Bayesian Inference
Vertical Consensus Inference for High-Dimensional Random Partition
Nguyen, Khai, Ni, Yang, Mueller, Peter
We review recently proposed Bayesian approaches for clustering high-dimensional data. After identifying the main limitations of available approaches, we introduce an alternative framework based on vertical consensus inference (VCI) to mitigate the curse of dimensionality in high-dimensional Bayesian clustering. VCI builds on the idea of consensus Monte Carlo by dividing the data into multiple shards (smaller subsets of variables), performing posterior inference on each shard, and then combining the shard-level posteriors to obtain a consensus posterior. The key distinction is that VCI splits the data vertically, producing vertical shards that retain the same number of observations but have lower dimensionality. We use an entropic regularized Wasserstein barycenter to define a consensus posterior. The shard-specific barycenter weights are constructed to favor shards that provide meaningful partitions, distinct from a trivial single cluster or all singleton clusters, favoring balanced cluster sizes and precise shard-specific posterior random partitions. We show that VCI can be interpreted as a variational approximation to the posterior under a hierarchical model with a generalized Bayes prior. For relatively low-dimensional problems, experiments suggest that VCI closely approximates inference based on clustering the entire multivariate data. For high-dimensional data and in the presence of many noninformative dimensions, VCI introduces a new framework for model-based and principled inference on random partitions. Although our focus here is on random partitions, VCI can be applied to any dimension-independent parameters and serves as a bridge to emerging areas in statistics such as consensus Monte Carlo, optimal transport, variational inference, and generalized Bayes.
Mixture-Model Preference Learning for Many-Objective Bayesian Optimization
Dubey, Manisha, De Peuter, Sebastiaan, Wang, Wanrong, Kaski, Samuel
Preference-based many-objective optimization faces two obstacles: an expanding space of trade-offs and heterogeneous, context-dependent human value structures. Towards this, we propose a Bayesian framework that learns a small set of latent preference archetypes rather than assuming a single fixed utility function, modelling them as components of a Dirichlet-process mixture with uncertainty over both archetypes and their weights. To query efficiently, we designing hybrid queries that target information about (i) mode identity and (ii) within-mode trade-offs. Under mild assumptions, we provide a simple regret guarantee for the resulting mixture-aware Bayesian optimization procedure. Empirically, our method outperforms standard baselines on synthetic and real-world many-objective benchmarks, and mixture-aware diagnostics reveal structure that regret alone fails to capture.
Profile Graphical Models
Avalos-Pacheco, Alejandra, Lupparelli, Monia, Stingo, Francesco C.
We introduce a novel class of graphical models, termed profile graphical models, that represent, within a single graph, how an external factor influences the dependence structure of a multivariate set of variables. This class is quite general and includes multiple graphs and chain graphs as special cases. Profile graphical models capture the conditional distributions of a multivariate random vector given different levels of a risk factor, and learn how the conditional independence structure among variables may vary across these risk profiles; we formally define this family of models and establish their corresponding Markov properties. We derive key structural and probabilistic properties that underpin a more powerful inferential framework than existing approaches, underscoring that our contribution extends beyond a novel graphical representation.Furthermore, we show that the resulting profile undirected graphical models are independence-compatible with two-block LWF chain graph models.We then develop a Bayesian approach for Gaussian undirected profile graphical models based on continuous spike-and-slab priors to learn shared sparsity structures across different levels of the risk factor. We also design a fast EM algorithm for efficient inference. Inferential properties are explored through simulation studies, including the comparison with competing methods. The practical utility of this class of models is demonstrated through the analysis of protein network data from various subtypes of acute myeloid leukemia. Our results show a more parsimonious network and greater patient heterogeneity than its competitors, highlighting its enhanced ability to capture subject-specific differences.
AutoStan: Autonomous Bayesian Model Improvement via Predictive Feedback
We present AutoStan, a framework in which a command-line interface (CLI) coding agent autonomously builds and iteratively improves Bayesian models written in Stan. The agent operates in a loop, writing a Stan model file, executing MCMC sampling, then deciding whether to keep or revert each change based on two complementary feedback signals: the negative log predictive density (NLPD) on held-out data and the sampler's own diagnostics (divergences, R-hat, effective sample size). We evaluate AutoStan on five datasets with diverse modeling structures. On a synthetic regression dataset with outliers, the agent progresses from naive linear regression to a model with Student-t robustness, nonlinear heteroscedastic structure, and an explicit contamination mixture, matching or outperforming TabPFN, a state-of-the-art black-box method, while remaining fully interpretable. Across four additional experiments, the same mechanism discovers hierarchical partial pooling, varying-slope models with correlated random effects, and a Poisson attack/defense model for soccer. No search algorithm, critic module, or domain-specific instructions are needed. This is, to our knowledge, the first demonstration that a CLI coding agent can autonomously write and iteratively improve Stan code for diverse Bayesian modeling problems.
Complete Causal Identification from Ancestral Graphs under Selection Bias
Many causal discovery algorithms, including the celebrated FCI algorithm, output a Partial Ancestral Graph (PAG). PAGs serve as an abstract graphical representation of the underlying causal structure, modeled by directed acyclic graphs with latent and selection variables. This paper develops a characterization of the set of extended-type conditional independence relations that are invariant across all causal models represented by a PAG. This theory allows us to formulate a general measure-theoretic version of Pearl's causal calculus and a sound and complete identification algorithm for PAGs under selection bias. Our results also apply when PAGs are learned by certain algorithms that integrate observational data with experimental data and incorporate background knowledge.
