The Inference Report

Multicollinearity is a long lasting challenge in observational causal inference, especially in regressions -- highly correlated independent variables make it hard to isolate their individual impacts on outcomes of interest. While common solutions such as shrinkage estimators and principal component regressions are helpful in prediction problems, a crucial limitation hinders their applicability to causal inference problems -- they cannot provide the original causal relationships. To fill the gap, we present an innovative and intuitive solution, by employing hierarchical clustering to aggregate data in a way that effectively alleviates collinearity. This method is generally applicable to causal problems featuring multicollinearity. We use a marketing application to demonstrate how and why it works. Expenditures on different advertising channels often exhibit correlations, making it exceedingly difficult to separately measure their impact. Many previous studies proposed to leverage granular cross-sectional data for better identification but, to our knowledge, none explicitly addressed multicollinearity, which undermines causal identification even with granular data. We propose to hierarchically cluster geographic units based on marketing spend correlation to reduce collinearity, and to implement a Bayesian Marketing Mix Model with cluster-level data. Such clustering happens in two steps -- we first normalize and demean geo-level data to establish a common scale and to eliminate the common trends; we then calculate pairwise distance to summarize marketing spend correlation between geos and cluster the ones with moderate to strong correlation. Both descriptive evidence and regression analysis affirm that such hierarchical clustering effectively mitigates collinearity and facilitates the separate identification of the impact of different marketing channels.

Reliable generative AI models critically rely on expert human annotations to evaluate output quality, yet these "gold" labels are expensive to collect and limited in quantity. Organizations thus often turn to collecting vast but noisy "silver" labels from crowdsourced workers or vendor annotators as proxies for gold labels. Because gold remains the evaluation target, naively aggregating noisy silver labels may introduce bias, and estimators built on sparsely observed gold labels may have high variance to resolve the model performance gaps that guide practical decisions. Model evaluation has become an ongoing operational practice rather than a one-time exercise, with evaluation rounds repeating across model versions, releases, and content domains. A natural question is whether the previous historical evaluation data can be used to improve each new round of evaluation. We introduce HERO (History Enhanced RObust model evaluation), a novel framework that uses historical data to suppress bias (improve reliability) and reduce variance (improve sensitivity) in model performance evaluation. HERO calibrates silver labelers' performance learned from historical gold annotations, and stabilizes the resulting estimator by anchoring it to covariate information measured with high precision in the historical data. HERO can be broadly applied across multiple common evaluation tasks, and remains valid when only a subset of historical labelers appears in the current round. We establish conditions under which the bias and variance reductions hold, showcase HERO's performance in simulation studies, and demonstrate its effectiveness on real-world model evaluation benchmarking datasets.

As machine learning models and datasets continue to grow, developing complex models has become increasingly computationally demanding. Knowledge distillation reduces deployment cost by compressing a large, well-trained teacher model into a compact student model, but it does not address settings where constructing the teacher itself is the bottleneck. Motivated by this challenge, we introduce Knowledge Cascade (KCas), a reverse knowledge distillation framework that uses information from a small, inexpensive student model to guide the development of a more complex teacher model. Although this direction is counterintuitive because the teacher typically has greater representational capacity, we show that student-to-teacher transfer can be principled when supported by statistical scaling relationships. We first develop KCas for nonparametric multivariate functional estimation in reproducing kernel Hilbert spaces via smoothing splines, where selecting multiple smoothing parameters is a major computational bottleneck. KCas transfers student-selected smoothing parameters to the full-sample regime through asymptotic scaling laws, substantially reducing computational cost for high-dimensional and large-scale datasets while retaining theoretical guarantees. Beyond smoothing splines, we illustrate the same principle through kernel density estimation and deep learning hyperparameter transfer. Simulations and real-data experiments show that KCas achieves substantial computational savings while maintaining strong statistical performance, and can sometimes outperform the corresponding full-sample procedure.

