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.

Toaddressthesechallenges,weproposeMiSO(MicroStimulationOptimization), a closed-loop stimulation framework to drive neural population activity toward specified states by optimizing over a large stimulation parameter space.

Vision Transformers (ViTs) have recently achieved comparable or superior performance to Convolutional neural networks (CNNs) in computer vision. This empirical breakthrough is even more remarkable since ViTs discards spatial information by mixing patch embeddings and positional encodings and do not embed any visual inductive bias (e.g.\ spatial locality). Yet, recent work showed that while minimizing their training loss, ViTs specifically learn spatially delocalized patterns. This raises a central question: how do ViTs learn this pattern by solely minimizing their training loss using gradient-based methods from \emph{random initialization}? We propose a structured classification dataset and a simplified ViT model to provide preliminary theoretical justification of this phenomenon. Our model relies on a simplified attention mechanism --the positional attention mechanism-- where the attention matrix solely depends on the positional encodings. While the problem admits multiple solutions that generalize, we show that our model implicitly learns the spatial structure of the dataset while generalizing. We finally prove that learning the structure helps to sample-efficiently transfer to downstream datasets that share the same structure as the pre-training one but with different features. We empirically verify that ViTs using only the positional attention mechanism perform similarly to the original one on CIFAR-10/100, SVHN and ImageNet.

Multivariate time series forecasting is of central importance in modern intelligent decision systems. The dynamics of multivariate time series are jointly characterized by temporal dependencies and spatial correlations. Hence, it is equally important to build the forecasting models from both perspectives. The real-world multivariate time series data often presents spatial correlations that show structures and evolve dynamically. To capture such dynamic spatial structures, the existing forecasting approaches often rely on a two-stage learning process (learning dynamic series representations and then generating spatial structures), which is sensitive to the small time-window input data and has high variance. To address this, we propose a novel forecasting model with a structured matrix basis. At its core is a dynamic spatial structure generation function whose output space is well-constrained and the generated structures have lower variance, meanwhile, it is more expressive and can offer interpretable dynamics. This is achieved via a novel structured parameterization and imposing structure regularization on the matrix basis. The resulting forecasting model can achieve up to $8.5\%$ improvements over the existing methods on six benchmark datasets, and meanwhile, it enables us to gain insights into the dynamics of underlying systems.

Representation alignment (REPA) guides generative training by distilling representations from a strong, pretrained vision encoder to intermediate diffusion features. We investigate a fundamental question: what aspect of the target representation matters for generation, its \textit{global} \revision{semantic} information (e.g., measured by ImageNet-1K accuracy) or its spatial structure (i.e. pairwise cosine similarity between patch tokens)? Prevalent wisdom holds that stronger global semantic performance leads to better generation as a target representation. To study this, we first perform a large-scale empirical analysis across 27 different vision encoders and different model scales. The results are surprising; spatial structure, rather than global performance, drives the generation performance of a target representation. To further study this, we introduce two straightforward modifications, which specifically accentuate the transfer of \emph{spatial} information. We replace the standard MLP projection layer in REPA with a simple convolution layer and introduce a spatial normalization layer for the external representation. Surprisingly, our simple method (implemented in $<$4 lines of code), termed iREPA, consistently improves convergence speed of REPA, across a diverse set of vision encoders, model sizes, and training variants (such as REPA, REPA-E, Meanflow, JiT etc). %, etc. Our work motivates revisiting the fundamental working mechanism of representational alignment and how it can be leveraged for improved training of generative models. The code and project page are available at https://end2end-diffusion.github.io/irepa

This is achieved via a novel structured parameterization and imposing structure regularization on the matrix basis.