Foundation models for biology and physics optimize predictive accuracy, but their internal representations systematically fail to preserve the continuous geometry of the systems they model. We identify the root cause: the Geometric Alignment Tax, an intrinsic cost of forcing continuous manifolds through discrete categorical bottlenecks. Controlled ablations on synthetic dynamical systems demonstrate that replacing cross-entropy with a continuous head on an identical encoder reduces geometric distortion by up to 8.5x, while learned codebooks exhibit a non-monotonic double bind where finer quantization worsens geometry despite improving reconstruction. Under continuous objectives, three architectures differ by 1.3x; under discrete tokenization, they diverge by 3,000x. Evaluating 14 biological foundation models with rate-distortion theory and MINE, we identify three failure regimes: Local-Global Decoupling, Representational Compression, and Geometric Vacuity. A controlled experiment confirms that Evo 2's reverse-complement robustness on real DNA reflects conserved sequence composition, not learned symmetry. No model achieves simultaneously low distortion, high mutual information, and global coherence.

Aligning language models with human preferences is essential for ensuring their safety and reliability. Although most existing approaches assume specific human preference models such as the Bradley-Terry model, this assumption may fail to accurately capture true human preferences, and consequently, these methods lack statistical consistency, i.e., the guarantee that language models converge to the true human preference as the number of samples increases. In contrast, direct density ratio optimization (DDRO) achieves statistical consistency without assuming any human preference models. DDRO models the density ratio between preferred and non-preferred data distributions using the language model, and then optimizes it via density ratio estimation. However, this density ratio is unstable and often diverges, leading to training instability of DDRO. In this paper, we propose a novel alignment method that is both stable and statistically consistent. Our approach is based on the relative density ratio between the preferred data distribution and a mixture of the preferred and non-preferred data distributions. Our approach is stable since this relative density ratio is bounded above and does not diverge. Moreover, it is statistically consistent and yields significantly tighter convergence guarantees than DDRO. We experimentally show its effectiveness with Qwen 2.5 and Llama 3.

Quasi-experimental evaluations are central for generating real-world causal evidence and complementing insights from randomized trials. The regression discontinuity design (RDD) is a quasi-experimental design that can be used to estimate the causal effect of treatments that are assigned based on a running variable crossing a threshold. Such threshold-based rules are ubiquitous in healthcare, where predictive and prognostic biomarkers frequently guide treatment decisions. However, standard RD estimators rely on complete outcome data, an assumption often violated in time-to-event analyses where censoring arises from loss to follow-up. To address this issue, we propose a nonparametric approach that leverages doubly robust censoring corrections and can be paired with existing RD estimators. Our approach can handle multiple survival endpoints, long follow-up times, and covariate-dependent variation in survival and censoring. We discuss the relevance of our approach across multiple areas of applications and demonstrate its usefulness through simulations and the prostate component of the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial where our new approach offers several advantages, including higher efficiency and robustness to misspecification. We have also developed an open-source software package, $\texttt{rdsurvival}$, for the $\texttt{R}$ language.

We study robust regression under a contamination model in which covariates are clean while the responses may be corrupted in an adaptive manner. Unlike the classical Huber's contamination model, where both covariates and responses may be contaminated and consistent estimation is impossible when the contamination proportion is a non-vanishing constant, it turns out that the clean-covariate setting admits strictly improved statistical guarantees. Specifically, we show that the additional information in the clean covariates can be carefully exploited to construct an estimator that achieves a better estimation rate than that attainable under Huber contamination. In contrast to the Huber model, this improved rate implies consistency even when the contamination is a constant. A matching minimax lower bound is established using Fano's inequality together with the construction of contamination processes that match $m> 2$ distributions simultaneously, extending the previous two-point lower bound argument in Huber's setting. Despite the improvement over the Huber model from an information-theoretic perspective, we provide formal evidence -- in the form of Statistical Query and Low-Degree Polynomial lower bounds -- that the problem exhibits strong information-computation gaps. Our results strongly suggest that the information-theoretic improvements cannot be achieved by polynomial-time algorithms, revealing a fundamental gap between information-theoretic and computational limits in robust regression with clean covariates.

Damped sinusoidal oscillations are widely observed in many physical systems, and their analysis provides access to underlying physical properties. However, parameter estimation becomes difficult when the signal decays rapidly, multiple components are superposed, and observational noise is present. In this study, we develop an autoencoder-based method that uses the latent space to estimate the frequency, phase, decay time, and amplitude of each component in noisy multi-component damped sinusoidal signals. We investigate multi-component cases under Gaussian-distribution training and further examine the effect of the training-data distribution through comparisons between Gaussian and uniform training. The performance is evaluated through waveform reconstruction and parameter-estimation accuracy. We find that the proposed method can estimate the parameters with high accuracy even in challenging setups, such as those involving a subdominant component or nearly opposite-phase components, while remaining reasonably robust when the training distribution is less informative. This demonstrates its potential as a tool for analyzing short-duration, noisy signals.

