Stefan Klus

On the numerical approximation of the Perron-Frobenius and Koopman operator

Information about the behavior of dynamical systems can often be obtained by analyzing the eigenvalues and corresponding eigenfunctions of linear operators associated with a dynamical system. Examples of such operators are the Perron-Frobenius and the Koopman operator. In this paper, we will review different methods that have been developed over the last decades to compute finite-dimensional approximations of these infinite-dimensional operators - e.g. Ulams method and Extended Dynamic Mode Decomposition (EDMD) - and highlight the similarities and differences between these approaches. The results will be illustrated using simple stochastic differential equations and molecular dynamics examples.

Variational Koopman models: Slow collective variables and molecular kinetics from short off-equilibrium simulations

Markov state models (MSMs) and master equation models are popular approaches to approximate molecular kinetics, equilibria, metastable states, and reaction coordinates in terms of a state space discretization usually obtained by clustering. Recently, a powerful generalization of MSMs has been introduced, the variational approach conformation dynamics/molecular kinetics (VAC) and its special case the time-lagged independent component analysis (TICA), which allow us to approximate slow collective variables and molecular kinetics by linear combinations of smooth basis functions or order parameters. While it is known how to estimate MSMs from trajectories whose starting points are not sampled from an equilibrium ensemble, this has not yet been the case for TICA and the VAC. Previous estimates from short trajectories have been strongly biased and thus not variationally optimal. Here, we employ the Koopman operator theory and the ideas from dynamic mode decomposition to extend the VAC and TICA to non-equilibrium data. The main insight is that the VAC and TICA provide a coefficient matrix that we call Koopman model, as it approximates the underlying dynamical (Koopman) operator in conjunction with the basis set used. This Koopman model can be used to compute a stationary vector to reweight the data to equilibrium. From such a Koopman-reweighted sample, equilibrium expectation values and variationally optimal reversible Koopman models can be constructed even with short simulations. The Koopman model can be used to propagate densities, and its eigenvalue decomposition provides estimates of relaxation time scales and slow collective variables for dimension reduction. Koopman models are generalizations of Markov state models, TICA, and the linear VAC and allow molecular kinetics to be described without a cluster discretization.

Data-Driven Model Reduction and Transfer Operator Approximation

In this review paper, we will present different data-driven dimension reduction techniques for dynamical systems that are based on transfer operator theory as well as methods to approximate transfer operators and their eigenvalues, eigenfunctions, and eigenmodes. The goal is to point out similarities and differences between methods developed independently by the dynamical systems, fluid dynamics, and molecular dynamics communities such as time-lagged independent component analysis, dynamic mode decomposition, and their respective generalizations. As a result, extensions and best practices developed for one particular method can be carried over to other related methods.

Towards tensor-based methods for the numerical approximation of the Perron-Frobenius and Koopman operator

The global behavior of dynamical systems can be studied by analyzing the eigenvalues and corresponding eigenfunctions of linear operators associated with the system. Two important operators which are frequently used to gain insight into the systems behavior are the Perron-Frobenius operator and the Koopman operator. Due to the curse of dimensionality, computing the eigenfunctions of high-dimensional systems is in general infeasible. We will propose a tensor-based reformulation of two numerical methods for computing finite-dimensional approximations of the aforementioned infinite-dimensional operators, namely Ulams method and Extended Dynamic Mode Decomposition (EDMD). The aim of the tensor formulation is to approximate the eigenfunctions by low-rank tensors, potentially resulting in a significant reduction of the time and memory required to solve the resulting eigenvalue problems, provided that such a low-rank tensor decomposition exists. Typically, not all variables of a high-dimensional dynamical system contribute equally to the systems behavior, often the dynamics can be decomposed into slow and fast processes, which is also reflected in the eigenfunctions. Thus, some variables might be approximable by low-rank tensors while other variables require more information. We will illustrate the efficiency of the tensor-based formulation of Ulams method and EDMD using simple stochastic differential equations.

