Learning partially observed systems with neural Hamiltonian ordinary differential equations

When learning dynamical systems from data, embedding physical structure can constrain the solution space and improve generalization, but many physics-informed models assume access to the full system state. This limits their use in partially observed settings, where some state variables are completely unobserved and must be inferred without direct supervision. Here, we present neural Hamiltonian ordinary differential equations (NHODE), a framework that combines Hamiltonian neural networks (HNNs) with neural ordinary differential equations (neural ODEs) to learn partially observed dynamical systems from data. The Hamiltonian structure enforces energy conservation by construction, while the neural ODE framework enables a flexible training procedure that allows the loss to be defined only on observed variables. We also incorporate additional physical constraints through symmetry-aware coordinate transformations and separable energy formulations. The framework is evaluated on systems of increasing complexity, from linear and nonlinear mass-spring systems to the chaotic three-body problem. Across all examples, increasing the amount of embedded physical structure improves the accuracy and long-horizon stability of the predictions. Even in the most challenging regimes, the NHODE framework captures both observed and latent dynamics, whereas purely data-driven baselines become unstable.