Accurately identifying patients with specific medical conditions is a key challenge when using clinical data from electronic health records. Our objective was to comprehensively assess when weakly-supervised prediction methods, which use silver-standard labels (proxy measures of the true outcome) rather than gold-standard true labels, perform well in rare-outcome settings like vaccine safety studies. We compared three methods (PheNorm, MAP, and sureLDA) that combine structured features and features derived from clinical text using natural language processing, through an extensive simulation study with data-generating mechanisms ranging from simple to complex, varying outcome rates, and varying degrees of informative silver labels. We also considered using predicted probabilities to design a chart review validation study. No single method dominated the other across all prediction performance metrics. Probability-guided sampling selected a cohort enriched for patients with more mentions of important concepts in chart notes. SureLDA, the most complex of the three algorithms we considered, often performed well in simulations. Performance depended greatly on selected tuning parameters. Care should be taken when using weakly-supervised prediction methods in rare-outcome settings, particularly if the probabilities will be used in downstream analysis, but these methods can work well when silver labels are strong predictors of true outcomes.

We study the problem of identifying change points in high-dimensional generalized linear models, and propose an approach based on sample-weighted empirical risk minimization. Our method, Weighted ERM, encodes priors on the change points via weights assigned to each sample, to obtain weighted versions of standard estimators such as M-estimators and maximum-likelihood estimators. Under mild assumptions on the data, we obtain a precise asymptotic characterization of the performance of our method for general Gaussian designs, in the high-dimensional limit where the number of samples and covariate dimension grow proportionally. We show how this characterization can be used to efficiently construct a posterior distribution over change points. Numerical experiments on both simulated and real data illustrate the efficacy of Weighted ERM compared to existing approaches, demonstrating that sample weights constructed with weakly informative priors can yield accurate change point estimators. Our method is implemented as an open-source package, weightederm, available in Python and R.

While the manifold hypothesis is widely adopted in modern machine learning, complex data is often better modeled as stratified spaces -- unions of manifolds (strata) of varying dimensions. Stratified learning is challenging due to varying dimensionality, intersection singularities, and lack of efficient models in learning the underlying distributions. We provide a deep generative approach to stratified learning by developing two generative frameworks for learning distributions on stratified spaces. The first is a sieve maximum likelihood approach realized via a dimension-aware mixture of variational autoencoders. The second is a diffusion-based framework that explores the score field structure of a mixture. We establish the convergence rates for learning both the ambient and intrinsic distributions, which are shown to be dependent on the intrinsic dimensions and smoothness of the underlying strata. Utilizing the geometry of the score field, we also establish consistency for estimating the intrinsic dimension of each stratum and propose an algorithm that consistently estimates both the number of strata and their dimensions. Theoretical results for both frameworks provide fundamental insights into the interplay of the underlying geometry, the ambient noise level, and deep generative models. Extensive simulations and real dataset applications, such as molecular dynamics, demonstrate the effectiveness of our methods.

In many problems of data-driven modeling for dynamical systems, the governing equations are not known a priori and must be selected phenomenologically from a large set of candidate interactions and basis functions. In such situations, point estimates alone can be misleading, because multiple model components may explain the observed data comparably well, especially when the data are limited or the dynamics exhibit poor identifiability. Quantifying the uncertainty associated with model selection is therefore essential for constructing reliable dynamical models from data. In this work, we develop a Bayesian sparse identification framework for dynamical systems with coupled components, aimed at inferring both interaction structure and functional form together with principled uncertainty quantification. The proposed method combines sparse modeling with Bayesian model averaging, yielding posterior inclusion probabilities that quantify the credibility of each candidate interaction and basis component. Through numerical experiments on oscillator networks, we show that the framework accurately recovers sparse interaction structures with quantified uncertainty, including higher-order harmonic components, phase-lag effects, and multi-body interactions. We also demonstrate that, even in a phenomenological setting where the true governing equations are not contained in the assumed model class, the method can identify effective functional components with quantified uncertainty. These results highlight the importance of Bayesian uncertainty quantification in data-driven discovery of dynamical models.

Computational models support high-stakes decisions across engineering and science, and practitioners increasingly seek probabilistic predictions to quantify uncertainty in such models. Existing approaches generate predictions either by sampling input parameter distributions or by augmenting deterministic outputs with uncertainty representations, including distribution-free and distributional methods. However, sampling-based methods are often computationally prohibitive for real-time applications, and many existing uncertainty representations either ignore input dependence or rely on restrictive Gaussian assumptions that fail to capture asymmetry and heavy-tailed behavior. Therefore, we extend the ACCurate and Reliable Uncertainty Estimate (ACCRUE) framework to learn input-dependent, non-Gaussian uncertainty distributions, specifically two-piece Gaussian and asymmetric Laplace forms, using a neural network trained with a loss function that balances predictive accuracy and reliability. Through synthetic and real-world experiments, we show that the proposed approach captures an input-dependent uncertainty structure and improves probabilistic forecasts relative to existing methods, while maintaining flexibility to model skewed and non-Gaussian errors.