Distribution shift between training and deployment is a pervasive challenge for modern AI systems. In many cases, the target marginals of covariates and response are known or specified through population-level observations, boundary conditions, properties of simulator configurations, or alignment-time distributional constraints. Such knowledge may provide valuable side information for regression estimation. We study this problem in the multivariate linear regression setting with a stable conditional mean $E[Y\mid X]$ across source and target, and identify the hybrid-loss estimator, which jointly incorporates both target marginals, as a benchmark target-aware estimator. Its direct computation, however, requires solving a coupled nonlinear optimization that is expensive at scale. Our main contribution is to develop and evaluate two computationally tractable alternatives: a constrained moment-matching estimator and a two-stage estimator that augments ordinary least squares with a calibration step. For all three estimators, we derive and compare closed-form asymptotic mean squared errors, yielding conditions under which the tractable alternatives match or closely approximate the hybrid benchmark, and regimes in which they do not. Monte Carlo experiments across three controlled shift regimes validate the theoretical results, investigate the accuracy-runtime tradeoffs among the three estimators, and translate into guidance on estimator choice. In particular, the two-stage estimator nearly matches the hybrid benchmark in the high signal-to-noise regime at essentially no additional cost, providing theoretical grounding for empirical observations in nonlinear settings.

Multi-cause observational studies contain information about unmeasured confounding through the dependence structure among causes. However, literal imputation of the unobserved confounder is often more complex than learning a lower-dimensional substitute score that preserves the shared assignment variation needed for stable causal adjustment. The deconfounder (Wang and Blei, 2019) and related substitute confounder methods exploit this idea, but flexible assignment models can fit the joint distribution of the causes while producing scores that over-encode the treatment vector, collapse overlap, or capture single-cause variation. We develop a Bayesian factor assignment framework for learning sparse substitute confounders that retain coarse multi-cause dependence with shrinkage priors. The theory is stated at the level of posterior concentration, factor score contraction, and overlap-preserving assignment geometry and therefore does not rely on a particular shrinkage prior. Under these conditions, the proposed regression-adjusted estimators are consistent for mean potential outcomes when the corresponding latent variable identification assumptions hold. Shrinkage priors provide a natural tool for latent structural learning: they favour low-dimensional factors supported by multiple causes, discourage effectively single-cause factors, and induce an ordering of the latent factors through progressive shrinkage. Synthetic experiments illustrate the roles of signal strength, outcome validity, and geometry-aware regularization. In an Alzheimer's Disease Neuroimaging Initiative (ADNI) baseline analysis, sparse substitute scores recover much of the adjustment obtained by directly conditioning on invasive cerebrospinal-fluid biomarkers, while collapse diagnostics identify when fitted factors reduce to individual observed measurements.

Offline policy learning has received growing attention in causal inference. The primary objective is to learn a policy (individualized treatment rule) as a mapping from covariates to treatment that maximizes the empirical welfare defined as the mean of scalar-valued potential outcomes. In this paper, we study offline policy learning with distribution-valued outcomes, where each potential outcome is a probability measure on $\mathbb{R}$ and the reward is defined through a utility functional applied to the Wasserstein barycenter of induced outcome distributions. We establish statistical guarantees for the policy learning framework based on both Inverse Probability Weighting (IPW) and Doubly Robust (DR) estimators. By handling the challenging uniform deviation over the product of the combinatorial policy class and the infinite-dimensional quantile domain, we prove that the finite-sample regret has leading dependence $\widetilde{\mathcal{O}}(\sqrt{\mathrm{N\text{-}dim}(Π)/N})$. In the one-dimensional Wasserstein setting and under the stated regularity conditions, the leading regret rate is still governed by the policy-class complexity. Moreover, we provide a minimax lower bound establishing the sharpness of the leading dependence on $N$ and $\mathrm{N\text{-}dim}(Π)$.

