DisKO: Deep Koopman Learning in Distribution Space from Unpaired Snapshots

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.

Learning population dynamics from temporally sparse, unpaired distribution snapshots is a fundamental challenge in developmental biology. Recent approaches based on neural differential equations and flow matching can interpolate between observed population snapshots, but may struggle to extrapolate beyond the training horizon and often lack an explicit mechanism for modeling developmental branching. We propose KoopCell, a unified generative framework based on Koopman-Mori-Zwanzig theory that jointly learns representations and predictive linear latent dynamics. Theoretically, using the weak continuity equation, we derive a closed-form least-squares estimator for the Koopman generator from distribution snapshots and establish convergence guarantees under suitable assumptions. To model branching dynamics, we further develop KoopCell-M, which incorporates non-Markovian memory into the latent Koopman dynamics through a Markovian embedding. Experiments on synthetic systems and three scRNA-seq datasets demonstrate the ability of our framework to recover Koopman spectra, model branching through memory, and scale to predicting high-dimensional gene expression distributions, achieving state-of-the-art performance among the evaluated methods.

The Koopman operator has been widely used for time-series prediction in dynamical systems. However, prior work that learns latent ``Koopman spaces'' using neural networks often did not construct a valid Koopman space for forecasting, as these representations may be mathematically inconsistent with the operator-theoretic formulation and fail to capture the intrinsic low-rank structure of system dynamics. To address this issue, we introduce K$^2$SVD, a method that explicitly learns the leading singular functions of the Koopman operator by optimizing a Hilbert-Schmidt objective. This yields a well-defined low-rank approximation of the Koopman operator with an interpretable linear combination, featuring a compact latent space with less than $10\%$ of the dimensions used in previous work. In the learned Koopman space, K$^2$SVD further captures temporal evolution with a linear Gaussian state-space model and performs inference via Kalman filtering, mitigating noise accumulation during multi-step prediction. Empirical results show that K$^2$SVD outperforms state-of-the-art methods across multiple datasets, with significantly faster prediction speeds and lower computational cost than previous efficiency-focused models. This highlights the benefits of principled low-rank Koopman representations and opens up broader potential for applications.