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Feliks Nüske

Publications and source records attributed to Feliks Nüske.

At least 19 recordsLinked to original sources

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

Koopman operator theory provides a linear framework for analyzing nonlinear dynamical systems and has become a major tool for data-driven modeling. A central challenge, however, is that finite-dimensional approximations computed by methods such as extended dynamic mode decomposition (EDMD) require the dictionary to be specified a priori. Recent machine-learning approaches address this limitation by learning the dictionary from data, predominantly using artificial neural network (ANN) autoencoder architectures. Although kernel methods offer an alternative with greater interpretability and tractability for theoretical analysis, they have received little attention in this setting. We introduce extended dynamic mode decomposition with kernel-based dictionary learning (EDMD-kDL), a kernel-based method for learning finite-dimensional Koopman embeddings directly from data. The method combines ideas from collocation methods and bilevel optimization to simultaneously learn a kernel dictionary and the corresponding Koopman approximation. We evaluate EDMD-kDL against state-of-the-art ANN-based approaches on a range of numerical experiments, including global sea-surface-temperature forecasting and learning directly from video data. Across all tested settings, EDMD-kDL achieves performance comparable to or better than the ANN-based methods. Moreover, in contrast to standard kernel methods, the proposed approach is scalable to large datasets by design since the size of the required kernel matrices depends on the number of collocation points rather than the size of the training dataset.

cs.LG↗

Numerical approximation of the Koopman-von Neumann equation: Operator learning and quantum computing

The Koopman-von Neumann equation describes the evolution of wavefunctions associated with autonomous ordinary differential equations and can be regarded as a quantum physics-inspired formulation of classical mechanics. The main advantage compared to conventional transfer operators such as Koopman and Perron-Frobenius operators is that the Koopman-von Neumann operator is unitary even if the dynamics are non-Hamiltonian. Projecting this operator onto a finite-dimensional subspace allows us to represent it by a unitary matrix, which in turn can be expressed as a quantum circuit. We will exploit relationships between the Koopman-von Neumann framework and classical transfer operators in order to derive numerical methods to approximate the Koopman-von Neumann operator and its eigenvalues and eigenfunctions from data. Furthermore, we will show that the choice of basis functions and domain are crucial to ensure that the operator is well-defined. We will illustrate the results with the aid of guiding examples, including simple undamped and damped oscillators and the Lotka-Volterra model.

math.DS↗

Optimal Bias Potentials via Ergodic Optimal Control and Generator Learning

We investigate the computation of optimal bias potentials for accelerating transitions between metastable states and for computation of equilibrium properties in molecular dynamics simulations. We formulate optimal biasing as an ergodic optimal control problem (OCP), which can be recast as a linear eigenvalue problem for the infinitesimal generator of the unbiased dynamics. We demonstrate that data-driven learning methods for the generator enable reliable solution of the OCP, computation of biasing potentials, extraction of equilibrium properties, and acceleration of state transitions. We also explore the relation of the control problem to coarse grained representations and learning of coarse grained dynamics.

physics.comp-ph↗

Tensor-based Approximation of Molecular Kinetics: Generator Learning, Reaction Coordinates and Incremental Updating

We present an approach to analyze long-timescale kinetics of molecular dynamics simulations - meta-stable states and transition timescales - by a tensor-based approximation of the infinitesimal generator. We start from the variational approximation of low-lying generator eigenvalues, and discretize the associated eigenvalue problem using a tensor-product basis. We derive analytical expressions for the resulting tensor operators in tensor train (TT) format, and provide efficient algorithms to solve the corresponding linear problems. We also treat the case of a state-dependent diffusion field, which is relevant when working in reaction coordinates. We show how the number of reaction coordinates can be gradually increased without having to solve the variational problem from scratch. Using MD simulations of fast-folding proteins and TICA coordinates as reaction coordinates, we demonstrate the effectiveness of the proposed method at identifying long-timescale transitions and meta-stable states.

physics.chem-ph↗

Consistent Projection of Langevin Dynamics: Preserving Thermodynamics and Kinetics in Coarse-Grained Models

Coarse graining (CG) is an important task for efficient modeling and simulation of complex multi-scale systems, such as the conformational dynamics of biomolecules. This work presents a projection-based coarse-graining formalism for general underdamped Langevin dynamics. Following the Zwanzig projection approach, we derive a closed-form expression for the coarse grained dynamics. In addition, we show how the generator Extended Dynamic Mode Decomposition (gEDMD) method, which was developed in the context of Koopman operator methods, can be used to model the CG dynamics and evaluate its kinetic properties, such as transition timescales. Finally, we combine our approach with thermodynamic interpolation (TI), a generative approach to transform samples between thermodynamic conditions, to extend the scope of the approach across thermodynamic states without repeated numerical simulations. Using a two-dimensional model system, we demonstrate that the proposed method allows to accurately capture the thermodynamic and kinetic properties of the full-space model.

