Euclidean Distance Matrix Optimization for Sensor Network Localization∗
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Graph Equivalence Classes for Spectral Projector-Based Graph Fourier Transforms Joya A
1 Graph Equivalence Classes for Spectral Projector-Based Graph Fourier Transforms Joya A. Deri, Member, IEEE, and José M. F. Moura, Fellow, IEEE Abstract—We define and discuss the utility of two equiv- Consider a graph G = G(A) with adjacency matrix alence graph classes over which a spectral projector-based A 2 CN×N with k ≤ N distinct eigenvalues and Jordan graph Fourier transform is equivalent: isomorphic equiv- decomposition A = VJV −1. The associated Jordan alence classes and Jordan equivalence classes. Isomorphic equivalence classes show that the transform is equivalent subspaces of A are Jij, i = 1; : : : k, j = 1; : : : ; gi, up to a permutation on the node labels. Jordan equivalence where gi is the geometric multiplicity of eigenvalue 휆i, classes permit identical transforms over graphs of noniden- or the dimension of the kernel of A − 휆iI. The signal tical topologies and allow a basis-invariant characterization space S can be uniquely decomposed by the Jordan of total variation orderings of the spectral components. subspaces (see [13], [14] and Section II). For a graph Methods to exploit these classes to reduce computation time of the transform as well as limitations are discussed. signal s 2 S, the graph Fourier transform (GFT) of [12] is defined as Index Terms—Jordan decomposition, generalized k gi eigenspaces, directed graphs, graph equivalence classes, M M graph isomorphism, signal processing on graphs, networks F : S! Jij i=1 j=1 s ! (s ;:::; s ;:::; s ;:::; s ) ; (1) b11 b1g1 bk1 bkgk I. INTRODUCTION where sij is the (oblique) projection of s onto the Jordan subspace Jij parallel to SnJij. -
EUCLIDEAN DISTANCE MATRIX COMPLETION PROBLEMS June 6
EUCLIDEAN DISTANCE MATRIX COMPLETION PROBLEMS HAW-REN FANG∗ AND DIANNE P. O’LEARY† June 6, 2010 Abstract. A Euclidean distance matrix is one in which the (i, j) entry specifies the squared distance between particle i and particle j. Given a partially-specified symmetric matrix A with zero diagonal, the Euclidean distance matrix completion problem (EDMCP) is to determine the unspecified entries to make A a Euclidean distance matrix. We survey three different approaches to solving the EDMCP. We advocate expressing the EDMCP as a nonconvex optimization problem using the particle positions as variables and solving using a modified Newton or quasi-Newton method. To avoid local minima, we develop a randomized initial- ization technique that involves a nonlinear version of the classical multidimensional scaling, and a dimensionality relaxation scheme with optional weighting. Our experiments show that the method easily solves the artificial problems introduced by Mor´e and Wu. It also solves the 12 much more difficult protein fragment problems introduced by Hen- drickson, and the 6 larger protein problems introduced by Grooms, Lewis, and Trosset. Key words. distance geometry, Euclidean distance matrices, global optimization, dimensional- ity relaxation, modified Cholesky factorizations, molecular conformation AMS subject classifications. 49M15, 65K05, 90C26, 92E10 1. Introduction. Given the distances between each pair of n particles in Rr, n r, it is easy to determine the relative positions of the particles. In many applications,≥ though, we are given only some of the distances and we would like to determine the missing distances and thus the particle positions. We focus in this paper on algorithms to solve this distance completion problem. -
On Asymmetric Distances
Analysis and Geometry in Metric Spaces Research Article • DOI: 10.2478/agms-2013-0004 • AGMS • 2013 • 200-231 On Asymmetric Distances Abstract ∗ In this paper we discuss asymmetric length structures and Andrea C. G. Mennucci asymmetric metric spaces. A length structure induces a (semi)distance function; by using Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy the total variation formula, a (semi)distance function induces a length. In the first part we identify a topology in the set of paths that best describes when the above operations are idempo- tent. As a typical application, we consider the length of paths Received 24 March 2013 defined by a Finslerian functional in Calculus of Variations. Accepted 15 May 2013 In the second part we generalize the setting of General metric spaces of Busemann, and discuss the newly found aspects of the theory: we identify three interesting classes of paths, and compare them; we note that a geodesic segment (as defined by Busemann) is not necessarily continuous in our setting; hence we present three different notions of intrinsic metric space. Keywords Asymmetric metric • general metric • quasi metric • ostensible metric • Finsler metric • run–continuity • intrinsic metric • path metric • length structure MSC: 54C99, 54E25, 26A45 © Versita sp. z o.o. 1. Introduction Besides, one insists that the distance function be symmetric, that is, d(x; y) = d(y; x) (This unpleasantly limits many applications [...]) M. Gromov ([12], Intr.) The main purpose of this paper is to study an asymmetric metric theory; this theory naturally generalizes the metric part of Finsler Geometry, much as symmetric metric theory generalizes the metric part of Riemannian Geometry. -
