Machine Learning Hamiltonian Dynamical Systems with Sparse and Noisy Data
Authors: Vedanta Thapar, Abhinav Gupta
Organizations: The Mathematical Institute, University of Oxford, Oxford OX2 6GG, United Kingdom · Center for Theoretical Physics, St. Stephen’s College, University of Delhi, Delhi 110007, India
Machine learning has become a powerful tool for discovering governing laws of dynamical systems from data. However, most existing approaches degrade severely when observations are sparse, noisy, or irregularly sampled. In this work, we address the problem of learning symbolic representations of nonlinear Hamiltonian dynamical systems under extreme data scarcity by explicitly incorporating physical structure into the learning architecture. We introduce Adaptable Symplectic Recurrent Neural Networks (ASRNNs), a parameter-cognizant, structure-preserving model that combines Hamiltonian learning with symplectic recurrent integration, avoiding time derivative estimation, and enabling stable learning under noise. We demonstrate that ASRNNs can accurately predict long-term dynamics even when each training trajectory consists of only two irregularly spaced time points, possibly corrupted by correlated noise. Leveraging ASRNNs as structure-preserving data generators, we further enable symbolic discovery using independent regression methods (SINDy and PySR), recovering exact symbolic equations for polynomial systems and consistent polynomial approximations for non-polynomial Hamiltonians. Our results show that such architectures can provide a robust pathway to interpretable discovery of Hamiltonian dynamics from sparse and noisy data.
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.
Sunniva Meltzer, Sølve Eidnes, Alexander Johannes Stasik
Discovering governing equations from observational data remains a fundamental challenge in scientific modeling, particularly when the underlying mathematical structure is unknown. Traditional sparse identification methods like SINDy excel at discovering parsimonious models but require researchers to specify candidate basis functions a priori, a limitation that often leads to model failure when critical terms are omitted or when systems exhibit unconventional dynamics. Purely symbolic regression approaches offer unlimited flexibility but struggle with noise sensitivity and frequently produce overly complex, unstable equations. We present AutoSINDy, a hybrid Discovery-then-Solve framework that combines the exploratory power of symbolic regression with the robust sparsity-promoting capabilities of SINDy. Our method operates in three stages: (1) PySR-based symbolic regression discovers candidate functional forms from bootstrapped data chunks; (2) a curation pipeline decomposes, expands, and filters these expressions using collinearity analysis to construct a minimal yet comprehensive library; and (3) SINDy identifies sparse governing equations from this custom-tailored library. Extensive experiments across canonical nonlinear systems demonstrate that AutoSINDy consistently recovers ground-truth equations even under high observational noise, achieving a ground-truth recovery rate of 92.8% across all trials. Compared with standard SINDy using enriched libraries and standalone symbolic regression, AutoSINDy achieves higher predictive accuracy, superior generalization to unseen trajectories, and substantially lower symbolic complexity.
Hamiltonian Neural Networks (HNNs) integrate physical priors into neural models by learning a system's Hamiltonian, improving generalization and sample efficiency. Identifying the system Hamiltonian from noisy observations of state variables is a challenging task. For simulations to faithfully reflect the long-term behavior of Hamiltonian systems, especially energy conservation, it is essential to use symplectic integrators, which preserve the system's geometric structure. This fidelity comes at a cost: implicit symplectic integrators are more computationally intensive and make backpropagation through the ODE solver non-trivial. However, by leveraging the fact that symplectic discretizations of the adjoint system yield the same sensitivities associated by backpropagation, we obtain an efficient method of training the Neural Network parameters. In our work, we explore this alternate method of HNN training under noisy observation of trajectories with our HNN model based on an implicit symplectic integrator. Computationally, a predictor-corrector based ODE solver and fixed point iteration help to mitigate the computational cost of the implicit timestepping, resulting in more efficient generation of gradient updates. We showcase the numerical advantage, in experiments, in system identification and energy preservation on a range of non-separable, chaotic systems and the efficient computation and memory complexity of our method. We also observe that the post-processing of the learned Hamiltonian using backward error analysis yields a modified Hamiltonian that is a more accurate approximation of the true Hamiltonian without the need to use more accurate discretizations of the flow map.