Predicting disease risk from DNA presents an unprecedented emerging challenge as biobanks approach population scale sizes (N > 106 individuals) with ultra-highdimensional features (L > 105 genotypes). Current methods, often linear and reliant on summary statistics, fail to capture complex genetic interactions and discard valuable individual-level information. We introduce PRSformer, a scalable deep learning architecture designed for end-to-end, multitask disease prediction directly from million-scale individual genotypes. PRSformer employs neighborhood attention, achieving linear O(L) complexity per layer, making Transformers tractable for genome-scale inputs. Crucially, PRSformer utilizes a stacking of these efficient attention layers, progressively increasing the effective receptive field to model local dependencies (e.g., within linkage disequilibrium blocks) before integrating information across wider genomic regions. This design, tailored for genomics, allows PRSformer to learn complex, potentially non-linear and long-range interactions directly from raw genotypes. We demonstrate PRSformer's effectiveness using a unique large private cohort (N 5M) for predicting 18 autoimmune and inflammatory conditions using L 140k variants. PRSformer significantly outperforms highly optimized linear models trained on the same individual-level data and state-of-the-art summary-statistic-based methods (LDPred2) derived from the same cohort, quantifying the benefits of non-linear modeling and multitask learning at scale. Furthermore, experiments reveal that the advantage of non-linearity emerges primarily at large sample sizes (N > 1M), and that a multi-ancestry trained model improves generalization, establishing PRSformer as a new framework for deep learning in population-scale genomics.

In this manuscript, we analyze a solvable model of flow or diffusion-based generative model. We consider the problem of learning a model parametrized by a two-layer auto-encoder, trained with online stochastic gradient descent, on a highdimensional target density with an underlying low-dimensional manifold structure. We derive a tight asymptotic characterization of low-dimensional projections of the distribution of samples generated by the learned model, ascertaining in particular its dependence on the number of training samples. Building on this analysis, we discuss how mode collapse can arise, and lead to model collapse when the generative model is re-trained on generated synthetic data.

Neural networks trained with gradient-based methods exhibit a strong simplicity bias: they learn simpler statistical features of their data before moving to more complex features. Previous analyses of this phenomenon have largely focused on settings with (quasi-)isotropic inputs. In this work, we study the simplicity bias from a Fourier perspective, which allows us to include two key features of natural images in the analysis: approximate translation-invariance and power-law spectra. We first show experimentally that simple neural networks trained on image classification tasks first rely on amplitude information -- related to pair-wise correlations between pixels -- before exploiting phase information, which encodes edges and higher-order correlations. In view of this, we introduce a synthetic data model for translation-invariant inputs that allows precise control over amplitudes and phases while remaining tractable. We rigorously establish that for isotropic and high-dimensional inputs, classification based on phase information alone is a genuinely hard task: online stochastic gradient descent (SGD) cannot distinguish the structured inputs from noise within $n \ll N^3$ steps, but needs at least $n \gg N^3 \log^2{N}$ steps. In contrast, we show both experimentally and theoretically that power-law spectra can dramatically accelerate the speed of learning phase information, even if the spectra do not help with classification. Simulations with two-layer networks trained on textures and with deep convolutional networks on ImageNet and CIFAR100 confirm this non-trivial interaction between amplitudes and phases, providing mechanistic insights into how deep neural networks can learn natural image distributions efficiently.

Chaos arises in many complex dynamical systems, from weather to power grids, but is difficult to accurately model using data-driven emulators, including neural operator architectures. For chaotic systems, the inherent sensitivity to initial conditions makes exact long-term forecasts theoretically infeasible, meaning that traditional squared-error losses often fail when trained on noisy data. Recent work has focused on training emulators to match the statistical properties of chaotic attractors by introducing regularization based on handcrafted local features and summary statistics, as well as learned statistics extracted from a diverse dataset of trajectories. In this work, we propose a family of adversarial optimal transport objectives that jointly learn high-quality summary statistics and a physically consistent emulator. We theoretically analyze and experimentally validate a Sinkhorn divergence formulation (2-Wasserstein) and a WGAN-style dual formulation (1-Wasserstein). Our experiments across a variety of chaotic systems, including systems with high-dimensional chaotic attractors, show that emulators trained with our approach exhibit significantly improved long-term statistical fidelity.

Agent-based models (ABMs) are proliferating as decision-making tools across policy areas in transportation, economics, and epidemiology.

The proofs of Lemmas A.2 and A.3 follow from covering arguments and Bernstein's inequality; refer

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