Organizations and researchers show increasing interest in using large language models (LLMs) in place of human participants in A/B tests, in the hope of experimenting faster and at lower cost. We study when a treatment effect estimated on LLM outcomes recovers the effect that would have been measured on the human population of interest. Distributional equivalence between LLM and human outcomes would make any standard estimator valid but is unrealistic. We therefore develop a statistical framework that adapts surrogate endpoint theory to LLMs. The framework shows that calibrating LLM outcomes to human outcomes identifies the average treatment effect under surrogacy and comparability conditions that are jointly weaker than distributional equivalence. When these conditions fail, the effect of interest is only partially identified, and we provide diagnostics that can falsify surrogacy on historical experiments together with a bound on the worst-case bias from limited overlap. We further show that the stochasticity inherent to LLMs introduces both bias and variance, but using an average of multiple draws as the surrogate mitigates both. We illustrate the methods and theory in simulations and an application to A/B tests on Upworthy headlines. A central takeaway from our work is that the validity of LLM outcomes as surrogates can only be falsified for past treatments and never verified for new ones, so human experiments remain indispensable for novel interventions. We discuss the role of LLM choice, prompting, and temperature as design variables, and how to size human experiments for validation.

We introduce biarchetype analysis for the first time in the context of univariate functional data. This unsupervised methodology extends archetype analysis by simultaneously identifying archetypal structures across both the cases (countries, in our application) and the temporal argument. Both cases and time points are expressed as mixtures of biarchetypes, yielding a concise and highly interpretable representation of complex functional observations. Although biarchetype analysis is not intended as a clustering technique, it offers superior interpretability compared with biclustering approaches, as it is based on extreme, representative patterns rather than average centroids, thereby enhancing human comprehension. We apply the proposed method to 10-year government bond yields of European countries over the period 2001-2025. The results identify three distinct time regimes (the pre-crisis period, the euro-area sovereign debt crisis, and the post-crisis period), and reveal Germany, Greece, and Hungary as country archetypes.

Finding D-optimal designs for generalized linear models (GLMs) is challenging due to the dependence of the Fisher information matrix on unknown parameters and the lack of closed-form solutions, particularly when input factors include both discrete and continuous variables. Although classical algorithms and recent metaheuristic approaches have offered partial solutions, there remains a need for robust and computationally efficient methods. In this paper, we propose a penalized Particle Swarm Optimization (PSO) approach, named $p$-PSO. Here we introduce a new, general-purpose penalty formulation for constrained optimization and demonstrate its effectiveness in optimal design problems. The formulation is algorithm-agnostic and applicable to a broad class of black-box optimization methods. Results show that the method is highly efficient, with its primary contribution being a penalty formulation that enables the direct use of an off-the-shelf PSO algorithm and extends naturally to more general constrained optimization tasks.

We develop a new, differentially private mean estimator called the balloon mean. The main features of the balloon mean are that it is computationally tractable and enjoys robustness to outlying observations. It is based on an iterative clipping procedure over expanding Mahalanobis balls, or ``balloons.'' The method satisfies zero-concentrated differential privacy and depends on a small number of interpretable tuning parameters. We provide theoretical guarantees under heavy-tailed and contaminated elliptical models, characterizing its statistical performance and robustness to outliers. Extensive simulations demonstrate that the balloon mean is robust to heavy-tailed and contaminated data, and outperforms existing differentially private mean estimators in contaminated settings.

There is a proliferation of work arguing for the use of synthetic data in scientific research. For example, social scientists are arguing for the use of LLM-generated "silicon samples" in pilot studies; AI evaluations increasingly rely on "LLM-as-a-judge" outputs; and proteomics research is accelerated by generative models that produce synthetic protein structures. These developments raise an intriguing possibility: synthetic data may help researchers ask more questions, run more studies, and accelerate discovery. But they also raise a fundamental concern: synthetic data can be biased, noisy, and misspecified. In this work, we propose statistical principles for using synthetic data in scientific research with provable validity guarantees. The key insight is a new technical condition that we call task exchangeability. Informally, this is a requirement that the researcher can identify historical tasks, for which real data is available, such that their current task of interest is exchangeable with the historical tasks in an appropriate mathematical sense. We develop methods for valid inference under task exchangeability, together with extensions that provide guarantees even beyond exchangeability. We demonstrate the framework on public opinion surveys with silicon samples and AI evaluation with autoraters.