Dimensionality Reduction
CHAPTER 7 Dimensionality Reduction We saw in Chapter 6 that high-dimensional data has some peculiar characteristics, some of which are counterintuitive. For example, in high dimensions the center of the space is devoid of points, with most of the points being scattered along the surface of the space or in the corners. There is also an apparent proliferation of orthogonal axes. As a consequence high-dimensional data can cause problems for data mining and analysis, although in some cases high-dimensionality can help, for example, for nonlinear classification. Nevertheless, it is important to check whether the dimensionality can be reduced while preserving the essential properties of the full data matrix. This can aid data visualization as well as data mining. In this chapter we study methods that allow us to obtain optimal lower-dimensional projections of the data. 7.1 BACKGROUND Let the data D consist of n points over d attributes, that is, it is an n × d matrix, given as ⎛ ⎞ X X ··· Xd ⎜ 1 2 ⎟ ⎜ x x ··· x ⎟ ⎜x1 11 12 1d ⎟ ⎜ x x ··· x ⎟ D =⎜x2 21 22 2d ⎟ ⎜ . ⎟ ⎝ . .. ⎠ xn xn1 xn2 ··· xnd T Each point xi = (xi1,xi2,...,xid) is a vector in the ambient d-dimensional vector space spanned by the d standard basis vectors e1,e2,...,ed ,whereei corresponds to the ith attribute Xi . Recall that the standard basis is an orthonormal basis for the data T space, that is, the basis vectors are pairwise orthogonal, ei ej = 0, and have unit length ei = 1. T As such, given any other set of d orthonormal vectors u1,u2,...,ud ,withui uj = 0 T and ui = 1(orui ui = 1), we can re-express each point x as the linear combination x = a1u1 + a2u2 +···+adud (7.1) 183 184 Dimensionality Reduction T where the vector a = (a1,a2,...,ad ) represents the coordinates of x in the new basis. -
Linear Algebra
Linear Algebra July 28, 2006 1 Introduction These notes are intended for use in the warm-up camp for incoming Berkeley Statistics graduate students. Welcome to Cal! We assume that you have taken a linear algebra course before and that most of the material in these notes will be a review of what you already know. If you have never taken such a course before, you are strongly encouraged to do so by taking math 110 (or the honors version of it), or by covering material presented and/or mentioned here on your own. If some of the material is unfamiliar, do not be intimidated! We hope you find these notes helpful! If not, you can consult the references listed at the end, or any other textbooks of your choice for more information or another style of presentation (most of the proofs on linear algebra part have been adopted from Strang, the proof of F-test from Montgomery et al, and the proof of bivariate normal density from Bickel and Doksum). Go Bears! 1 2 Vector Spaces A set V is a vector space over R and its elements are called vectors if there are 2 opera- tions defined on it: 1. Vector addition, that assigns to each pair of vectors v ; v V another vector w V 1 2 2 2 (we write v1 + v2 = w) 2. Scalar multiplication, that assigns to each vector v V and each scalar r R another 2 2 vector w V (we write rv = w) 2 that satisfy the following 8 conditions v ; v ; v V and r ; r R: 8 1 2 3 2 8 1 2 2 1. -
Linear Algebra with Exercises B
Linear Algebra with Exercises B Fall 2017 Kyoto University Ivan Ip These notes summarize the definitions, theorems and some examples discussed in class. Please refer to the class notes and reference books for proofs and more in-depth discussions. Contents 1 Abstract Vector Spaces 1 1.1 Vector Spaces . .1 1.2 Subspaces . .3 1.3 Linearly Independent Sets . .4 1.4 Bases . .5 1.5 Dimensions . .7 1.6 Intersections, Sums and Direct Sums . .9 2 Linear Transformations and Matrices 11 2.1 Linear Transformations . 11 2.2 Injection, Surjection and Isomorphism . 13 2.3 Rank . 14 2.4 Change of Basis . 15 3 Euclidean Space 17 3.1 Inner Product . 17 3.2 Orthogonal Basis . 20 3.3 Orthogonal Projection . 21 i 3.4 Orthogonal Matrix . 24 3.5 Gram-Schmidt Process . 25 3.6 Least Square Approximation . 28 4 Eigenvectors and Eigenvalues 31 4.1 Eigenvectors . 31 4.2 Determinants . 33 4.3 Characteristic polynomial . 36 4.4 Similarity . 38 5 Diagonalization 41 5.1 Diagonalization . 41 5.2 Symmetric Matrices . 44 5.3 Minimal Polynomials . 46 5.4 Jordan Canonical Form . 48 5.5 Positive definite matrix (Optional) . 52 5.6 Singular Value Decomposition (Optional) . 54 A Complex Matrix 59 ii Introduction Real life problems are hard. Linear Algebra is easy (in the mathematical sense). We make linear approximations to real life problems, and reduce the problems to systems of linear equations where we can then use the techniques from Linear Algebra to solve for approximate solutions. Linear Algebra also gives new insights and tools to the original problems. -