physics.comp-ph↗

Group-Convolutional Extended Dynamic Mode Decomposition

This paper explores the integration of symmetries into the Koopman-operator framework for the analysis and efficient learning of equivariant dynamical systems using a group-convolutional approach. Approximating the Koopman operator by finite-dimensional surrogates, e.g., via extended dynamic mode decomposition (EDMD), is challenging for high-dimensional systems due to computational constraints. To tackle this problem with a particular focus on EDMD, we demonstrate -- under suitable equivarance assumptions on the system and the observables -- that the optimal EDMD matrix is equivariant. That is, its action on states can be described by group convolutions and the generalized Fourier transform. We show that this structural property has many advantages for equivariant systems, in particular, that it allows for data-efficient learning, fast predictions and fast eigenfunction approximations. We conduct numerical experiments on the Kuramoto-Sivashinsky equation and a $λ$-$ω$ spiraling wave system, both nonlinear partial differential equations, providing evidence of the effectiveness of this approach, and highlighting its potential for broader applications in dynamical systems analysis.

math.DS↗

Kinetically Consistent Coarse Graining using Kernel-based Extended Dynamic Mode Decomposition

In this paper, we show how kernel-based models for the Koopman generator -- the gEDMD method -- can be used to identify coarse-grained dynamics on reduced variables, which retain the slowest transition timescales of the original dynamics. The centerpiece of this study is a learning method to identify an effective diffusion in coarse-grained space, which is similar in spirit to the force matching method. By leveraging the gEDMD model for the Koopman generator, the kinetic accuracy of the CG model can be evaluated. By combining this method with a suitable learning method for the effective free energy, such as force matching, a complete model for the effective dynamics can be inferred. Using a two-dimensional model system and molecular dynamics simulation data of alanine dipeptide and the Chignolin mini-protein, we demonstrate that the proposed method successfully and robustly recovers the essential kinetic and also thermodynamic properties of the full model. The parameters of the method can be determined using standard model validation techniques.

physics.comp-ph↗

Thermodynamic Interpolation: A generative approach to molecular thermodynamics and kinetics

Using normalizing flows and reweighting, Boltzmann Generators enable equilibrium sampling from a Boltzmann distribution, defined by an energy function and thermodynamic state. In this work, we introduce Thermodynamic Interpolation (TI), which allows for generating sampling statistics in a temperature-controllable way. We introduce TI flavors that work directly in the ambient configurational space, mapping between different thermodynamic states or through a latent, normally distributed reference state. Our ambient-space approach allows for the specification of arbitrary target temperatures, ensuring generalizability within the temperature range of the training set and demonstrating the potential for extrapolation beyond it. We validate the effectiveness of TI on model systems that exhibit metastability and non-trivial temperature dependencies. Finally, we demonstrate how to combine TI-based sampling to estimate free energy differences through various free energy perturbation methods and provide corresponding approximated kinetic rates estimated through generator extended dynamic mode decomposition (gEDMD).

physics.chem-ph↗

Equivariance and partial observations in Koopman operator theory for partial differential equations

The Koopman operator has become an essential tool for data-driven analysis, prediction and control of complex systems. The main reason is the enormous potential of identifying linear function space representations of nonlinear dynamics from measurements. This equally applies to ordinary, stochastic, and partial differential equations (PDEs). Until now, with a few exceptions only, the PDE case is mostly treated rather superficially, and the specific structure of the underlying dynamics is largely ignored. In this paper, we show that symmetries in the system dynamics can be carried over to the Koopman operator, which allows us to significantly increase the model efficacy. Moreover, the situation where we only have access to partial observations (i.e., measurements, as is very common for experimental data) has not been treated to its full extent, either. Moreover, we address the highly-relevant case where we cannot measure the full state, where alternative approaches (e.g., delay coordinates) have to be considered. We derive rigorous statements on the required number of observables in this situation, based on embedding theory. We present numerical evidence using various numerical examples including the wave equation and the Kuramoto-Sivashinsky equation.

math.DS↗

Koopman-based Control for Stochastic Systems: Application to Enhanced Sampling

We present a data-driven approach to use the Koopman generator for prediction and optimal control of control-affine stochastic systems. We provide a novel conceptual approach and a proof-of-principle for the determination of optimal control policies which accelerate the simulation of rare events in metastable stochastic systems.

math.OC↗

Variance representations and convergence rates for data-driven approximations of Koopman operators

We rigorously derive novel error bounds for extended dynamic mode decomposition (EDMD) to approximate the Koopman operator for discrete- and continuous time (stochastic) systems; both for i.i.d. and ergodic sampling under non-restrictive assumptions. We show exponential convergence rates for i.i.d. sampling and provide the first superlinear convergence rates for ergodic sampling of deterministic systems. The proofs are based on novel exact variance representations for the empirical estimators of mass and stiffness matrix. Moreover, we verify the accuracy of the derived error bounds and convergence rates by means of numerical simulations for highly-complex dynamical systems including a nonlinear partial differential equation.

math.DS↗

Invariance of Gaussian RKHSs under Koopman operators of stochastic differential equations with constant matrix coefficients

