Library

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
Source
Years
Language
  • 11
    facet.materialart.
    Unknown
    Spectral Clustering for Non-Reversible Markov Chains (2018)
    Details
    Publication Date: 2023-11-03
    Description: Spectral clustering methods are based on solving eigenvalue problems for the identification of clusters, e.g., the identification of metastable subsets of a Markov chain. Usually, real-valued eigenvectors are mandatory for this type of algorithms. The Perron Cluster Analysis (PCCA+) is a well-known spectral clustering method of Markov chains. It is applicable for reversible Markov chains, because reversibility implies a real-valued spectrum. We also extend this spectral clustering method to non-reversible Markov chains and give some illustrative examples. The main idea is to replace the eigenvalue problem by a real-valued Schur decomposition. By this extension non-reversible Markov chains can be analyzed. Furthermore, the chains do not need to have a positive stationary distribution. In addition to metastabilities, dominant cycles and sinks can also be identified. This novel method is called GenPCCA (i.e., generalized PCCA), since it includes the case of non-reversible processes. We also apply the method to real-world eye-tracking data.
    Language: English
    Type: article , doc-type:article
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    OPUS
  • 12
    facet.materialart.
    Unknown
    Spectral Clustering for Non-reversible Markov Chains (2018)
    Details
    Publication Date: 2023-11-03
    Description: Spectral clustering methods are based on solving eigenvalue problems for the identification of clusters, e.g. the identification of metastable subsets of a Markov chain. Usually, real-valued eigenvectors are mandatory for this type of algorithms. The Perron Cluster Analysis (PCCA+) is a well-known spectral clustering method of Markov chains. It is applicable for reversible Markov chains, because reversibility implies a real-valued spectrum. We also extend this spectral clustering method to non-reversible Markov chains and give some illustrative examples. The main idea is to replace the eigenvalue problem by a real-valued Schur decomposition. By this extension non-reversible Markov chains can be analyzed. Furthermore, the chains do not need to have a positive stationary distribution. In addition to metastabilities, dominant cycles and sinks can also be identified. This novel method is called GenPCCA (i.e. Generalized PCCA), since it includes the case of non reversible processes. We also apply the method to real world eye tracking data.
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    OPUS
  • 13
    facet.materialart.
    Unknown
    Spectral clustering of Markov chain transition matrices with complex eigenvalues (2024)
    Details
    Publication Date: 2024-01-29
    Description: The Robust Perron Cluster Analysis (PCCA+) has become a popular spectral clustering algorithm for coarse-graining transition matrices of nearly decomposable Markov chains with transition states. Originally developed for reversible Markov chains, the algorithm only worked for transition matrices with real eigenvalues. In this paper, we therefore extend the theoretical framework of PCCA+ to Markov chains with a complex eigen-decomposition. We show that by replacing a complex conjugate pair of eigenvectors by their real and imaginary components, a real representation of the same subspace is obtained, which is suitable for the cluster analysis. We show that our approach leads to the same results as the generalized PCCA+ (GPCCA), which replaces the complex eigen-decomposition by a conceptually more difficult real Schur decomposition. We apply the method on non-reversible Markov chains, including circular chains, and demonstrate its efficiency compared to GPCCA. The experiments are performed in the Matlab programming language and codes are provided.
    Language: German
    Type: article , doc-type:article
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    OPUS
  • 14
    facet.materialart.
    Unknown
    cmdtools (2021)
    Details
    Publication Date: 2024-03-18
    Description: Python implementation of severals tools (PCCA, AJC, SQRA, P/Q estimation) for the analysis of dynamical systems from the transfer operator perspective.
    Language: English
    Type: software , doc-type:Other
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    OPUS
  • 15
    facet.materialart.
    Unknown
    Tensor-SqRA: Modeling the transition rates of interacting molecular systems in terms of potential energies (2024)
    Details
    Publication Date: 2024-03-26
    Description: Estimating the rate of rare conformational changes in molecular systems is one of the goals of molecular dynamics simulations. In the past few decades, a lot of progress has been done in data-based approaches toward this problem. In contrast, model-based methods, such as the Square Root Approximation (SqRA), directly derive these quantities from the potential energy functions. In this article, we demonstrate how the SqRA formalism naturally blends with the tensor structure obtained by coupling multiple systems, resulting in the tensor-based Square Root Approximation (tSqRA). It enables efficient treatment of high-dimensional systems using the SqRA and provides an algebraic expression of the impact of coupling energies between molecular subsystems. Based on the tSqRA, we also develop the projected rate estimation, a hybrid data-model-based algorithm that efficiently estimates the slowest rates for coupled systems. In addition, we investigate the possibility of integrating low-rank approximations within this framework to maximize the potential of the tSqRA.
    Language: English
    Type: article , doc-type:article
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    OPUS
  • 16
    facet.materialart.
    Unknown
    Capturing the Macroscopic Behaviour of Molecular Dynamics with Membership Functions (2024)
    Details
    Publication Date: 2024-03-22
    Description: Markov processes serve as foundational models in many scientific disciplines, such as molecular dynamics, and their simulation forms a common basis for analysis. While simulations produce useful trajectories, obtaining macroscopic information directly from microstate data presents significant challenges. This paper addresses this gap by introducing the concept of membership functions being the macrostates themselves. We derive equations for the holding times of these macrostates and demonstrate their consistency with the classical definition. Furthermore, we discuss the application of the ISOKANN method for learning these quantities from simulation data. In addition, we present a novel method for extracting transition paths based on the ISOKANN results and demonstrate its efficacy by applying it to simulations of the 𝜇-opioid receptor. With this approach we provide a new perspective on analyzing the macroscopic behaviour of Markov systems.
    Language: English
    Type: article , doc-type:article
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    OPUS
  • 17
    facet.materialart.
    Unknown
    Learning Koopman eigenfunctions of stochastic diffusions with optimal importance sampling and ISOKANN (2024)
    Details
    Publication Date: 2024-03-21
    Description: The dominant eigenfunctions of the Koopman operator characterize the metastabilities and slow-timescale dynamics of stochastic diffusion processes. In the context of molecular dynamics and Markov state modeling, they allow for a description of the location and frequencies of rare transitions, which are hard to obtain by direct simulation alone. In this article, we reformulate the eigenproblem in terms of the ISOKANN framework, an iterative algorithm that learns the eigenfunctions by alternating between short burst simulations and a mixture of machine learning and classical numerics, which naturally leads to a proof of convergence. We furthermore show how the intermediate iterates can be used to reduce the sampling variance by importance sampling and optimal control (enhanced sampling), as well as to select locations for further training (adaptive sampling). We demonstrate the usage of our proposed method in experiments, increasing the approximation accuracy by several orders of magnitude.
    Language: English
    Type: article , doc-type:article
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    OPUS
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...