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Register a new userKinetic Euclidean Distance Matrices
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Added by
Puoya Tabaghi
Publication date
2018
fields
Electronic Engineering
and research's language is
English
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Euclidean distance matrices (EDMs) are a major tool for localization from distances, with applications ranging from protein structure determination to global positioning and manifold learning. They are, however, static objects which serve to localize points from a snapshot of distances. If the objects move, one expects to do better by modeling the motion. In this paper, we introduce Kinetic Euclidean Distance Matrices (KEDMs)---a new kind of time-dependent distance matrices that incorporate motion. The entries of KEDMs become functions of time, the squared time-varying distances. We study two smooth trajectory models---polynomial and bandlimited trajectories---and show that these trajectories can be reconstructed from incomplete, noisy distance observations, scattered over multiple time instants. Our main contribution is a semidefinite relaxation (SDR), inspired by SDRs for static EDMs. Similarly to the static case, the SDR is followed by a spectral factorization step; however, because spectral factorization of polynomial matrices is more challenging than for constant matrices, we propose a new factorization method that uses anchor measurements. Extensive numerical experiments show that KEDMs and the new semidefinite relaxation accurately reconstruct trajectories from noisy, incomplete distance data and that, in fact, motion improves rather than degrades localization if properly modeled. This makes KEDMs a promising tool for problems in geometry of dynamic points sets.
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Euclidean distance matrices (EDM) are matrices of squared distances between points. The definition is deceivingly simple: thanks to their many useful properties they have found applications in psychometrics, crystallography, machine learning, wireless sensor networks, acoustics, and more. Despite the usefulness of EDMs, they seem to be insufficiently known in the signal processing community. Our goal is to rectify this mishap in a concise tutorial. We review the fundamental properties of EDMs, such as rank or (non)definiteness. We show how various EDM properties can be used to design algorithms for completing and denoising distance data. Along the way, we demonstrate applications to microphone position calibration, ultrasound tomography, room reconstruction from echoes and phase retrieval. By spelling out the essential algorithms, we hope to fast-track the readers in applying EDMs to their own problems. Matlab code for all the described algorithms, and to generate the figures in the paper, is available online. Finally, we suggest directions for further research.
In this paper, we present an acoustic localization system for multiple devices. In contrast to systems which localise a device relative to one or several anchor points, we focus on the joint localisation of several devices relative to each other. We present a prototype of our system on off-the-shelf smartphones. No user interaction is required, the phones emit acoustic pulses according to a precomputed schedule. Using the elapsed time between two times of arrivals (ETOA) method with sample counting, distances between the devices are estimated. These, possibly incomplete, distances are the input to an efficient and robust multi-dimensional scaling algorithm returning a position for each phone. We evaluated our system in real-world scenarios, achieving error margins of 15 cm in an office environment.
In this note we reexamine the possibility of extracting parton distribution functions from lattice simulations. We discuss the case of quasi-parton distribution functions, the possibility of using the reduced Ioffe-time distributions and the more recent proposal of directly making reference to the computation of the current-current $T$-product. We show that in all cases the process of renormalization hindered by lattice momenta limitation represents an obstruction to a direct Euclidean calculation of the parton distribution function.
Considering the wide application of network embedding methods in graph data mining, inspired by the adversarial attack in deep learning, this paper proposes a Genetic Algorithm (GA) based Euclidean Distance Attack strategy (EDA) to attack the network embedding, so as to prevent certain structural information from being discovered. EDA focuses on disturbing the Euclidean distance between a pair of nodes in the embedding space as much as possible through minimal modifications of the network structure. Since a large number of downstream network algorithms, such as community detection and node classification, rely on the Euclidean distance between nodes to evaluate the similarity between them in the embedding space, EDA can be considered as a universal attack on a variety of network algorithms. Different from traditional supervised attack strategies, EDA does not need labeling information, and, in other words, is an unsupervised network embedding attack method.
Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly-interconverting states. Here we build upon diffusion map theory and define a kinetic distance for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine pancreatic trypsin inhibitor and protein-inhibitor association in trypsin and benzamidine.
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