Diffusion learning reveals viable parameter manifolds and compensation geometry in biological dynamical systems

We study the theoretical behavior of denoising score matching--the learning task associated to diffusion models--when the data distribution is supported on a low-dimensional manifold and the score is parameterized using a random feature neural network. We derive asymptotically exact expressions for the test, train, and score errors in the high-dimensional limit. Our analysis reveals that, for linear manifolds the sample complexity required to learn the score function scales linearly with the intrinsic dimension of the manifold, rather than with the ambient dimension. Perhaps surprisingly, the benefits of low-dimensional structure starts to diminish once we have a non-linear manifold. These results indicate that diffusion models can benefit from structured data; however, the dependence on the specific type of structure is subtle and intricate.

Diffusion models have recently emerged as powerful learners for simulation-based inference (SBI), enabling fast and accurate estimation of latent parameters from simulated and real data. Their score-based formulation offers a flexible way to learn conditional or joint distributions over parameters and observations, thereby providing a versatile solution to various modeling problems. In this tutorial review, we synthesize recent developments on diffusion models for SBI, covering design choices for training, inference, and evaluation. We highlight opportunities created by various concepts such as guidance, score composition, flow matching, consistency models, and joint modeling. Furthermore, we discuss how efficiency and statistical accuracy are affected by noise schedules, parameterizations, and samplers. Finally, we illustrate these concepts with case studies across parameter dimensionalities, simulation budgets, and model types, and outline open questions for future research.

Computational sampling has been central to the sciences since the mid-20th century. While machine-learning-based approaches have recently enabled major advances, their behavior remains poorly understood, with limited theoretical control over when and why they succeed. Here we provide such insight for diffusion models-a class of generative schemes highly effective in practice-by analyzing their application to the $O(n)$ model of statistical field theory in the Gaussian limit $n \to \infty$. In this analytically tractable setting, we show that training a score model with a one-layer network architecture matching the exact solution exhibits a form of critical slowing down in parameter learning. This slowing down also impacts the generation process, indicating that the well-known difficulties of sampling near criticality persist even for learned generative models. To overcome this bottleneck, we demonstrate the power of combining architectural depth with physical locality. We find that using a two-layer architecture drastically reduces the critical slowing down, with the training time scaling logarithmically rather than quadratically with system size. By introducing a local score approximation we show that this acceleration in training time can be achieved without increasing the number of neural network parameters. Taken together, these results demonstrate that diffusion models can overcome the critical slowing down through appropriate architectural design, and establish a controlled framework for understanding and improving learned sampling methods in statistical physics and beyond.