Hierarchical Empirical-Bayes Naive Bayes: Minimax Smoothing and Calibration with AODE Extension

The Naive Bayes (NB) classifier remains a standard choice for categorical data, yet its widely used smoothing rules, such as Laplace, Lidstone, Krichevsky-Trofimov, and the $m$-estimate, all prescribe a fixed smoothing strength that ignores feature cardinality, sample size, and class imbalance, inducing a non-vanishing bias on modern high-cardinality tabular data. We propose hierarchical empirical-Bayes Naive Bayes (HEB-NB), in which each class-feature conditional probability is smoothed by a Dirichlet prior whose concentration is learned data-adaptively via Type-II maximum likelihood, enabling principled information sharing across classes while retaining closed-form inference. We further introduce HEB average one-dependence estimators (HEB-AODE), showing that the adaptive smoothing transfers cleanly to structural relaxations of NB. Theoretically, we establish a non-asymptotic $\ell_1$ error bound for HEB-NB matching the empirical-distribution minimax rate plus a vanishing data-adaptive bias, together with a matching Laplace-tight lower bound that yields a finite-sample, risk-level strict separation from Laplace. We further derive a plug-in excess Bayes-risk bound via total-variation tensorization and a population top-1 expected calibration error (ECE) corollary. Empirically, across 31 UCI and OpenML benchmarks, HEB-NB attains the best average Friedman rank on probabilistic metrics, with up to 22.1% log-loss reductions on high-cardinality datasets and consistent improvements of HEB-AODE over vanilla AODE. Combining HEB-NB with mutual-information weighting reduces top-1 ECE by 41%-70%, demonstrating substantial gains in probabilistic accuracy and calibration.

Personalized Federated Learning via Variance-Aware Nonparametric Empirical Bayes

We develop a new approach to Personalized Federated Learning across heterogeneous clients using Nonparametric Empirical Bayes (NPEB). Leveraging the asymptotic normality of local parameter estimates obtained from Empirical Risk Minimization or M-estimation, our method formulates these estimates as noisy observations to estimate an unknown shared prior via Nonparametric Maximum Likelihood. A key challenge in applying NPEB in this setting is that existing approaches assume known fixed variances, which is not true in practice. To address this, we introduce a Variance-Aware Nonparametric Empirical Bayes (VANEB) framework that leverages the parameter-dependent asymptotic variance of local M-estimators. A key technical contribution is a generalized Tweedie's formula for this heteroskedastic setting. We then establish non-asymptotic error rates for density estimation in the average squared Hellinger distance and derive an oracle denoising inequality that provides error bounds for our estimator. While our theoretical guarantees are rooted in the asymptotic regime of M-estimators, we empirically explore heuristic extensions of VANEB to modern federated learning settings involving Deep Neural Networks (DNNs). For DNNs, we propose VANEB-head and VANEB-FT, which personalize the last fully connected layer via an NPEB step using an approximate diagonal variance estimator. We show that our method has strong performance on popular vision datasets MNIST and CIFAR-10, using a convolutional neural network architecture.

DAIF: A Data-Driven Intermediate Fusion Framework for Multimodal Supervised Learning via Approximate Message Passing

Multimodal supervised learning seeks to leverage multiple heterogeneous data sources to improve predictive performance. A central challenge is determining the fusion granularity across modalities: over-integration may amplify noise while under-integration fails to exploit cross-modal dependence. Existing approaches rely on pre-specified fusion architectures, from early to late fusion, that may not adapt to the underlying dependence structure among modalities. We propose DAIF, a data adaptive intermediate fusion framework that combines random matrix theory and non-parametric dependence measures to learn fusion structure directly from data. We operate under a Bayesian multimodal factor model where the prior on the latent factors determines the cross-modal dependence. Our method clusters modalities based on estimated intermodal dependence, then performs clusterwise empirical Bayes estimation of the priors. These estimated priors are used to construct denoisers within an approximate message passing (AMP) framework, yielding denoised low-dimensional features that borrow strength across related modalities while preserving modality-specific signal. The resulting embeddings are used for downstream supervised prediction. We evaluate the framework through simulations under varying dependence structures and signal regimes, comparing against several benchmark methods, and demonstrate its practical utility on two multimodal datasets, namely a trimodal TEA-seq dataset (Swanson et al., 2021) and TCGA-BRCA dataset (Goldman et al., 2020). In the first example, we predict the expression level of a T-cell differentiation marker protein and in the second case we analyze patient survival prediction based on multimodal information. Our method competes with or outperforms the state-of-the-art techniques in both prediction problems, demonstrating its versatility across diverse supervised learning tasks.