Variable importance produced by Random Forests (RF) is used widely in statistical data analysis, and has played an important role in a variety of tasks such as assisting model interpretation, model selection and diagnosis, and cost-bounded learning etc. However, the calculation of variable importance in RF does not take into account of the correlations among variables, and variables that are correlated to many other variables tend to receive a lower importance index or being completely masked (i.e., with an importance index near zero) by other strongly correlated variables. To prevent influence from unwanted correlated variables in calculating variable importance, we propose to group variables by their conditional correlations (conditional on the response variable). We explore two computationally efficient options, with one grouping variables individually, and then separates the variable of interest from all correlated variables, while the other uses clustering to group variables according to their pair-wise conditional correlations. Our experiments show that both lead to sensible corrections to the importance of variables.

We propose the data augmented bootstrap (DAB), a framework for constructing confidence intervals from approximately invariant transformations of the data. As special cases, DAB recovers popular methods that rely on exact group symmetries, such as conformal prediction, wild bootstrap for Maximum Mean Discrepancy U-statistics and the recently proposed SymmPI. Meanwhile, DAB also recovers the classical bootstrap method, which exploits the dataset's approximate invariance under uniform sampling of data indices as the dataset size grows. For all DAB methods, we establish theoretical coverage results that interpolate between finite-sample and asymptotic guarantees according to the strength of the invariance, and without assuming a group structure. The approximate invariance is measured in the Kolmogorov distance and, for statistics that satisfy Gaussian universality, reduces to conditional mean and variance matching. This allows us to incorporate data augmentation (DA), a widely used machine learning heuristic based on approximate invariances, into known statistical methods. We empirically test the performance of incorporating DA into bootstrap, wild bootstrap and conformal prediction for simulated settings as well as for image, language and scientific data.

Causal discovery from multivariate time series is challenging when causal effects may occur both across time and within the same sampling interval. This issue is especially important in applications such as neuroscience, where the sampling rate may be coarse relative to the underlying dynamics and contemporaneous effects need not form an acyclic graph. We study causal discovery in linear Gaussian structural VAR models under an equal noise variance assumption, meaning that the structural noise terms have a common variance. Unlike the DAG-based cross-sectional equal noise variance setting, the time-series setting considered here does not generally yield point identification of a unique causal graph. Instead, multiple structural VAR parameterizations can induce the same stationary observed process law. We introduce a notion of observational equivalence tailored to this setting and show that the corresponding equivalence class is characterized by orthogonal transformations of the structural equations together with a global positive scale. This characterization leads to an equivalence-aware model discrepancy, the observational alignment discrepancy, which compares structural models modulo transformations that preserve the observed law. Building on this theory, we propose ENVAR, a sparsity-based procedure that searches over the induced observational equivalence class for a sparse normalized structural representative. We evaluate the proposed methodology on synthetic structural VAR data and on an fMRI dataset.

Large-scale hypothesis testing is central to modern science, where controlling the False Discovery Rate (FDR) has become the standard approach to managing false positives across many simultaneous tests. Hypotheses rarely exist in isolation; they often exhibit structure through proximity, connectivity, or hierarchy. This structure represents both a challenge and an opportunity: while classical methods treat these dependencies as obstacles requiring conservative correction, leveraging them can substantially increase discovery power. Here, we reframe structured FDR control as a regularized learning problem. By optimizing within a suitable Reproducing Kernel Hilbert Space (RKHS), we introduce a framework that unifies continuous domains, graphs, and hierarchies under a single algorithm through kernel choice alone. This formulation enables smooth solutions in place of the piecewise-constant fits of prior methods, principled likelihood-based hyperparameter selection rather than heuristic tuning, and inference at unobserved locations which in turn supports sample-efficient experimental design. Building on this estimator, we provide two decision rules which we prove to control the FDR. We validate our method on two sources: spatial locations derived from high-dimensional real-world datasets, and a differential gene expression task utilizing protein-protein interaction graphs.

