4,339 research outputs found
Large Scale Spectral Clustering Using Approximate Commute Time Embedding
Spectral clustering is a novel clustering method which can detect complex
shapes of data clusters. However, it requires the eigen decomposition of the
graph Laplacian matrix, which is proportion to and thus is not
suitable for large scale systems. Recently, many methods have been proposed to
accelerate the computational time of spectral clustering. These approximate
methods usually involve sampling techniques by which a lot information of the
original data may be lost. In this work, we propose a fast and accurate
spectral clustering approach using an approximate commute time embedding, which
is similar to the spectral embedding. The method does not require using any
sampling technique and computing any eigenvector at all. Instead it uses random
projection and a linear time solver to find the approximate embedding. The
experiments in several synthetic and real datasets show that the proposed
approach has better clustering quality and is faster than the state-of-the-art
approximate spectral clustering methods
Erratum: Signal propagation in proteins and relation to equilibrium fluctuations (PLoS Computational Biology (2007) 3, 9, (e172) DOI: 10.1371/journal.pcbi.0030172))
Elastic network (EN) models have been widely used in recent years for describing protein dynamics, based on the premise that the motions naturally accessible to native structures are relevant to biological function. We posit that equilibrium motions also determine communication mechanisms inherent to the network architecture. To this end, we explore the stochastics of a discrete-time, discrete-state Markov process of information transfer across the network of residues. We measure the communication abilities of residue pairs in terms of hit and commute times, i.e., the number of steps it takes on an average to send and receive signals. Functionally active residues are found to possess enhanced communication propensities, evidenced by their short hit times. Furthermore, secondary structural elements emerge as efficient mediators of communication. The present findings provide us with insights on the topological basis of communication in proteins and design principles for efficient signal transduction. While hit/commute times are information-theoretic concepts, a central contribution of this work is to rigorously show that they have physical origins directly relevant to the equilibrium fluctuations of residues predicted by EN models
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