Simulation-Based Empirical Bayes

Empirical Bayes (EB) performs simultaneous inference across many related latent variables. Classical EB assumes that the likelihood p(x | z) is tractable. In many scientific applications, however, the likelihood is available only through a simulator. This paper develops EB for such implicit likelihoods. We introduce simulation-based empirical Bayes (SBEB), which connects nonparametric EB to simulation-based inference (SBI). SBEB computes EB estimates without an explicit density by using the observed data, simulator samples, and an amortized inference network. SBEB iteratively refines the fitted EB prior toward the population prior. With several scientific simulators and real-world data, we demonstrate that SBEB improves accuracy over SBI with a fixed prior.

Spectrally Deconfounded Gradient Boosting

Flexible machine-learning methods can be sensitive to hidden confounding: they may learn associations induced by unobserved confounders rather than stable signals. Spectral deconfounding mitigates this problem by shrinking high-variance directions of the covariate matrix that, under dense confounding, carry latent confounder information. Existing work has largely focused on linear models. We develop a nonlinear spectral deconfounding framework for gradient boosting. Our approach replaces the ordinary squared-error loss by a spectral loss, which alters the boosting dynamics by slowing down learning in confounding-aligned directions. We show that deconfounding is not achieved by the spectral loss alone, but by the interaction between spectral shrinkage and regularization, especially in terms of early stopping. Moreover, we provide a mixed-model interpretation that connects LAVA-type shrinkage to random-effects adjustment and yields an empirical-Bayes procedure for tuning the spectral loss. We also extend the method to general likelihoods and nonlinear confounding using Laplace approximations and kernel random effects. Across synthetic and real-world experiments, spectrally deconfounded boosting improves estimation of the target function under hidden confounding and is substantially more scalable than existing nonlinear spectral deconfounding baselines.

Robust Bayes-Assisted Conformal Prediction

Bayes-assisted conformal prediction combines the strengths of Bayesian modelling with exact, distribution-free frequentist coverage guarantees. Although conformal validity is preserved even when the Bayesian working model (BWM) is misspecified, the size of the resulting prediction sets can degrade substantially when the prior is poorly aligned with the observed data. We address this limitation by introducing RoBAS (Robust Bayes-Assisted Shrinkage): a Bayes-assisted framework for constructing robust nonconformity scores, with two instantiations: one induced by a heavy-tailed BWM, and a closed-form empirical Bayes shrinkage score. The resulting scores adapt to the quality of the working information encoded in the prior: when this information is reliable, they exploit it to produce efficient prediction sets; when it is weak or inaccurate, they revert to the Distance-To-Average (DTA) score, a robust non-informative baseline. We evaluate the proposed scores on tabular and image regression tasks where the training distribution may differ from the calibration and test distributions, while the calibration and test data themselves remain exchangeable. We find that they are competitive with widely used scores in the absence of such shift, while substantially reducing interval widths in shifted settings.

Empirical Bayes for correlated Gaussian sequence model

Empirical Bayes methods are among the most widely used statistical methods for large-scale inference. A central paradigm is the NPMLE, whose theoretical guarantees are by now well understood for the independent Gaussian sequence model. In this paper, we study empirical Bayes estimation from dependent observations in the Gaussian sequence model. We show that the maximum Composite Marginal Likelihood (CML) estimator, which ignores all correlations in the likelihood, converges in weighted Hellinger distance at the rate $n_*^{-1/2}$, where $n_*=n/κ_0$ is the `effective sample size' determined solely by the number of observations $n$ and the spectral radius $κ_0$ of the correlation matrix of the Gaussian observations. A complementary minimax lower bound shows that $n_*$ indeed serves as the right complexity measure, and that the CML estimator is nearly rate optimal under general dependence. We consider two concrete applications. In the first, we consider Bayesian linear regression, where the signal prior is estimated via CML applied to the least squares estimator. In the second, we consider the more challenging Bayesian nonlinear single-index model, where prior is estimated by CML applied to a one-step debiased gradient descent. In both applications, although the full likelihood landscape can be arbitrarily complicated and intractable, our CML method is facilitated by exploiting the high-dimensional distribution of the auxiliary statistics through a correlated Gaussian sequence model. The key ingredient in the proof of our results is a sharp local maximal inequality for the log composite marginal likelihood process under dependent Gaussian observations. In contrast to standard empirical process methods, we prove this inequality by leveraging a recent geometric Brascamp-Lieb inequality for Gaussian measures.