Accurate estimates of item difficulty are essential for valid assessment and effective adaptive learning. However, for newly created tasks, response data are typically unavailable. Pretesting and expert judgement can be costly and slow, while machine learning methods often require large labelled training datasets. Recent work suggests that large language models (LLMs) may help. However, there is limited evidence on the elicitation procedures and prompt configurations used to emulate experts for difficulty estimation. This study addresses this gap by evaluating three off-the-shelf LLMs as difficulty raters for newly created items without access to response data. Using an item bank from an online learning system, the study examined 6 domains of primary-school mathematics, with empirical difficulty estimates treated as empirical reference. The study used a full factorial design crossing three factors: judgement format (absolute vs pairwise), decision type (hard decisions vs token-probability-based estimates), and prompting strategy (zero-shot vs few-shot). LLM-derived difficulty estimates were compared with empirical difficulties using Spearman rank correlations. Across domains, LLM-based estimates exhibited moderate to strong positive correlations with empirical item difficulties. For simpler arithmetic tasks, some configurations approached the upper end of the accuracy range reported for human experts in previous research. Pairwise comparison consistently outperformed absolute judgement in the absence of additional refinements. However, when token-level probabilities were incorporated and examples of items with known empirical difficulty were provided, the absolute judgement configuration likewise demonstrated moderate-to-high alignment. The study positions LLMs as a promising tool for initial item calibration and offers insights into effective workflow configuration.

Deep learning excels at prediction but often lacks finite-sample guarantees and calibrated uncertainty; RKHS (Reproducing Kernel Hilbert Space)-based methods provide those guarantees but struggle to adapt in high dimensions. We propose Wahkon, a deep RKHS superposition network that unifies Kolmogorov's superposition principle with RKHS regularization in the smoothing-spline tradition of Wahba. This yields a finite-dimensional deep representer theorem that makes training tractable and provides explicit layerwise complexity control. We show the penalized estimator is exactly the MAP (maximum a posteriori) estimate under a hierarchical Gaussian-process prior, extending the spline/GP duality to deep compositions. Using metric-entropy arguments, we establish minimax-optimal convergence rates under mild smoothness and clarify how depth and width trade off with regularity. Empirically, Wahkon outperforms multilayer perceptrons, Neural Tangent Kernels, and Kolmogorov--Arnold Networks across simulation benchmarks and a single-cell CITE-seq study. By unifying Kolmogorov's superposition principle with RKHS regularization, Wahkon delivers accuracy, interpretability, and statistical rigor in a single framework.

Background: External validation is essential for assessing the transportability of predictive models. However, its interpretation is often confounded by differences between external and development populations. This study introduces a framework to distinguish model deficiencies from case-mix effects. Method: We propose a framework that quantifies each external patient's similarity to the development data and measures performance in subgroups with varying levels of alignment to the development distribution. We use generative models, specifically autoencoders, to estimate similarity, offering a more flexible alternative to traditional linear approaches and enabling validation without sharing the original development data. The utility of autoencoder-based similarity measure is demonstrated using synthetic data, and the framework's application is illustrated using data from the Netherlands Heart Registration (NHR) to predict mortality after transcatheter aortic valve implantation. Results: Our framework revealed substantial variation in model performance across similarity-defined subgroups, differences that remain hidden under conventional external validation yet can meaningfully alter conclusions. In several settings, conventional external validation suggested poor overall performance. However, after accounting for differences in patient characteristics, for some sub-groups, the model performance was consistent with internal validation results. Conversely, apparently acceptable overall performance could mask clinically relevant performance deficits in specific subgroups. Conclusion: The proposed framework enhances the interpretability of external validation by linking model performance to population alignment with the development data. This provides a more principled basis for deciding whether a model is transportable and to which patients it can be safely applied.

Random directed acyclic graphs (DAGs) based on imposing an order on Erdős-Rényi and scale free random graphs are widely used for evaluating causal discovery algorithms. We show that in such DAGs, the set of nodes reachable via open paths, termed relatives, increases monotonically along the causal order. We assess the prevalence of this pattern numerically, and demonstrate that it can be exploited for causal order recovery via sorting by the estimated number of relatives. We note that many simulations in the literature feature settings where this yields an excellent proxy for the causal order, and show that a strict increase of relatives along the causal order leads to a singular Markov equivalence class. We propose sampling time-series DAGs as a possible alternative and discuss implications for causal discovery algorithms and their evaluation on synthetic data.

