Learning Graphical Models
Bayesian Multiplicity Correction in the Probabilistic Forward Stepwise Framework
Womack, Andrew, Taylor-Rodriguez, Daniel
We develop a natural Bayesian multiplicity-correcting prior distribution within the probabilistic forward stepwise representation of model space priors for regression problems. The proposed prior, obtained from making an analogy to the Holm procedure, exhibits behavior closely aligned with that of the Matryoshka doll prior. We compare both priors to several other priors, including some recently put forward as objective choices for model space prior probabilities. Our comparisons indicate that adequate multiplicity correction requires a degree of sparsity that many recommended priors do not provide, and we argue that multiplicity correction itself offers a principled and transparent criterion for specifying model space priors in regression.
The Good, the Bad, and the Ugly of Markov Boundary for Tabular Prediction
Wan, Shu, Gorantla, Abhinav, Liu, Huan, Candan, K. Selçuk
Under standard graphical assumptions, the Markov boundary of a target variable is the smallest set of features that renders every other feature redundant. Once the boundary is observed, the target is conditionally independent of the rest of the table. This is a tempting object for tabular prediction, since it names exactly the columns a model should need. Yet modern regressors are still trained on the full feature set. We ask whether the Markov boundary is genuinely useful for prediction on SCM3K, a 3,450-task synthetic SCM benchmark with feature counts from 40 to 1000 and six SCM families, evaluated with six regressors. The answer is more nuanced than the theory suggests. Restricting a regressor to the oracle boundary often improves prediction substantially, and the improvement grows as the feature space becomes larger and sparser. But the natural pipeline of recovering the boundary with causal discovery and training on the recovered mask does not deliver. Existing estimators exhaust the compute budget before reaching the regime where the boundary helps most, and even where they run they rarely beat the full feature set. We trace this to three causes. Discovery optimizes structural recovery rather than prediction. False negatives and false positives carry sharply asymmetric predictive cost. The exact boundary is only one of many feature sets that beat all features. We then develop what these facts imply for prediction-aligned feature selection and for tabular models that learn to use causal structure.
On the Construction and Implications of Low-Loss Valleys in LoRA-based Bayesian Inference
Dold, Daniel, Sommer, Emanuel, Kobialka, Julius, Dürr, Oliver, Rügamer, David
While parameter-efficient fine-tuning methods like low-rank adaptation (LoRA) are standard for large language models, principled estimation of epistemic uncertainty remains challenging. Recent results in the LoRA regime suggest that discrete multi-mode approaches such as deep ensembles offer little benefit over single-mode methods. This contradicts broader observations in deep learning, where ensembling independent optima typically improves generalization, and linking these modes through continuous low-loss valleys further enhances Bayesian model averaging (BMA). Whether such structure exists in the LoRA space and whether it yields functional diversity missed by local or discrete methods has not been studied. We introduce LoRA-Curve, a segmented Bézier curve parameterization in the LoRA space, with two variants: a free configuration that jointly optimizes all control points, and an anchored configuration that connects independently fine-tuned LoRA optima. We prove pathwise continuity and Lipschitz regularity of the loss along the curve and empirically show, across reasoning and classification benchmarks with Qwen2.5 7B, that linear interpolation encounters loss barriers, while our anchored multi-segment curves connect independent optima through continuous low-loss valleys. Combined with flat-minima perturbations and a Jensen-Shannon divergence regularizer, LoRA-Curve yields measurably higher mutual information of the predictive distribution without sacrificing performance, and links continuous parameter-space traversal to functional diversity.