We consider the problem of conditional independence (CI) testing and adopt a kernel-based approach. Kernel-based CI tests embed variables in reproducing kernel Hilbert spaces, regress their embeddings on the conditioning variables, and test the resulting residuals for marginal independence. This approach yields tests that are sensitive to a broad range of conditional dependencies. Existing methods, however, rely heavily on kernel ridge regression, which is computationally expensive when properly tuned and yields poorly calibrated tests when left untuned, which limits their practical usefulness. We propose the Generalised Kernel Covariance Measure (GKCM), a regression-model-agnostic kernel-based CI test that accommodates a broad class of regression estimators. Building on the Generalised Hilbertian Covariance Measure framework (Lundborg et al., 2022), we characterise conditions under which GKCM satisfies uniform asymptotic level guarantees. In simulations, GKCM paired with tree-based regression models frequently outperforms state-of-the-art CI tests across a diverse range of data-generating processes, achieving better type I error control and competitive or superior power.

This paper studies the problem of recovering a hidden vertex correspondence between two correlated graphs when both edge weights and node features are observed. While most existing work on graph alignment relies primarily on edge information, many real-world applications provide informative node features in addition to graph topology. To capture this setting, we introduce the featured correlated Gaussian Wigner model, where two graphs are coupled through an unknown vertex permutation, and the node features are correlated under the same permutation. We characterize the optimal information-theoretic thresholds for exact recovery and partial recovery of the latent mapping. On the algorithmic side, we propose QPAlign, an algorithm based on a quadratic programming relaxation, and demonstrate its strong empirical performance on both synthetic and real datasets. Moreover, we also derive theoretical guarantees for the proposed procedure, supporting its reliability and providing convergence guarantees.

Many data-driven decision problems are formulated using a nominal distribution estimated from historical data, while performance is ultimately determined by a deployment distribution that may be shifted, context-dependent, partially observed, or stress-induced. This tutorial presents modern generative models, particularly flow- and score-based methods, as mathematical tools for constructing decision-relevant distributions. From an operations research perspective, their primary value lies not in unconstrained sample synthesis but in representing and transforming distributions through transport maps, velocity fields, score fields, and guided stochastic dynamics. We present a unified framework based on pushforward maps, continuity, Fokker-Planck equations, Wasserstein geometry, and optimization in probability space. Within this framework, generative models can be used to learn nominal uncertainty, construct stressed or least-favorable distributions for robustness, and produce conditional or posterior distributions under side information and partial observation. We also highlight representative theoretical guarantees, including forward-reverse convergence for iterative flow models, first-order minimax analysis in transport-map space, and error-transfer bounds for posterior sampling with generative priors. The tutorial provides a principled introduction to using generative models for scenario generation, robust decision-making, uncertainty quantification, and related problems under distributional shift.

Learning the potentials of interacting particle systems is a fundamental task across various scientific disciplines. A major challenge is that unlabeled data collected at discrete time points lack trajectory information due to limitations in data collection methods or privacy constraints. We address this challenge by introducing a trajectory-free self-test loss function that leverages the weak-form stochastic evolution equation of the empirical distribution. The loss function is quadratic in potentials, supporting parametric and nonparametric regression algorithms for robust estimation that scale to large, high-dimensional systems with big data. Systematic numerical tests show that our method outperforms baseline methods that regress on trajectories recovered via label matching, tolerating large observation time steps. We establish the convergence of parametric estimators as the sample size increases, providing a theoretical foundation for the proposed approach.

We study privacy-preserving sparse linear regression in the high-dimensional regime, focusing on the LASSO estimator. We analyze two widely used mechanisms for differential privacy: output perturbation, which injects noise into the estimator, and objective perturbation, which adds a random linear term to the loss function. Using approximate message passing (AMP), we characterize the typical behavior of these estimators under random design and privacy noise. To quantify privacy, we adopt typical-case measures, including the on-average KL divergence, which admits a hypothesis-testing interpretation in terms of distinguishability between neighboring datasets. Our analysis reveals that sparsity plays a central role in shaping the privacy-accuracy trade-off: stronger regularization can improve privacy by stabilizing the estimator against single-point data changes. We further show that the two mechanisms exhibit qualitatively different behaviors. In particular, for objective perturbation, increasing the noise level can have non-monotonic effects, and excessive noise may destabilize the estimator, leading to increased sensitivity to data perturbations. Our results demonstrate that AMP provides a powerful framework for analyzing privacy-accuracy trade-offs in high-dimensional sparse models.