We consider the problem of clustering nested or hierarchical data, where observations are grouped and there are both group-level and observation-level variables. In our motivating OneK1K dataset, observations consist of single-cell RNA-sequencing (scRNA-seq) data from 982 individuals (groups), totaling 1.27 million cells (observations), along with individual-specific genotype data. This type of data would enable the identification of cell types and the investigation of how genetic variations among individuals influence differences in cell-type profiles. Our goal, therefore, is to jointly cluster cells and individuals to capture the heterogeneity across both levels using cell-specific gene expressions as well as individual-specific genotypes. However, existing grouped clustering methods do not incorporate group-level variables, thereby limiting their ability to capture the heterogeneity of genotypes in our motivating application. To address this, we propose the Nested Atoms Model (NAM), a new Bayesian nonparametric approach that enables the desired two-layered clustering, accounting for both group-level and observation-level variables. To scale NAM for high-dimensional data, we develop a fast variational Bayesian inference algorithm. Simulations show that NAM outperforms existing methods that ignore group-level variables. Applied to the OneK1K dataset, NAM identifies clusters of genetically similar individuals with homogeneous cell-type profiles. The resulting cell clusters align with known immune cell types based on differential gene expression, underscoring the ability of NAM to capture nested heterogeneity and provide biologically meaningful insights.

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.

Preprocessing leakage arises when scaling, imputation, or other data-dependent transformations are estimated before resampling, inflating apparent performance while remaining hard to detect. We present fastml, an R package that provides a single-call interface for leakage-aware machine learning through guarded resampling, where preprocessing is re-estimated inside each resample and applied to the corresponding assessment data. The package supports grouped and time-ordered resampling, blocks high-risk configurations, audits recipes for external dependencies, and includes sandboxed execution and integrated model explanation. We evaluate fastml with a Monte Carlo simulation contrasting global and fold-local normalization, a usability comparison with tidymodels under matched specifications, and survival benchmarks across datasets of different sizes. The simulation demonstrates that global preprocessing substantially inflates apparent performance relative to guarded resampling. fastml matched held-out performance obtained with tidymodels while reducing workflow orchestration, and it supported consistent benchmarking of multiple survival model classes through a unified interface.

Conditional effects are commonly used measures for understanding how treatment effects vary across different groups, and are often used to target treatments/interventions to groups who benefit most. In this work we review existing methods and propose novel ones, focusing on the odds ratio (OR) and the risk ratio (RR). While estimation of the conditional average treatment effect (ATE) has been widely studied, estimators for the OR and RR lag behind, and cutting edge estimators such as those based on doubly robust transformations or orthogonal risk functions have not been generalized to these parameters. We propose such a generalization here, focusing on the DR-learner and the R-learner. We derive orthogonal risk functions for the OR and RR and show that the associated pseudo-outcomes satisfy second-order conditional-mean remainder properties analogous to the ATE case. We also evaluate estimators for the conditional ATE, OR, and RR in a comprehensive nonparametric Monte Carlo simulation study to compare them with common alternatives under hundreds of different data-generating distributions. Our numerical studies provide empirical guidance for choosing an estimator. For instance, they show that while parametric models are useful in very simple settings, the proposed nonparametric estimators significantly reduce bias and mean squared error in the more complex settings expected in the real world. We illustrate the methods in the analysis of physical activity and sleep trouble in U.S. adults using data from the National Health and Nutrition Examination Survey (NHANES). The results demonstrate that our estimators uncover substantial treatment effect heterogeneity that is obscured by traditional regression approaches and lead to improved treatment decision rules, highlighting the importance of data-adaptive methods for advancing precision health research.