In many scientific domains, including experimentation, researchers rely on measurements of proxy outcomes to achieve faster and more frequent reads, especially when the primary outcome of interest is challenging to measure directly. While proxies offer a more readily accessible observation for inference, the ultimate goal is to draw statistical inferences about the primary outcome parameter and proxy data are typically imperfect in some ways. To correct for these imperfections, current statistical inference methods often depend on strict identifying assumptions (such as surrogacy, covariate/label shift, or missingness assumptions). These assumptions can be difficult to validate and may be violated by various additional sources of distribution shift, potentially leading to biased parameter estimates and miscalibrated uncertainty quantification. We introduce an estimate-level framework, inspired by domain adaptation techniques, to empirically calibrate proxy-based inference. This framework models the proxy-primary metric discrepancy as a random effect at the parameter level, estimating its distribution from aggregated historical observations across past domains (e.g., experiments, time periods, or distinct segments). This method avoids the requirement for retaining individual-level response data. Additionally, this adjustment can be layered on top of existing proxy-correction methods (such as prediction-powered inference or importance weighting) to account for additional biases not addressed by those corrections. To manage uncertainty when the number of historical domains is limited, we provide both a method-of-moments estimator and a domain bootstrap procedure. We further validate this approach using publicly available datasets and real-world experiments.

We study the problem of denoising observations \(Y_i=X_i+Z_i\), where the latent variables \(X_i\) are sampled from a low-dimensional manifold in \(\mathbb{R}^n\) and the noise variables \(Z_i\) are isotropic Gaussian. We propose a convex-relaxation estimator that first reduces dimension by principal component analysis and then projects the observations onto the convex hull of the projected latent manifold. We construct a statistical oracle that estimates its supporting hyperplanes from empirical Gaussian tail probabilities of the noisy sample. Under a lower-mass condition on the latent distribution, we prove finite-sample guarantees for the oracle and derive error bounds for the resulting denoiser. The analysis combines risk bounds for least-squares projection under convex constraints with entropy bounds for convex hulls. We also verify the assumptions of the framework for a Cryo-Electron Microscopy observation model by establishing suitable covering number and Lipschitz estimates for the associated group action and imaging operators.

Doubly Robust (DR) estimation of treatment effect relies on an untestable assumption that is the absence of unobserved confounding. This assumption is par- ticularly problematic in the context of healthcare research, where variables like pre- scription refill rates serve as proxies for unobserved behaviors such as medication adherence. These proxy variables are often endogenous, exhibiting correlation with the regression error term due to unmeasured confounding or measurement error. We propose a copula-corrected doubly robust estimator that addresses endogeneity in both the treatment and outcome models without requiring instrumental variables. Gaussian copulas model the joint distribution of endogenous covariates and the error term, enabling consistent estimation while preserving the doubly robust property that requires correct specification of either the treatment or outcome model, not both. Monte Carlo simulations demonstrate that naive DR estimation exhibits substantial bias under endogeneity, whereas our corrected estimator recovers unbiased treatment effects across different data-generating processes. We apply our method to examine the effect of nutritional counseling on blood pressure using the National Health and Nutrition Examination Survey (NHANES) data. Naive DR estimation suggests counseling is associated with increased blood pressure. After copula correction, this effect becomes statistically insignificant, consistent with literature showing modest effects of nutri- Counseling in reducing blood pressure. Our methodology provides researchers with a practical tool for obtaining treatment effects in the presence of endogeneity.

