Journal ArticleDOI
Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification
Susanna Röblitz,Marcus Weber +1 more
TLDR
It is demonstrated in this paper that PCCA+ always delivers an optimal fuzzy clustering for nearly uncoupled, not necessarily reversible, Markov chains with transition states.Abstract:
Given a row-stochastic matrix describing pairwise similarities between data objects, spectral clustering makes use of the eigenvectors of this matrix to perform dimensionality reduction for clustering in fewer dimensions. One example from this class of algorithms is the Robust Perron Cluster Analysis (PCCA+), which delivers a fuzzy clustering. Originally developed for clustering the state space of Markov chains, the method became popular as a versatile tool for general data classification problems. The robustness of PCCA+, however, cannot be explained by previous perturbation results, because the matrices in typical applications do not comply with the two main requirements: reversibility and nearly decomposability. We therefore demonstrate in this paper that PCCA+ always delivers an optimal fuzzy clustering for nearly uncoupled, not necessarily reversible, Markov chains with transition states.read more
Citations
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Proceedings ArticleDOI
Online Classification of Dynamic Multilayer-Network Time Series in Riemannian Manifolds
TL;DR: Riemannian manifolds are exploited to introduce a geometric framework for online state and community classification in dynamic multilayer networks where nodes are annotated with time series, and it is shown that the proposed geometric framework outperforms state-of-the-art deep-learning models in classification accuracy.
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Investigating the folding mechanism of the N-terminal domain of ribosomal protein L9
TL;DR: In this paper, a mixing replica exchange molecular dynamics method was used to study the folding of the N-terminal domain of ribosomal protein L9 (NTL9).
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Non-equilibrium Markov state modeling of periodically driven biomolecules.
Fabian Knoch,Thomas Speck +1 more
TL;DR: This work introduces a method to construct Markov state models for systems that are driven through periodically changing one (or several) external parameter, and illustrates the method for alanine dipeptide exposed to a time-dependent electric field.
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Molecular dynamics analysis of the structural properties of the transglutaminases of Kutzneria albida and Streptomyces mobaraensis
De Lima Raquel Camargo Giordano,Cassiano Langini,Amedeo Caflisch,Anna Marabotti,Angelo Facchiano +4 more
TL;DR: In this article , the authors compared KalbTGase and MTGase structural flexibility by molecular dynamics simulations at different conditions and found that at room temperature, the enhanced specificity of Kutzneria albida could be related to a more closed catalytic pocket and lower flexibility.
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pH-Induced Local Unfolding of the Phl p 6 Pollen Allergen From cpH-MD.
TL;DR: In this paper, the impact of endosomal acidification on the conformational stability of the major timothy grass pollen allergen Phl p 6 was quantified using state of the art sampling approaches in combination with constant pH MD techniques to profile pH-dependent local unfolding events in atomistic detail.
References
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Journal ArticleDOI
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