Bilevel optimization for data-driven learning of Koopman embeddings using kernel-based autoencoders

Studying nonlinear dynamical systems through their state space behavior can be challenging, and one possible alternative is to analyze them via their associated Koopman operator. This turns the nonlinear problem into a linear, infinite-dimensional one. To approximate the operator in finite dimensions, extended dynamic mode decomposition (EDMD) is a commonly used algorithm. It requires a finite list of functionals and a set of snapshots from the system to compute an approximation of the operator and its corresponding spectrum. Instead of choosing the list of functionals directly, it can be implicitly defined via kernels, a method known as kernel extended dynamic mode decomposition (kEDMD). However, one still needs to define the kernel and choose its parameter values. In this paper, we aim to streamline this process by extending dictionary learning for EDMD to kernel learning in kEDMD. By simplifying kEDMD we show how to perform gradient-based optimization over the learnable kernel parameters, and demonstrate that this method leads to useful kernels for the original kEDMD. The focus of our work is a method that takes a weighted list of kernels with randomly initialized values as input and outputs a list of kernels and parameter values suitable for approximating the Koopman operator of the underlying system. We demonstrate that unimportant kernels can be removed from the list by analyzing the weights in the weighted sum. We evaluate the method across several experiments, including the Duffing oscillator and the Kuramoto-Sivashinsky PDE, showcasing the method's different strengths.

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.

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.