Probabilistic Geometric Alignment via Bayesian Latent Transport for Domain-Adaptive Foundation Models
Aueawatthanaphisut, Aueaphum, Auewattanapisut, Kuepon
Adapting large-scale foundation models to new domains with limited supervision remains a fundamental challenge due to latent distribution mismatch, unstable optimization dynamics, and miscalibrated uncertainty propagation. This paper introduces an uncertainty-aware probabilistic latent transport framework that formulates domain adaptation as a stochastic geometric alignment problem in representation space. A Bayesian transport operator is proposed to redistribute latent probability mass along Wasserstein-type geodesic trajectories, while a PAC-Bayesian regularization mechanism constrains posterior model complexity to mitigate catastrophic overfitting. The proposed formulation yields theoretical guarantees on convergence stability, loss landscape smoothness, and sample efficiency under distributional shift. Empirical analyses demonstrate substantial reduction in latent manifold discrepancy, accelerated transport energy decay, and improved covariance calibration compared with deterministic fine-tuning and adversarial domain adaptation baselines. Furthermore, bounded posterior uncertainty evolution indicates enhanced probabilistic reliability during cross-domain transfer. By establishing a principled connection between stochastic optimal transport geometry and statistical generalization theory, the proposed framework provides new insights into robust adaptation of modern foundation architectures operating in heterogeneous environments. These findings suggest that uncertainty-aware probabilistic alignment constitutes a promising paradigm for reliable transfer learning in next-generation deep representation systems.
Identification of physiological shock in intensive care units via Bayesian regime switching models
Kendall, Emmett B., Williams, Jonathan P., Storlie, Curtis B., Radosevich, Misty A., Wittwer, Erica D., Warner, Matthew A.
Detection of occult hemorrhage (i.e., internal bleeding) in patients in intensive care units (ICUs) can pose significant challenges for critical care workers. Because blood loss may not always be clinically apparent, clinicians rely on monitoring vital signs for specific trends indicative of a hemorrhage event. The inherent difficulties of diagnosing such an event can lead to late intervention by clinicians which has catastrophic consequences. Therefore, a methodology for early detection of hemorrhage has wide utility. We develop a Bayesian regime switching model (RSM) that analyzes trends in patients' vitals and labs to provide a probabilistic assessment of the underlying physiological state that a patient is in at any given time. This article is motivated by a comprehensive dataset we curated from Mayo Clinic of 33,924 real ICU patient encounters. Longitudinal response measurements are modeled as a vector autoregressive process conditional on all latent states up to the current time point, and the latent states follow a Markov process. We present a novel Bayesian sampling routine to learn the posterior probability distribution of the latent physiological states, as well as develop an approach to account for pre-ICU-admission physiological changes. A simulation and real case study illustrate the effectiveness of our approach.
Elements of Conformal Prediction for Statisticians
Sesia, Matteo, Favaro, Stefano
Predictive inference is a fundamental task in statistics, traditionally addressed using parametric assumptions about the data distribution and detailed analyses of how models learn from data. In recent years, conformal prediction has emerged as a rapidly growing alternative framework that is particularly well suited to modern applications involving high-dimensional data and complex machine learning models. Its appeal stems from being both distribution-free -- relying mainly on symmetry assumptions such as exchangeability -- and model-agnostic, treating the learning algorithm as a black box. Even under such limited assumptions, conformal prediction provides exact finite-sample guarantees, though these are typically of a marginal nature that requires careful interpretation. This paper explains the core ideas of conformal prediction and reviews selected methods. Rather than offering an exhaustive survey, it aims to provide a clear conceptual entry point and a pedagogical overview of the field.
SPDE Methods for Nonparametric Bayesian Posterior Contraction and Laplace Approximation
Alberola-Boloix, Enric, Casado-Telletxea, Ioar
We derive posterior contraction rates (PCRs) and finite-sample Bernstein von Mises (BvM) results for non-parametric Bayesian models by extending the diffusion-based framework of Mou et al. (2024) to the infinite-dimensional setting. The posterior is represented as the invariant measure of a Langevin stochastic partial differential equation (SPDE) on a separable Hilbert space, which allows us to control posterior moments and obtain non-asymptotic concentration rates in Hilbert norms under various likelihood curvature and regularity conditions. We also establish a quantitative Laplace approximation for the posterior. The theory is illustrated in a nonparametric linear Gaussian inverse problem.
Decorrelation, Diversity, and Emergent Intelligence: The Isomorphism Between Social Insect Colonies and Ensemble Machine Learning
Fokoué, Ernest, Babbitt, Gregory, Levental, Yuval
Social insect colonies and ensemble machine learning methods represent two of the most successful examples of decentralized information processing in nature and computation respectively. Here we develop a rigorous mathematical framework demonstrating that ant colony decision-making and random forest learning are isomorphic under a common formalism of \textbf{stochastic ensemble intelligence}. We show that the mechanisms by which genetically identical ants achieve functional differentiation -- through stochastic response to local cues and positive feedback -- map precisely onto the bootstrap aggregation and random feature subsampling that decorrelate decision trees. Using tools from Bayesian inference, multi-armed bandit theory, and statistical learning theory, we prove that both systems implement identical variance reduction strategies through decorrelation of identical units. We derive explicit mappings between ant recruitment rates and tree weightings, pheromone trail reinforcement and out-of-bag error estimation, and quorum sensing and prediction averaging. This isomorphism suggests that collective intelligence, whether biological or artificial, emerges from a universal principle: \textbf{randomized identical agents + diversity-enforcing mechanisms $\rightarrow$ emergent optimality}.