Variable selection in linear regression models has been a problem since hypothesis testing began. Which variables to include or exclude from a model is not an easy task. Techniques such as Forward, Back ward, Stepwise Regression sequentially add or delete variables from a model. Penalized likelihood methods such as AIC, BIC, etc. seek to choose variables that have a significant contribution to the likelihood. Penalized sum of square methods such as LASSO and Elastic Net have been used to penalize small coefficients to only allow variables with large coefficients in the model. This work introduces an Artificial Intelligence approach to model selection where an ANN is trained to determine the significance of the variables based on OLS estimates. A simulation study shows the accuracy across various sample sizes and variances. Furthermore, a simulation study is conducted to compare the performance of the approach against Forward, Backward, AIC, BIC and LASSO. The approach is illustrated using a dataset from the World Health Organization regarding Life Expectancy. A github link is provided to the pretrained ANN that can handle up to 100 predictor variables, the original WHO dataset and the subset used in this work.

Fractionally supervised classification (FSC) offers a flexible framework for combining labeled and unlabeled data in model-based classification, but existing formulations assume simple random sampling. In many applications, however, the retained observation is an extreme order statistic from a set rather than a randomly selected unit. This is particularly appealing when the target population is rare, since maxima nomination sampling (NS) can enrich the sample with the most informative observations, as in screening, environmental monitoring, repeated testing, and reliability studies. Under such designs, the likelihood function changes fundamentally, and the usual FSC EM construction is no longer valid. We develop FSC for nominated samples by introducing a latent representation that accounts for both the class membership of the observed maximum and the latent composition of the remaining units in the set. The resulting method yields a proper EM algorithm and a coherent weighted-likelihood FSC procedure for NS data. We present the methodology in general form, illustrate it for a rare-event contamination normal mixtures, and show through simulation that it substantially improves on the misspecified alternative by ignoring the extra rank information of such data. A real-data analysis demonstrates its practical value.

Nonlinear Mixed Effects models (NLME) models are widely used in pharmacometrics and related fields to analyze hierarchical and longitudinal data. However, as the number of parameters and random effects increases, traditional methods for maximizing the marginal likelihood become computationally expensive. This paper explores the Variational Expectation Maximization (VEM) algorithm, a scalable alternative for fitting NLME models. Originally introduced in the context of probabilistic graphical models and later popularized through variational autoencoders, VEM has not been extensively applied to NLME modeling. By leveraging flexible variational families and reverse-mode automatic differentiation, VEM can efficiently maximize the marginal likelihood, scaling to NLME models with over 15,000 population parameters. This work provides a detailed description of VEM, compares it to other NLME fitting algorithms, and highlights its scalability through computational experiments. Using the Pumas statistical software, we fit two test models: 1) a standard warfarin model, and 2) a DeepNLME Friberg model with 15,410 population parameters and 16 random effects. The warfarin model was fitted to completion to demonstrate the correctness of VEM, while the DeepNLME Friberg model was fitted for a limited number of iterations to measure the time per iteration and demonstrate VEM's scalability.

Safety-critical prediction systems, such as autonomous vehicles, weather forecasters, and medical monitors, commonly rely on probabilistic forecasters. These forecasters make predictions about possible future outcomes, and their quality and robustness needs to be validated and certified. Often, only accuracy -- the mean of the predictions -- is evaluated against true outcomes. However, for safety-critical scenarios and decision making under uncertainty, the full distributional properties of the forecasts should be checked: do the observed prediction errors actually follow the forecasted probability distributions? To this end, we introduce a framework for calibration checks: statistical tests that validate distributional properties of forecasts when measured over many samples. In order to support ease-of-use in real-world operations, these checks produce a single accept/reject decision for data collected from a forecaster. This contrasts typical calibration calculations which produce one or multiple continuous calibration scores and require expertise to implement in a validation workflow. We further support operationalization by introducing modifications to calibration testing that (a) reject only overconfident predictions, allowing for pessimistic or cautious predictions in safety-critical settings, and (b) tolerate small, operationally acceptable deviations even for large numbers of validation samples. We organize the calibration checking process into a modular pipeline comprising four steps: (i) the data model, (ii) the chosen metric, (iii) the hypothesis formulation, and (iv) the testing procedure. Each step consists of independently swappable components, thereby supporting a large variety of possible use-cases and trade-offs. We demonstrate the applicability of the framework on two complementary example problems, weather forecasting and robot pose estimation.

