Geometric Dictionary Learning of Dynamical Systems with Optimal Transport

Koopman theory promises linear structure in nonlinear dynamics, but numerical Koopman spectra are easy to compute and hard to trust. A finite EDMD matrix always has eigenvalues; the problem is that many of them may have nothing to do with the infinite-dimensional operator. In this paper we make spectral reliability the objective of dictionary learning. We train neural-network dictionaries not merely to predict the next snapshot, but to minimize Residual Dynamic Mode Decomposition residuals: operator-level a posteriori errors that test whether computed eigenvalues and modes are genuine Koopman spectral objects. To keep the learned observables from collapsing into an unstable coordinate system, the loss also penalizes the condition number of the lifted data matrix. Thus the method couples two requirements that should not be separated: small Koopman residuals and a well-conditioned representation. The result is a learned dictionary that is expressive, numerically stable, and spectrally disciplined. Across conservative and dissipative benchmark systems, the method sharply reduces spectral pollution, improves residual pseudospectral inclusion, and lowers forecast error relative to standard fixed dictionaries. On sea-surface temperature data, it gives cleaner Koopman diagnostics and substantially better one-step forecasts from noisy observations with no governing equations. The message is simple: neural Koopman learning should be judged not by prediction alone, but by whether its spectral claims can be certified. Residuals provide the certificate; conditioning makes it computable.

We propose a spectral learning method for stochastic nonlinear dynamical systems represented with embedded latent transfer operators in deep feature spaces. We instantiate the method as Deep Spectral Encoder (DSE), an operator-based latent state-space model in which a time-invariant neural encoder implements learnable nonlinear feature maps from observations, and these features define Markovian latent states whose temporal evolution and observation mapping are described by the transfer and observation operators, respectively. Functional canonical correlation analysis in a learnable Galerkin-projected feature space provides state coordinates from past and future observations, and the two linear operators are estimated on the state coordinates as ridge-regularized closed-form solutions that coincide with Galerkin projections of the associated covariance operators. On this representation, we generalize sequential Bayesian filtering and Koopman spectral mode decomposition in feature space. Experiments on several scenarios show stable and superior performance with sequential Bayesian filtering and dynamic mode decomposition baselines even under noise and partial observability.

Koopman theory turns nonlinear dynamics into a linear spectral problem. In computation, however, everything depends on a hard finite-dimensional choice: the observables must be expressive, nearly invariant under the dynamics, and, ideally, compatible with composition. Deep Koopman methods learn flexible coordinates, whereas structure-preserving methods enforce operator identities on fixed dictionaries. We combine these ideas by introducing Deep Embedded Multiplicative Dynamic Mode Decomposition (DeepMDMD), a method that learns a latent space and a partition of it, while enforcing the Koopman product rule as an exact algebraic constraint. Training alternates between an exact multiplicative operator update and a differentiable latent-clustering step that promotes Koopman closure. The result is a finite transition map on learned latent cells. Its nonzero spectrum lies on the unit circle, its dictionary is shaped by the dynamics rather than by ambient geometry, and forecasts are made in latent coordinates before being decoded to physical space. Across Hamiltonian, chaotic, and fluid examples, DeepMDMD learns dictionaries that are far more compact and dynamically coherent than those produced by geometric MDMD partitions. It reduces spectral pollution, reveals richer continuous-spectrum structure, and gives stable forecasts under severe noise. In high-dimensional flows, including a 158,624-dimensional cylinder wake and a noisy $Re=20,000$ lid-driven cavity, it preserves coherent structures and long-time spectral statistics where state-space MDMD fails. These results suggest a practical rule for Koopman learning: learn the coordinates, constrain the algebra.