Accurate representation of non-Gaussian distributions of quantities of interest in nonlinear dynamical systems is critical for estimation, control, and decision-making, but can be challenging when forward propagations are expensive to carry out. This paper presents an approach for estimating probability density functions of states evolving under nonlinear dynamics using Seminonparametric (SNP), or Gallant-Nychka, densities. SNP densities employ a probabilists' Hermite polynomial basis to model non-Gaussian behavior and are positive everywhere on the support by construction. We use Monte Carlo to approximate the expectation integrals that arise in the maximum likelihood estimation of SNP coefficients, and introduce a convex relaxation to generate effective initial estimates. The method is demonstrated on density and quantile estimation for the chaotic Lorenz system. The results demonstrate that the proposed method can accurately capture non-Gaussian density structure and compute quantiles using significantly fewer samples than raw Monte Carlo sampling.

Time-series analysis is often affected by missing data, a common problem across several fields, including healthcare and environmental monitoring. Multiple Imputation by Chained Equations (MICE) has been prominent for imputing missing values through "fully conditional specification". We extend MICE using the Bayesian framework (tBayes-MICE), utilising Bayesian inference to impute missing values via Markov Chain Monte Carlo (MCMC) sampling to account for uncertainty in MICE model parameters and imputed values. We also include temporally informed initialisation and time-lagged features in the model to respect the sequential nature of time-series data. We evaluate the tBayes-MICE method using two real-world datasets (AirQuality and PhysioNet), and using both the Random Walk Metropolis (RWM) and the Metropolis-Adjusted Langevin Algorithm (MALA) samplers. Our results demonstrate that tBayes-MICE reduces imputation errors relative to the baseline methods over all variables and accounts for uncertainty in the imputation process, thereby providing a more accurate measure of imputation error. We also found that MALA mixed better than RWM across most variables, achieving comparable accuracy while providing more consistent posterior exploration. Overall, these findings suggest that the tBayes-MICE framework represents a practical and efficient approach to time-series imputation, balancing increased accuracy with meaningful quantification of uncertainty in various environmental and clinical settings.

Multivariate Hawkes processes are a widely used class of self-exciting point processes, but maximum likelihood estimation naively scales as $O(N^2)$ in the number of events. The canonical linear exponential Hawkes process admits a faster $O(N)$ recurrence, but prior work evaluates this recurrence sequentially, without exploiting parallelization on modern GPUs. We show that the Hawkes process intensity can be expressed as a product of sparse transition matrices admitting a linear-time associative multiply, enabling computation via a parallel prefix scan. This yields a simple yet massively parallelizable algorithm for maximum likelihood estimation of linear exponential Hawkes processes. Our method reduces the computational complexity to approximately $O(N/P)$ with $P$ parallel processors, and naturally yields a batching scheme to maintain constant memory usage, avoiding GPU memory constraints. Importantly, it computes the exact likelihood without any additional assumptions or approximations, preserving the simplicity and interpretability of the model. We demonstrate orders-of-magnitude speedups on simulated and real datasets, scaling to thousands of nodes and tens of millions of events, substantially beyond scales reported in prior work. We provide an open-source PyTorch library implementing our optimizations.

This research considers a scalable inference for spatial data modeled through Gaussian intrinsic conditional autoregressive (ICAR) structures. The classical estimation method, restricted maximum likelihood (REML), requires repeated inversion and factorization of large, sparse precision matrices, which makes this computation costly. To sort this problem out, we propose a variational restricted maximum likelihood (VREML) framework that approximates the intractable marginal likelihood using a Gaussian variational distribution. By constructing an evidence lower bound (ELBO) on the restricted likelihood, we derive a computationally efficient coordinate-ascent algorithm for jointly estimating the spatial random effects and variance components. In this article, we theoretically establish the monotone convergence of ELBO and mathematically exhibit that the variational family is exact under Gaussian ICAR settings, which is an indication of nullifying approximation error at the posterior level. We empirically establish the supremacy of our VREML over MLE and INLA.

In the last decades, energy-based models (EBMs) have become an important class of probabilistic models in which a component of the likelihood is intractable and therefore cannot be evaluated explicitly. Consequently, parameter estimation in EBMs is challenging for conventional inference methods. In this work, we provide a unified framework that connects noise contrastive estimation (NCE), reverse logistic regression (RLR), multiple importance sampling (MIS), and bridge sampling within the context of EBMs. We further show that these methods are equivalent under specific conditions. This unified perspective clarifies relationships among existing methods and enables the development of new estimators, with the potential to improve statistical and computational efficiency. Furthermore, this study helps elucidate the success of NCE in terms of its flexibility and robustness, while also identifying scenarios in which its performance can be further improved. Hence, rather than being a purely descriptive review, this work offers a unifying perspective and additional methodological contributions. The MATLAB code used in the numerical experiments is also made freely available to support the reproducibility of the results.