XMSE-Aware Adaptive Empirical Bayes Estimation

Empirical Bayes (EB) estimators can match the first-order asymptotic risk of maximum likelihood (ML) while behaving very differently at second order: recent excess mean squared error (XMSE) analysis shows that kernel-based EB estimation may be worse than ML when the kernel is poorly aligned with the true parameter. This paper turns that diagnostic into a design principle. We propose an XMSE-aware mixed estimator that interpolates between ML and EB shrinkage. Its fixed-weight XMSE is a scalar quadratic, yielding a closed-form oracle mixing weight that is no worse than both ML and the base EB estimator at the XMSE scale. A plug-in implementation based on finite-sample XMSE approximations is proved consistent, with a second-order oracle regret rate for an interior oracle weight. We further establish a transfer of the regret bound to the fixed-weight risk curve evaluated at the selected weight, a thresholded boundary rule, and extensions to compact kernel families and to finite and growing kernel dictionaries with high-probability oracle bounds. Finite impulse response simulations with SURE-tuned, hard-selection, and trace-corrected baselines, together with the public Silverbox and Cascaded Tanks benchmarks, show that the proposed estimator retains most of the benefit of regularization when it is helpful and retreats toward ML under kernel misspecification, with an identified finite-de analyzed on the benchmarks.

Nonparametric Deconvolution and Denoising using Simulation Based Inference

Latent signals are often obscured by measurement noise, yet encode the underlying laws and dynamics of complex systems; learning both the signals and their distributions remains a central challenge in scientific inference. The noise is often non-negligible, and the likelihoods for expressive generative models are often intractable. We utilize a convolutional maximum mean discrepancy (convMMD) loss and propose a likelihood-free framework for nonparametric density deconvolution and empirical Bayes denoising under additive measurement error. Our method learns a latent generative model by matching the observed data distribution to the noise-convolved model distribution. This yields a differentiable, simulation-based objective for multivariate homoscedastic or heteroscedastic noise, compatible with expressive sieve classes such as Gaussian mixtures and normalizing flows. The learned density then serves as an empirical prior for posterior denoising of individual latent values. Theoretically, we extend convMMD from parametric to nonparametric estimation, proving finite-sample bounds for empirical sieve minimizers and $L_2$ convergence rates under Sobolev smoothness. These rates recover the classical inverse-problem dependence: polynomial for ordinary-smooth and logarithmic for super-smooth noises. Our method provides a practical, theoretically grounded approach to deconvolution and denoising under generative latent distribution models.

Recovering Stranded Discrimination in Knowledge Tracing: Per-Item Bias Correction via Empirical-Bayes Shrinkage

Deployed knowledge-tracing models are typically frozen after training, yet systematic per-item logit bias arises, from limited per-item expressivity in backbone architectures and from post-deployment shifts in item properties, degrading prediction quality. Global post-hoc calibrators such as Platt scaling, temperature scaling, and isotonic regression improve probability estimates but leave discriminative ability, as measured by AUC, unchanged. This AUC invariance is a structural consequence of monotone score-only transforms; recovering the stranded discrimination requires conditioning on item identity. We propose SLC (State-space Logit Correction), which converts binary observations to Gaussian pseudo-observations via Laplace/IRLS, applies empirical-Bayes shrinkage through a Kalman smoother, and fits an offset-Platt link. The state-space formulation also yields a detectability bound that characterizes the Bernoulli information floor, explaining why temporal tracking provides no benefit at current data densities. Across four datasets, five backbones, and three seeds, SLC improves AUC on all four datasets and NLL on three, with the advantage concentrating on sparse items. Cross-domain controls suggest that the same phenomenon can arise beyond education when the deployed backbone leaves entity-level bias.

Environment-Robust Representation Learning with Empirical Bayes

We consider multi-environment prediction problems. We assume the environments change the distribution of a latent variable, while the mechanisms generating observed covariates and targets remain stable conditional on that variable. For example, hospitals or clinical cohorts may differ in the prevalence of latent patient states, even though the relationships between those states, physiological measurements, and outcomes remain unchanged. Given a dataset from multiple environments, we formulate a Bayesian model for such problems and derive the corresponding variational objective. We show that this objective decomposes into per-environment terms and an additional cross-environment balancing term induced by the model's structure. We use an empirical Bayes method to set the prior and incorporate it into the objective. Based on this objective, we develop an amortized variational algorithm for posterior approximation, and use the resulting learned latent variables to form predictions in new environments.We study our approach through simulations and real-world studies of astronomical source identification, microbiome-based disease detection, and ICU sepsis prediction. Across these settings, our method outperforms previous approaches for prediction in new environments.