arXiv:2610.11931v1 Announce Type: new Abstract: Structure-preserving numerical methods for gradient flows have been extensively developed when the governing equations and free energies are known. However, accurately predicting dynamics from observational data while preserving intrinsic physical properties remains challenging. Although neural operators, such as Fourier neural operators (FNOs), provide powerful data-driven approximations, their predictions do not inherently guarantee physical structure preservation. To address this challenge, we integrate deep learning with structure-preserving exponential time differencing (ETD) methods. Instead of directly learning the evolution operator, we introduce a *trajectory-inferred free energy* (TIFE), which reconstructs the unknown energy density from observed trajectories through a Duhamel-based learning framework. The learned energy determines the variational force and stabilization parameter, enabling structure-preserving numerical evolution. We further extend the framework to jointly identify the free energy and diffusion coefficient. Under suitable assumptions, we establish the maximum-bound principle, unconditional dissipation of the original learned energy, and error estimates incorporating discretization and inference errors. Numerical experiments demonstrate accurate energy recovery and reliable long-time predictions.