Kernel Renormalization in Bayesian Deep Neural Networks: the Equivalent Wishart Ansatz in the Proportional Regime
Baglioni, Paolo, Keup, Christian, Zimbardo, Vincenzo, Pacelli, Rosalba, Vezzani, Alessandro, Burioni, Raffaella, Rotondo, Pietro
The scaling limit where both the size of the training set $P$ and the width $N$ of a deep neural network grow at the same rate, the so-called proportional-width regime, has been intensely studied for shallow, single-hidden-layer networks. However, extending these non-perturbative results from shallow architectures to deep non-linear networks has proven very challenging. Here we present an effective approximate approach to predict the generalization performance of Bayesian multi-layer perceptrons (MLPs) of fixed depth $L$ on arbitrary high-dimensional data. We propose an equivalent Wishart Ansatz to capture the dominant stochastic fluctuations of the hierarchical empirical kernels of MLPs. This allows us to perform a large deviation analysis for the partition function of MLPs in the proportional limit, expressed in terms of a renormalized NNGP kernel. In this description, even strong representation learning in the proportional limit is encoded in at most $L$ scalar order parameters, determined self-consistently. Extending the approach to convolutional architectures (CNNs), we identify a hierarchical local kernel renormalization mechanism, which allows to quantify more complex data-dependent transformations of the large-width kernel in CNNs due to finite-width effects. We test our effective theory against sampling experiments from the Bayesian posterior of finite deep neural networks with depths $L \sim O(10)$ and $P\sim O(10^3)$ on classic benchmark datasets, finding overall very good agreement together with two distinct types of systematic deviations.
Joint Model and Data Sparsification via the Marginal Likelihood
Timans, Alexander, Möllenhoff, Thomas, Naesseth, Christian A., Khan, Mohammad Emtiyaz, Nalisnick, Eric
Sparse recovery in linear systems underpins applications from signal processing to high-dimensional regression. Sparse Bayesian Learning, grounded in the principle of automatic relevance determination (ARD), offers a practical Bayesian mechanism for feature sparsity via marginal likelihood optimization. Yet, its reliance on a homoscedastic noise model renders it sensitive to data contaminations such as outliers or misspecified noise, harming model fit and predictions. Instead, we propose jointly learning individual feature and sample relevancies, enabling simultaneous model and data sparsification via a single Bayesian objective. This symmetric pruning of model and data offers a natural extension that preserves conjugacy, admits closed-form updates for standard optimization procedures, and aligns with perspectives from robust regression and influence functions. Empirical results across diverse regression tasks affirm that a joint ARD approach consistently yields both sparse and robust prediction models.
Wasserstein Contraction of Coordinate Ascent Variational Inference
Caprio, Rocco, Corenflos, Adrien, Power, Sam
Finding approximations to an intractable probability distribution π of interest (usually known only up to a normalizing constant) is a key problem in scientific computing. Variational Inference stands out as a particularly attractive tool for this task, owing to its statistical and computational efficiency, and it has been the framework underlying many advances in computational statistics over the past half century (Parisi, 1980; Hinton and Van Camp, 1993; Jordan et al., 1999; Bishop and Nasrabadi, 2006). The central idea is to seek a tractable approximation to π within a chosen family of tractable distributions Q by minimizing a divergence to π over that'variational' family. Often, it is convenient or well-motivated to work with the family of product (or tensor, or factorized) distributions Q = P m, and define optimality through minimisation of the Kullback-Leibler (KL) divergence (also'relative entropy') min KL(ϱ||π): ϱ P m . A key practical aspect of working with this particular loss function is that in solving the associated optimisation problem, one is only required to compute expectations under the tractable variational distribution ϱ, rather than under the intractable target distribution π. In Bayesian statistics, π typically represents the joint posterior distribution of latent variables z Z and some parameters β B given observed data y Y. In these cases, we often choose m = 2 and seek the best variational approximation µ(dz) ν(dβ) to π to solve min KL(µ ν||π): µ P(Z), ν P(B) . The coordinate ascent variational inference algorithm (CAVI, Bishop and Nasrabadi, 2006; Blei et al., 2017) solves this problem by iteratively minimizing the Kullback-Leibler divergence with respect to one element at a time: given a starting point ν0, it iterates µk:= argmin
Leave a Window Out: Modifying the Jackknife for Predictive Inference in Time Series
Jiang, Hanyang, Barber, Rina Foygel, Pananjady, Ashwin, Xie, Yao
Conformal prediction methods enjoy strong theoretical and empirical predictive inference performance, provided the data is exchangeable, and predictors are trained in a memoryless fashion. However, these assumptions and constraints are impractical in many real-data settings, such as time series (where temporal dependence violates exchangeability, and where memoryless predictors will inevitably have poor predictive accuracy). Recent work shows that the split conformal prediction method is robust to these issues of memory-based predictors and deviations from exchangeability that are common features of time-series data. However, since using sample splitting can lead to lower accuracy, this motivates asking whether other predictive inference methods (that do not rely on data splitting) could also be reliably used in the time series setting. In this work, we show that the vanilla leave-one-out jackknife can suffer an arbitrary loss of coverage even in canonical time series models with mild temporal dependence. As a remedy, we propose a careful modification tailored to such settings, which we term the \emph{leave-a-window-out} (LWO) method, and show that it can achieve valid coverage provided that the model-fitting procedure satisfies mild stability properties. Our proofs are based on quantifying the degree to which the data departs from \emph{cyclic exchangeability}, and we introduce new coefficients to measure the extent of this departure. Experiments on time series data demonstrate that our LWO method often enjoys valid coverage when the vanilla jackknife fails to cover, while producing much narrower intervals than split conformal prediction.