Artificial intelligence (AI) is moving increasingly beyond prediction to support decisions in complex, uncertain, and dynamic environments. This shift creates a natural intersection with operations research and management sciences (OR/MS), which have long offered conceptual and methodological foundations for sequential decision-making under uncertainty. At the same time, recent advances in deep learning, including feedforward neural networks, LSTMs, transformers, and deep reinforcement learning, have expanded the scope of data-driven modeling and opened new possibilities for large-scale decision systems. This tutorial presents an OR/MS-centered perspective on deep learning for sequential decision-making under uncertainty. Its central premise is that deep learning is valuable not as a replacement for optimization, but as a complement to it. Deep learning brings adaptability and scalable approximation, whereas OR/MS provides the structural rigor needed to represent constraints, recourse, and uncertainty. The tutorial reviews key decision-making foundations, connects them to the major neural architectures in modern AI, and discusses leading approaches to integrating learning and optimization. It also highlights emerging impact in domains such as supply chains, healthcare and epidemic response, agriculture, energy, and autonomous operations. More broadly, it frames these developments as part of a wider transition from predictive AI toward decision-capable AI and highlights the role of OR/MS in shaping the next generation of integrated learning--optimization systems.

Partial observation is a pervasive obstacle in nonequilibrium physics: coarse graining may absorb hidden forcing into an apparently equilibrium-like reduced description, so a driven system can look reversible through the only variables one can measure. For scalar Gaussian observables of linear stochastic systems, no time-irreversibility statistic can detect the underlying drive. The Lucente--Crisanti ceiling constrains what one channel carries; what two channels carry is a different question, with a sharp closed-form answer. Two simultaneously observed channels retain an off-diagonal cross-spectral sector inaccessible to any scalar reduction; under channel-separable multiplicative structure the observed-channel response factors cancel identically, leaving a closed-form cross-spectral witness controlled only by the hidden spectrum, the loadings, and the innovation scales, strictly positive at every nonzero cross-coupling including at exact timescale coalescence where every scalar reduction is blind. Within general CSM this certifies shared hidden-sector drive; under the additional one-way coupling assumption the witness identifies the total entropy production rate at leading order with a square-root scaling.

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.

Since their introduction by Breiman (2001), permutation-based feature importance measures have been widely adopted. However, randomly permuting the entries of a dataset may create new points far from the original data or even "impossible data." In a permuted dataset, we may find children who are retired or individuals who graduated from high school before they were born (Mase et al. 2022, p. 1). Forcing ML models to make predictions at these points causes them to extrapolate, making explanations unreliable (Hooker et al. 2021). Every non-trivial permutation-based variable importance measure, including SHAP (Lundberg and Lee 2017), Knockoffs (Barber and Candés 2015), conditional model reliance (Fisher et al. 2019), and accumulated local effect (ALE) plots (Apley and Zhu 2020) suffer from this. We propose and compare three new strategies to address extrapolation issues. The first combines conditional model reliance from Fisher et al. (2019) with a Gaussian transformation. By mapping data quantiles to a Gaussian distribution and back, we adjust only the quantiles of point values, significantly reducing extrapolation. Under a Gaussian copula assumption for the feature distribution, we prove that the new data points follow the same probability distribution as the original data.

Generalized linear mixed-effects models (GLMMs) are widely used to analyze grouped and hierarchical data. In a GLMM, each response is assumed to follow an exponential-family distribution where the natural parameter is given by a linear function of observed covariates and a latent group-specific random effect. Since exact marginalization over the random effects is typically intractable, model parameters are estimated by maximizing an approximate marginal likelihood. In this paper, we replace the linear function with neural networks. The result is a more flexible model, the neural generalized mixed-effects model (NGMM), which captures complex relationships between covariates and responses. To fit NGMM to data, we introduce an efficient optimization procedure that maximizes the approximate marginal likelihood and is differentiable with respect to network parameters. We show that the approximation error of our objective decays at a Gaussian-tail rate in a user-chosen parameter. On synthetic data, NGMM improves over GLMMs when covariate-response relationships are nonlinear, and on real-world datasets it outperforms prior methods. Finally, we analyze a large dataset of student proficiency to demonstrate how NGMM can be extended to more complex latent-variable models.

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.