Nonlinear Mapping and Distance Geometry
Nonlinear Mapping and Distance Geometry Alain Franc, Pierre Blanchard , Olivier Coulaud arXiv:1810.08661v2 [cs.CG] 9 May 2019 RESEARCH REPORT N° 9210 October 2018 Project-Teams Pleiade & ISSN 0249-6399 ISRN INRIA/RR--9210--FR+ENG HiePACS Nonlinear Mapping and Distance Geometry Alain Franc ∗†, Pierre Blanchard ∗ ‡, Olivier Coulaud ‡ Project-Teams Pleiade & HiePACS Research Report n° 9210 — version 2 — initial version October 2018 — revised version April 2019 — 14 pages Abstract: Distance Geometry Problem (DGP) and Nonlinear Mapping (NLM) are two well established questions: Distance Geometry Problem is about finding a Euclidean realization of an incomplete set of distances in a Euclidean space, whereas Nonlinear Mapping is a weighted Least Square Scaling (LSS) method. We show how all these methods (LSS, NLM, DGP) can be assembled in a common framework, being each identified as an instance of an optimization problem with a choice of a weight matrix. We study the continuity between the solutions (which are point clouds) when the weight matrix varies, and the compactness of the set of solutions (after centering). We finally study a numerical example, showing that solving the optimization problem is far from being simple and that the numerical solution for a given procedure may be trapped in a local minimum. Key-words: Distance Geometry; Nonlinear Mapping, Discrete Metric Space, Least Square Scaling; optimization ∗ BIOGECO, INRA, Univ. Bordeaux, 33610 Cestas, France † Pleiade team - INRIA Bordeaux-Sud-Ouest, France ‡ HiePACS team, Inria Bordeaux-Sud-Ouest, -
Distance Geometry and Data Science1
TOP (invited survey, to appear in 2020, Issue 2) Distance Geometry and Data Science1 Leo Liberti1 1 LIX CNRS, Ecole´ Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France Email:[email protected] September 19, 2019 Dedicated to the memory of Mariano Bellasio (1943-2019). Abstract Data are often represented as graphs. Many common tasks in data science are based on distances between entities. While some data science methodologies natively take graphs as their input, there are many more that take their input in vectorial form. In this survey we discuss the fundamental problem of mapping graphs to vectors, and its relation with mathematical programming. We discuss applications, solution methods, dimensional reduction techniques and some of their limits. We then present an application of some of these ideas to neural networks, showing that distance geometry techniques can give competitive performance with respect to more traditional graph-to-vector map- pings. Keywords: Euclidean distance, Isometric embedding, Random projection, Mathematical Program- ming, Machine Learning, Artificial Neural Networks. Contents 1 Introduction 2 2 Mathematical Programming 4 2.1 Syntax . .4 2.2 Taxonomy . .4 2.3 Semantics . .5 2.4 Reformulations . .5 arXiv:1909.08544v1 [cs.LG] 18 Sep 2019 3 Distance Geometry 6 3.1 The distance geometry problem . .7 3.2 Number of solutions . .7 3.3 Applications . .8 3.4 Complexity . 10 1This research was partly funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement n. 764759 ETN \MINOA". 1 INTRODUCTION 2 4 Representing data by graphs 10 4.1 Processes . -
Applied Linear Algebra and Differential Equations
Applied Linear Algebra and Differential Equations Lecture notes for MATH 2350 Jeffrey R. Chasnov The Hong Kong University of Science and Technology Department of Mathematics Clear Water Bay, Kowloon Hong Kong Copyright ○c 2017-2019 by Jeffrey Robert Chasnov This work is licensed under the Creative Commons Attribution 3.0 Hong Kong License. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/hk/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA. Preface What follows are my lecture notes for a mathematics course offered to second-year engineering students at the the Hong Kong University of Science and Technology. Material from our usual courses on linear algebra and differential equations have been combined into a single course (essentially, two half-semester courses) at the request of our Engineering School. I have tried my best to select the most essential and interesting topics from both courses, and to show how knowledge of linear algebra can improve students’ understanding of differential equations. All web surfers are welcome to download these notes and to use the notes and videos freely for teaching and learning. I also have some online courses on Coursera. You can click on the links below to explore these courses. If you want to learn differential equations, have a look at Differential Equations for Engineers If your interests are matrices and elementary linear algebra, try Matrix Algebra for Engineers If you want to learn vector calculus (also known as multivariable calculus, or calcu- lus three), you can sign up for Vector Calculus for Engineers And if your interest is numerical methods, have a go at Numerical Methods for Engineers Jeffrey R. -