Iterative Causal Discovery: Per-Edge Impossibility Certificates, Tier-Aware Oracle Queries, and the $1+K$ Lower Bound
Causal-discovery algorithms return a directed graph, yet provide no principled means of distinguishing edge directions identified by the data from those assigned without an identifying assumption. Under the standard Markov and faithfulness conditions, the observational distribution identifies only a Markov equivalence class; orientations within that class are not determined by the joint distribution and cannot be recovered from additional samples alone, but require either a functional restriction or an intervention. We introduce a protocol for observational causal discovery on continuous data that attaches to each candidate edge a discrete impossibility certificate: a RESOLVED code records the identifiability theorem under which the direction was committed, while an IMPOSSIBLE code records the failure mode together with the specific question a domain expert must answer to resolve it. The bivariate cascade is extended with five gated identifiability tiers LSNM, IGCI, Stein, MDL, and PEIT that abstain when their precondition test rejects. Two oracle primitives, the meta-hub query and the node-children query, jointly establish an upper bound of $1+K$ expert interactions sufficient to recover any DAG, where $K$ denotes the number of non-leaf vertices. Under an ideal-oracle assumption, the bound is met exactly on the asia, sachs, child, and alarm benchmarks.
GenSBI: Generative Methods for Simulation-Based Inference in JAX
Flow and diffusion generative models have established themselves as widely adopted density estimators for simulation-based inference (SBI), extending naturally from neural posterior estimation to likelihood and joint density estimation. Their principled optimization objectives and freedom from architectural constraints have driven rapid adoption across the natural sciences. Yet the most widely used SBI libraries remain PyTorch-based, leaving researchers who develop their forward models and analysis pipelines in JAX without a native option. We present GenSBI, an open-source library that implements flow matching, score matching, and denoising diffusion entirely in JAX. The library offers three transformer-based architectures -- SimFormer, Flux1, and a novel Flux1Joint that extends gate-modulated transformer blocks to joint density estimation -- all interchangeable through a unified interface that decouples generative method, neural backbone, and inference mode. GenSBI provides an end-to-end workflow from training through posterior calibration (SBC, TARP, LC2ST) and supports custom architectures with domain-specific embedding networks.
Identifiable Bayesian Deep Generative Copulas with Unknown Layer Widths for Data with Arbitrary Marginal Distributions
Deep generative models offer powerful tools for multivariate data analysis, but their black-box architectures are often unidentified and difficult to interpret. We introduce the Deep Discrete Encoder (DDE) Copula, an identifiable and interpretable generative model for multivariate data with arbitrary marginal distributions. The model places a hierarchical directed network of binary latent variables inside a copula framework, enabling flexible dependence modeling for mixed discrete and continuous data. Estimation is based on rank likelihoods, which decouple marginal modeling from posterior inference on the DDE parameters and avoid specifying the marginal distributions. We establish conditions for identification of the DDE copula parameters, ensuring that layer-specific parameters provide meaningful summaries of multivariate dependence. We also prove quotient-space posterior consistency for continuous margins under the exact rank likelihood and treat the extended rank likelihood for tied or mixed margins as a generalized likelihood, with concentration under an additional contrast condition. For computation, we propose a stochastic expectation-maximization algorithm for \emph{maximum a posteriori} estimation, together with initialization strategies that improve convergence. To learn network dimension adaptively, we extend Bayesian rank-selection priors to infer layer-specific widths. Simulations show strong finite-sample performance, and a personality-survey analysis reveals interpretable hierarchical latent structure in complex multivariate data.