We consider the Koopman operator semigroup $(K^t)_{t\ge 0}$ associated with stochastic differential equations of the form $dX_t = AX_t\,dt + B\,dW_t$ with constant matrices $A$ and $B$ and Brownian motion $W_t$. We prove that the reproducing kernel Hilbert space $\bH_C$ generated by a Gaussian kernel with a positive definite covariance matrix $C$ is invariant under each Koopman operator $K^t$ if the matrices $A$, $B$, and $C$ satisfy the following Lyapunov-like matrix inequality: $AC^2 + C^2A^\top\le 2BB^\top$. In this course, we prove a characterization concerning the inclusion $\bH_{C_1}\subset\bH_{C_2}$ of Gaussian RKHSs for two positive definite matrices $C_1$ and $C_2$. The question of whether the sufficient Lyapunov-condition is also necessary is left as an open problem.

math.PR↗

Error bounds for kernel-based approximations of the Koopman operator

We consider the data-driven approximation of the Koopman operator for stochastic differential equations on reproducing kernel Hilbert spaces (RKHS). Our focus is on the estimation error if the data are collected from long-term ergodic simulations. We derive both an exact expression for the variance of the kernel cross-covariance operator, measured in the Hilbert-Schmidt norm, and probabilistic bounds for the finite-data estimation error. Moreover, we derive a bound on the prediction error of observables in the RKHS using a finite Mercer series expansion. Further, assuming Koopman-invariance of the RKHS, we provide bounds on the full approximation error. Numerical experiments using the Ornstein-Uhlenbeck process illustrate our results.

math.DS↗

Error analysis of kernel EDMD for prediction and control in the Koopman framework

Extended Dynamic Mode Decomposition (EDMD) is a popular data-driven method to approximate the Koopman operator for deterministic and stochastic (control) systems. This operator is linear and encompasses full information on the (expected stochastic) dynamics. In this paper, we analyze a kernel-based EDMD algorithm, known as kEDMD, where the dictionary consists of the canonical kernel features at the data points. The latter are acquired by i.i.d. samples from a user-defined and application-driven distribution on a compact set. We prove bounds on the prediction error of the kEDMD estimator when sampling from this (not necessarily ergodic) distribution. The error analysis is further extended to control-affine systems, where the considered invariance of the Reproducing Kernel Hilbert Space is significantly less restrictive in comparison to invariance assumptions on an a-priori chosen dictionary.

math.DS↗

Funnel Control for Langevin Dynamics

We study tracking control for stochastic differential equations of Langevin type and describe a new conceptual approach to the sampling problem for those systems. The objective is to guarantee the evolution of the mean value in a prescribed performance funnel around a given sufficiently smooth reference signal. To achieve this objective we design a novel funnel controller and show its feasibility under certain structural conditions on the potential energy. The control design does not require any specific knowledge of the shape of the potential energy. We illustrate the results by a numerical simulation for a double-well potential.

math.OC↗

Efficient Approximation of Molecular Kinetics using Random Fourier Features

Slow kinetic processes of molecular systems can be analyzed by computing dominant eigenpairs of the Koopman operator or its generator. In this context, the Variational Approach to Markov Processes (VAMP) provides a rigorous way of discerning the quality of different approximate models. Kernel methods have been shown to provide accurate and robust estimates for slow kinetic processes, but are sensitive to hyper-parameter selection, and require the solution of large-scale generalized eigenvalue problems, which can easily become computationally demanding for large data sizes. In this contribution, we employ a stochastic approximation of the kernel based on random Fourier features (RFFs), to derive a small-scale dual eigenvalue problem which can easily be solved. We provide an interpretation of this procedure in terms of a finite randomly generated basis set. By combining the RFF approach and model selection by means of the VAMP score, we show that kernel parameters can be efficiently tuned, and accurate estimates of slow molecular kinetics can be obtained for several benchmarking systems, such as deca alanine and the NTL9 protein.

physics.comp-ph↗

Towards reliable data-based optimal and predictive control using extended DMD

While Koopman-based techniques like extended Dynamic Mode Decomposition are nowadays ubiquitous in the data-driven approximation of dynamical systems, quantitative error estimates were only recently established. To this end, both sources of error resulting from a finite dictionary and only finitely-many data points in the generation of the surrogate model have to be taken into account. We generalize the rigorous analysis of the approximation error to the control setting while simultaneously reducing the impact of the curse of dimensionality by using a recently proposed bilinear approach. In particular, we establish uniform bounds on the approximation error of state-dependent quantities like constraints or a performance index enabling data-based optimal and predictive control with guarantees.

math.OC↗

Koopman analysis of quantum systems

Koopman operator theory has been successfully applied to problems from various research areas such as fluid dynamics, molecular dynamics, climate science, engineering, and biology. Applications include detecting metastable or coherent sets, coarse-graining, system identification, and control. There is an intricate connection between dynamical systems driven by stochastic differential equations and quantum mechanics. In this paper, we compare the ground-state transformation and Nelson's stochastic mechanics and demonstrate how data-driven methods developed for the approximation of the Koopman operator can be used to analyze quantum physics problems. Moreover, we exploit the relationship between Schrödinger operators and stochastic control problems to show that modern data-driven methods for stochastic control can be used to solve the stationary or imaginary-time Schrödinger equation. Our findings open up a new avenue towards solving Schrödinger's equation using recently developed tools from data science.

quant-ph↗