Synthetic data offers a promising tool for privacy-preserving data release, augmentation, and simulation, but its use in causal inference requires preserving more than predictive fidelity. We show that fully generative tabular synthesizers, including GAN- and LLM-based models, can achieve strong train-on-synthetic-test-on-real performance while substantially distorting causal estimands such as the average treatment effect (ATE). We formalize this failure through sensitivity and tradeoff results showing that ATE preservation requires control of both the generated covariate law and the treatment-effect contrast in the outcome regression. Motivated by this observation, we propose a hybrid synthetic-data framework that generates covariates separately from the treatment and outcome mechanisms, using distance-to-closest-record diagnostics to monitor covariate synthesis and separately learned nuisance models to construct (W, A, Y) triplets. We further study targeted synthetic augmentation for practical positivity problems and characterize when added overlap support helps by improving conditional-effect estimation more than it shifts the covariate distribution. Finally, we develop a synthetic simulation engine for pre-analysis estimator evaluation, enabling finite-sample comparison of OR, IPW, AIPW, and TMLE under realistic covariate structure. Across experiments, hybrid synthetic data substantially improve ATE preservation relative to fully generative baselines and provide a practical diagnostic tool for robust causal analysis.

When, in terms of the number of data points, the size of a dataset exceeds available computing resources, or when labeling is expensive, an attractive solution consists of selecting only some of the data points (subdata) for further consideration. A central question for selecting subdata of size $n$ from $N$ available data points is which $n$ points to select. While an answer to this question depends on the objective, one approach for a parametric model and a focus on parameter estimation is to select subdata that retains maximal information. Identifying such subdata is a classical NP-hard problem due to its inherent discreteness. Based on optimal approximate design theory, we develop a new methodology for information-based subdata selection, resulting in subdata that approaches the optimal solution. To achieve this, we develop a novel algorithm that applies to a general model, accommodates arbitrary choices of $N$ and $n$, and supports multiple optimality criteria, and we prove its convergence. Moreover, the new methodology facilitates an assessment of the efficiency of subdata selected by any method by obtaining tight lower and upper bounds for the efficiency. We show that the subdata obtained through the new methodology is highly efficient and outperforms all existing methods.

Predictions from machine learning algorithms can vary across random seeds, inducing instability in downstream debiased machine learning estimators. We formalize random seed stability via a concentration condition and prove that subbagging guarantees stability for any bounded-outcome regression algorithm. We introduce a new cross-fitting procedure, adaptive cross-bagging, which simultaneously eliminates seed dependence from both nuisance estimation and sample splitting in debiased machine learning. Numerical experiments confirm that the method achieves the targeted level of stability whereas alternatives do not. Our method incurs a small computational penalty relative to standard practice whereas alternative methods incur large penalties.

Targeted amplicon panels are widely used in oncology diagnostics, but providing per-gene performance guarantees for copy number variant (CNV) detection remains challenging due to amplification artifacts, process-mismatch heterogeneity, and limited validation sample sizes. While Bayesian CNV callers naturally quantify per-sample uncertainty, translating this into the frequentist population-level guarantees required for clinical validation, coverage rates, false-positive bounds, and minimum detectable copy-number changes, is a fundamentally different inferential problem. We show empirically that even robust Bayesian credible intervals, including coarsened posteriors and sandwich-adjusted intervals, are severely miscalibrated on panels with small amplicon counts per gene. To address this, we propose a hybrid framework that evaluates Bayesian posterior functionals on validation samples and models the resulting squared losses with a Gamma distribution, yielding tolerance intervals with valid frequentist coverage. Three components make the method practical under real-world constraints: (1) imputation that removes the influence of true CNV-positive samples without requiring known ground truth, (2) regularization to address small sample variability, and (3) evidence-based stratification on the log model evidence to accommodate non-exchangeable noise profiles arising from process mismatch. Evaluated on two targeted amplicon panels using leave-one-out cross-validation, the proposed method achieves single-digit mean absolute coverage error across all genes under both process-matched and unmatched conditions, whereas Bayesian comparators exhibit mean absolute errors exceeding 60\% on clinically relevant genes such as ERBB2.