When Does Jacobian Fine-Tuning Stabilize Neural PDE Emulators?

Neural autoregressive models have rapidly emerged as powerful emulators of high-dimensional chaotic systems, yet their long-term instability and error growth remain poorly understood, leading to ad-hoc solutions. Here, we develop an eigenanalysis framework that reveals the dynamical origin of this error growth. By analyzing the Jacobian of the learned one-step update map with respect to the state, we show how inference-time error growth, and thus model stability, is governed by its spectral radius. Direct-step architectures (models that predict the next state from the previous one) generically admit unstable eigenvalues with magnitudes exceeding one, explaining the rapid divergence of these widely used models. In contrast, integration-constrained models (where the time derivative is estimated and integrated with a higher-order integrator) collapse their eigenspectrum onto the unit circle, yielding neutral stability and a universal linear error-scaling law. The largest eigenvalue of this Jacobian provides an architecture-agnostic, a priori diagnostic of short-term skill, long-term stability, and spectral bias, without requiring an expensive rollout. Leveraging this theory, we introduce a stability-promoting loss that explicitly regularizes Jacobian-driven error amplification, improving both forecast accuracy and dynamical robustness. Demonstrated across $29$ models spanning two architectures, several explicit and implicit integrators, and multiple loss functions on the Kuramoto-Sivashinsky system, our results establish a theoretical foundation for the design and evaluation of neural emulators of chaotic multi-scale dynamics. More broadly, our framework is a step toward the kind of a priori stability analysis that numerical analysis provides for discretizations of differential equations and that scientific machine learning currently lacks.

Simulation is central to modern engineering and science, but the cost of numerical solvers for partial differential equations (PDEs) remains a bottleneck whenever fast or many-query evaluations are required. Neural emulators trained on solver-generated data promise significant speedups, yet they are usually framed as opaque alternatives to the very methods that produce their training signal. This thesis argues the two paradigms are more alike than different: neural architectures mirror classical discretizations, their errors are amenable to the same spectral analysis, and insight flows profitably in both directions. We approach the relationship by disentangling the multiple roles a solver plays in the emulator learning pipeline. Mode-wise Fourier analysis then provides a common language in which solver errors, architectural inductive biases, and training objectives can all be read off simultaneously. Taken together, this allows synthesizing three contributions. (1) APEBench, a comprehensive benchmarking suite for autoregressive neural emulators of PDEs that uses fast differentiable pseudo-spectral solvers in JAX. (2) Progressively Refined Differentiable Physics, an investigation of the effect of unconverged solvers on surrogate training. (3) Neural Emulator Superiority, an analysis of the influence of numerical errors and architectural inductive biases.

Neural surrogate models offer fast approximate mappings from PDE parameters to solutions, but they typically treat solving as a purely statistical task: once trained, they struggle to correct their own constraint violations and extrapolate beyond the training distribution. Recent hybrid methods promote physical correctness by targeting the PDE residual via gradient descent or Gauss--Newton steps, but inherit the compute cost and instability of the underlying classical optimizers. We show, theoretically and empirically, that numerically minimizing the PDE residual can be an unreliable proxy for reconstruction accuracy in ill-conditioned systems, explaining why these methods often do not make accurate predictions despite achieving low residuals. We propose error-conditioned Neural Solvers (ENS), built on a different principle: rather than an optimization target, the PDE residual field is passed as a direct input to the network at each iteration, enabling it to read the spatial structure of its own errors and learn an update policy to iteratively correct its predictions. Across four PDE families, ENS attains the highest prediction accuracy in the large majority of settings, with gains reaching $10\times$ on turbulent Kolmogorov flow, while avoiding the expensive compute cost of hybrid methods. ENS's learned correction policy generalizes under distribution shift, including zero-shot parameter changes and cross-equation transfer, where its relative advantage is largest in the ill-conditioned regimes where residual minimization is least reliable. Project website: https://neuralsolver.github.io/.