient matching methods that can be used to empirically estimate the implicit regularization. Our method works on networks with known regularization, recovering popular explicit penalties like $\ell_1$ and $\ell_2$. It also replicates known implicit effects, like the quadratic weight penalty induced by early stopping in gradient descent, demonstrating that it can be used to test theories of implicit regularization. Crucially, because our method is empirical, it can handle implicit regularization in arbitrary networks. We demonstrate this use by characterizing the effects of dropout in deep networks, showing implicit $\ell_2$ effects in this popular method. Our work shows that practitioners can use gradient matching to understand regularization in networks with implicit biases that are too complicated to derive analytically.


Non-Myopic Active Feature Acquisition via Pathwise Policy Gradients

arXiv.org Machine Learning

Active feature acquisition (AFA) considers prediction problems in which features are costly to obtain and the learner adaptively decides which feature values to acquire for each instance and when to stop and predict. AFA can be formulated as a partially observable Markov decision process (POMDP), which naturally admits a sequential decision-making perspective. In this paper, we present non-myopic pathwise policy gradients (NM-PPG), a new AFA method built around this formulation. We introduce a continuous relaxation of the acquisition process that enables pathwise gradients through the full acquisition trajectory, avoiding the high variance of standard score-function policy gradients while allowing end-to-end optimization of a non-myopic acquisition policy. To better align training with deployment, we further develop a straight-through rollout scheme that follows hard feature acquisitions in the forward pass while backpropagating through the corresponding soft relaxation in the backward pass. We stabilize optimization with entropy regularization and staged temperature sharpening. Experiments on both synthetic and real-world datasets demonstrate that NM-PPG yields superior performance relative to state-of-the-art AFA baselines.


Bayesian Rain Field Reconstruction using Commercial Microwave Links and Diffusion Model Priors

arXiv.org Machine Learning

Commercial Microwave Links (CMLs) offer dense spatial coverage for rainfall sensing but produce path-integrated measurements that make accurate ground-level reconstruction challenging. Existing methods typically oversimplify CMLs as point sensors and neglect line integration relating rainfall to signal attenuation, resulting in degraded performance under heterogeneous precipitation. In this work, we view rain field reconstruction as a Bayesian inverse problem with Diffusion Models (DMs) as high-fidelity spatial priors. We show that diffusion models better preserve key rainfall statistics compared to censored Gaussian processes. Framing rainfall estimation as a Bayesian inverse problem with a DM prior enables training-free posterior sampling using a broad family of methods, including Plug-and-Play, Sequential Monte Carlo, and Replica Exchange methods. Experiments on synthetic and real-world datasets demonstrate consistent improvements over established CML-based reconstruction baselines.


Relaxed Sparsest-Permutation Formulation for Causal Discovery at Scale

arXiv.org Machine Learning

Despite the growing availability of large datasets, causal structure learning remains computationally prohibitive at scale. We revisit sparsest-permutation learning for linear structural equation models and show that exact Cholesky factorization is unnecessary for structure recovery. This observation motivates a support-level relaxation that searches for sparse triangular factors over a precision-support screening graph. The relaxed formulation can be efficiently evaluated via masked zero-fill incomplete Cholesky factorization, enabling scalable comparison of candidate orderings. At the population level, we establish soundness for Markov equivalence class (MEC) recovery under no-cancellation and sparsest Markov representation assumptions, as well as robustness to ordering misspecification. Motivated by these guarantees, we introduce SCOPE, a sparse-Cholesky pipeline that provides a scalable implementation of the relaxed formulation. Experiments on synthetic and real datasets demonstrate that SCOPE matches the MEC recovery accuracy of substantially slower baselines, while achieving significantly reduced runtime and scaling to 10k variables.


Variational Smoothing and Inference for SDEs from Sparse Data with Dynamic Neural Flows

arXiv.org Machine Learning

Stochastic differential equations (SDEs) provide a flexible framework for modeling temporal dynamics in partially observed systems. A central task is to calibrate such models from data, which requires inferring latent trajectories and parameters from sparse, noisy observations. Classical smoothing methods for this problem are often limited by path degeneracy and poor scalability. In this work, we developed a novel method based on characterization of the posterior SDE in terms of conditional backward-in-time score defined as the gradient of a function solving a Kolmogorov backward equation with multiplicative updates at observation times. We learn this conditional score using neural networks trained to satisfy both the governing PDE and the observation-induced jump conditions, thereby integrating continuous-time dynamics with discrete Bayesian updates. The resulting score induces a posterior SDE with the same diffusion coefficient but a modified drift, enabling efficient posterior trajectory sampling. We further derive a likelihood-based objective for learning the SDE parameters, yielding an evidence lower bound (ELBO) for joint state smoothing and parameter estimation. This leads to a variational EM-style procedure, where the neural conditional score is optimized to approximate the smoothing distribution, followed by a maximization step over the SDE parameters using samples from the induced posterior. Experiments on nonlinear systems demonstrate accurate and stable inference with a very few observations demonstrating significant improved scalability compared to classical MCMC methods.


End-to-End Identifiable and Consistent Recurrent Switching Dynamical Systems

arXiv.org Machine Learning

Learning identifiable representations in deep generative models remains a fundamental challenge, particularly for sequential data with regime-switching dynamics. Existing approaches establish identifiability under restrictive assumptions, such as stationarity or limited emission models, and typically rely on variational autoencoder (VAE) estimators, which introduce approximation gaps that limit the recovery of the latent structure. In this work, we address both the theoretical and practical limitations of this setting. First, we establish identifiability of a broad class of recurrent nonlinear switching dynamical systems under flexible assumptions, significantly extending prior results. Second, we introduce $Ω$SDS, a flow-based estimator that enables exact likelihood optimization using expectation-maximisation. Through empirical validation on both synthetic and real-world data, our results demonstrate that $Ω$SDS achieves improved disentanglement compared to VAE-based estimators and more accurate forecasting of underlying dynamics.