Frequency-Structured Hamiltonian Neural Network for Multi-Timescale Dynamics

Hamiltonian Neural Networks and related structure-preserving dynamics models encode conservation laws, but their scalar Hamiltonian parameterizations inherit the spectral bias of deep networks, limiting their ability to learn stiff multi-timescale systems with coupled fast and slow dynamics. We introduce the Frequency-Structured Hamiltonian Neural Network (FS-HNN), which decomposes the system Hamiltonian into learned components trained on frequency-filtered views of observed trajectories, then recombines them into a single scalar Hamiltonian so that the learned ODE dynamics remain Hamiltonian by construction. For PDEs with unknown or problem-dependent structure, FS-HNN represents Hamiltonians as neural functionals, learns the action of the dynamics operator, and uses projection to enforce conservative structure when appropriate. Across ODE and PDE benchmarks, including the Fermi–Pasta–Ulam–Tsingou chain, shallow water equations, and incompressible Taylor–Green vortex, FS-HNN achieves improved long-horizon rollout accuracy and more accurate energy behavior than existing structure-preserving baselines.