Tensor-based dynamic mode decomposition

Dynamic mode decomposition (DMD) is a recently developed tool for the analysis of the behavior of complex dynamical systems. In this paper, we will propose an extension of DMD that exploits low-rank tensor decompositions of potentially high-dimensional data sets to compute the corresponding DMD modes and eigenvalues. The goal is to reduce the computational complexity and also the amount of memory required to store the data in order to mitigate the curse of dimensionality. The efficiency of these tensor-based methods will be illustrated with the aid of several different fluid dynamics problems such as the von Karman vortex street and the simulation of two merging vortices.

Transition manifolds of complex metastable systems: Theory and data-driven computation of effective dynamics

We consider complex dynamical systems showing metastable behavior, but no local separation of fast and slow time scales. The article raises the question of whether such systems exhibit a low-dimensional manifold supporting its effective dynamics. For answering this question, we aim at finding nonlinear coordinates, called reaction coordinates, such that the projection of the dynamics onto these coordinates preserves the dominant time scales of the dynamics. We show that, based on a specific reducibility property, the existence of good low-dimensional reaction coordinates preserving the dominant time scales is guaranteed. Based on this theoretical framework, we develop and test a novel numerical approach for computing good reaction coordinates. The proposed algorithmic approach is fully local and thus not prone to the curse of dimension with respect to the state space of the dynamics. Hence, it is a promising method for data-based model reduction of complex dynamical systems such as molecular dynamics.

An efficient algorithm for the parallel solution of high-dimensional differential equations

The study of high-dimensional differential equations is challenging and difficult due to the analytical and computational intractability. Here, we improve the speed of waveform relaxation (WR), a method to simulate high-dimensional differential-algebraic equations. This new method termed adaptive waveform relaxation (AWR) is tested on a communication network example. Further, we propose different heuristics for computing graph partitions tailored to adaptive waveform relaxation. We find that AWR coupled with appropriate graph partitioning methods provides a speedup by a factor between 3 and 16.

A Set-Oriented Numerical Approach for Dynamical Systems with Parameter Uncertainty

In this article, we develop a set-oriented numerical methodology which allows us to perform uncertainty quantification (UQ) for dynamical systems from a global point of view. That is, for systems with uncertain parameters we approximate the corresponding global attractors and invariant measures in the related stochastic setting. Our methods do not rely on generalized polynomial chaos techniques. Rather, we extend classical set-oriented methods designed for deterministic dynamical systems [M. Dellnitz and A. Hohmann, Numer. Math., 75 (1997), pp. 293--317; M. Dellnitz and O. Junge, SIAM J. Numer. Anal., 36 (1999), pp. 491--515] to the UQ-context, and this allows us to analyze the long-term uncertainty propagation. The algorithms have been integrated into the software package GAIO [M. Dellnitz, G. Froyland, and O. Junge, Ergodic Theory, Analysis, and Efficient Simulation of Dynamical Systems, Springer, Berlin, 2001, pp. 145--174], and we illustrate the use and efficiency of these techniques with a couple of numerical examples.

Nearest-neighbor interaction systems in the tensor-train format

Low-rank tensor approximation approaches have become an important tool in the scientific computing community. The aim is to enable the simulation and analysis of high-dimensional problems which cannot be solved using conventional methods anymore due to the so-called curse of dimensionality. This requires techniques to handle linear operators defined on extremely large state spaces and to solve the resulting systems of linear equations or eigenvalue problems. In this paper, we present a systematic tensor-train decomposition for nearest-neighbor interaction systems which is applicable to a host of different problems. With the aid of this decomposition, it is possible to reduce the memory consumption as well as the computational costs significantly. Furthermore, it can be shown that in some cases the rank of the tensor decomposition does not depend on the network size. The format is thus feasible even for high-dimensional systems. We will illustrate the results with several guiding examples such as the Ising model, a system of coupled oscillators, and a CO oxidation model.

A Spectral Assignment Approach for the Graph Isomorphism Problem

In this paper, we propose algorithms for the graph isomorphism (GI) problem that are based on the eigendecompositions of the adjacency matrices. The eigenvalues of isomorphic graphs are identical. However, two graphs