arXiv subjects

Stefan Klus

Publications and source records attributed to Stefan Klus.

66 records · Page 4Linked to original sources

arXiv2017

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.

math.DS↗

arXiv2017

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 (TICA), dynamic mode decomposition (DMD), and their respective generalizations. As a result, extensions and best practices developed for one particular method can be carried over to other related methods.

math.DS↗

arXiv2017

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.

math.NA↗

arXiv2017

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 (VA) of molecular kinetics 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 VA. Previous estimates from short trajectories, have been strongly biased and thus not variationally optimal. Here, we employ Koopman operator theory and ideas from dynamic mode decomposition (DMD) to extend the VA and TICA to non-equilibrium data. The main insight is that the VA 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 provide estimates of relaxation timescales and slow collective variables for dimension reduction. Koopman models are generalizations of Markov state models, TICA and the linear VA and allow molecular kinetics to be described without a cluster discretization.

stat.ML↗

arXiv2017

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 Kármán vortex street and the simulation of two merging vortices.

math.NA↗

arXiv2016

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 system's 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 Ulam's 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 system's behavior, often the dynamics can be decomposed into slow and fast processes, which is also reflected in the eigenfunctions. Thus, the weak coupling between different variables might be approximated by low-rank tensor cores. We will illustrate the efficiency of the tensor-based formulation of Ulam's method and EDMD using simple stochastic differential equations.

math.NA↗

arXiv2016

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. Ulam's 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.

math.DS↗

arXiv2016

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

In this article, we develop a set-oriented numerical methodology which allows 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 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, and we illustrate the use and efficiency of these techniques by a couple of numerical examples.

math.DS↗

arXiv2015

Sensing and Control in Symmetric Networks

In engineering applications, one of the major challenges today is to develop reliable and robust control algorithms for complex networked systems. Controllability and observability of such systems play a crucial role in the design process. The underlying network structure may contain symmetries -- caused for example by the coupling of identical building blocks -- and these symmetries lead to repeated eigenvalues in a generic way. This complicates the design of controllers since repeated eigenvalues might decrease the controllability of the system. In this paper, we will analyze the relationship between the controllability and observability of complex networked systems and graph symmetries using results from representation theory. Furthermore, we will propose an algorithm to compute sparse input and output matrices based on projections onto the isotypic components. We will illustrate our results with the aid of two guiding examples, a network with $ D_4 $ symmetry and the Petersen graph.

math.NA↗

arXiv2015

Signal-Flow Based Runge-Kutta Methods for the Simulation of Complex Networks

Complex dynamical networks appear in a wide range of physical, biological, and engineering systems. The coupling of subsystems with varying time scales often results in multirate behavior. During the simulation of highly integrated circuits, for example, only a few elements underlie changing signals whereas the major part -- usually up to 80 or even 90 per cent -- remains latent. Standard integration schemes discretize the entire circuit with a single step size which is mainly limited by the accuracy requirements of the rapidly changing subcircuits. It is of a particular interest to speed up the simulation without a significant loss of accuracy. By exploiting the latency of the system, only a fraction of the equations has to be formulated and solved at a given time point. Günther and Rentrop suggest that multirate strategies must be based both on the numerical information of the integration scheme and on the topology of the circuit. In this paper, we will introduce a directed graph describing the interdependency of the underlying system and propose Runge--Kutta methods which utilize the signal flow of the system in order to identify and exploit inactive regions. Furthermore, we describe an extension of these methods to identify and exploit periodic subsystems.

math.NA↗

arXiv2012

A Traveling Salesman Learns Bayesian Networks

Structure learning of Bayesian networks is an important problem that arises in numerous machine learning applications. In this work, we present a novel approach for learning the structure of Bayesian networks using the solution of an appropriately constructed traveling salesman problem. In our approach, one computes an optimal ordering (partially ordered set) of random variables using methods for the traveling salesman problem. This ordering significantly reduces the search space for the subsequent greedy optimization that computes the final structure of the Bayesian network. We demonstrate our approach of learning Bayesian networks on real world census and weather datasets. In both cases, we demonstrate that the approach very accurately captures dependencies between random variables. We check the accuracy of the predictions based on independent studies in both application domains.

cs.LG↗

arXiv2010

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.

cs.DC↗