Projection Matrices
Projection Matrices Ed Angel Professor of Computer Science, Electrical and Computer Engineering, and Media Arts University of New Mexico Angel: Interactive Computer Graphics 4E © Addison-Wesley 2005 1 Objectives • Derive the projection matrices used for standard OpenGL projections • Introduce oblique projections • Introduce projection normalization Angel: Interactive Computer Graphics 4E © Addison-Wesley 2005 2 Normalization • Rather than derive a different projection matrix for each type of projection, we can convert all projections to orthogonal projections with the default view volume • This strategy allows us to use standard transformations in the pipeline and makes for efficient clipping Angel: Interactive Computer Graphics 4E © Addison-Wesley 2005 3 Pipeline View modelview projection perspective transformation transformation division 4D → 3D nonsingular clipping Hidden surface removal projection 3D → 2D against default cube Angel: Interactive Computer Graphics 4E © Addison-Wesley 2005 4 Notes • We stay in four-dimensional homogeneous coordinates through both the modelview and projection transformations - Both these transformations are nonsingular - Default to identity matrices (orthogonal view) • Normalization lets us clip against simple cube regardless of type of projection • Delay final projection until end - Important for hidden-surface removal to retain depth information as long as possible Angel: Interactive Computer Graphics 4E © Addison-Wesley 2005 5 Orthogonal Normalization glOrtho(left,right,bottom,top,near,far) normalization -
Six Mathematical Gems from the History of Distance Geometry
Six mathematical gems from the history of Distance Geometry Leo Liberti1, Carlile Lavor2 1 CNRS LIX, Ecole´ Polytechnique, F-91128 Palaiseau, France Email:[email protected] 2 IMECC, University of Campinas, 13081-970, Campinas-SP, Brazil Email:[email protected] February 28, 2015 Abstract This is a partial account of the fascinating history of Distance Geometry. We make no claim to completeness, but we do promise a dazzling display of beautiful, elementary mathematics. We prove Heron’s formula, Cauchy’s theorem on the rigidity of polyhedra, Cayley’s generalization of Heron’s formula to higher dimensions, Menger’s characterization of abstract semi-metric spaces, a result of G¨odel on metric spaces on the sphere, and Schoenberg’s equivalence of distance and positive semidefinite matrices, which is at the basis of Multidimensional Scaling. Keywords: Euler’s conjecture, Cayley-Menger determinants, Multidimensional scaling, Euclidean Distance Matrix 1 Introduction Distance Geometry (DG) is the study of geometry with the basic entity being distance (instead of lines, planes, circles, polyhedra, conics, surfaces and varieties). As did much of Mathematics, it all began with the Greeks: specifically Heron, or Hero, of Alexandria, sometime between 150BC and 250AD, who showed how to compute the area of a triangle given its side lengths [36]. After a hiatus of almost two thousand years, we reach Arthur Cayley’s: the first paper of volume I of his Collected Papers, dated 1841, is about the relationships between the distances of five points in space [7]. The gist of what he showed is that a tetrahedron can only exist in a plane if it is flat (in fact, he discussed the situation in one more dimension). -
Questions for Linear Algebra
www.YoYoBrain.com - Accelerators for Memory and Learning Questions for Linear Algebra Category: Default - (148 questions) Linear Algebra: Wronskian of a set of Let (y1, y2, ... yn} be a set of functions which function have n-1 derivatives on an interval I. The determinant:| y1, y2, .... yn || y1', y2', ... yn'||.......................|| y1 (n-1 derivative)..... yn (n-1 derivative) | Linear Algebra: Wronskian test for linear Let { y1, y2, .... yn } be a set of nth order independence linear homogeneous differential equations.This set is linearly independent if and only if the Wronskian is not identically equal to zero Linear Algebra: define the dimension of a if w is a basis of vector space then the vector space number of elements in w is dimension Linear Algebra: if A is m x n matrix define row space - subspace of R^n spanned by row and column space of matrix row vectors of Acolum space subspace of R^m spanned by the column vectors of A Linear Algebra: if A is a m x n matrix, then have the same dimension the row space and the column space of A _____ Linear Algebra: if A is a m x n matrix, then have the same dimension the row space and the column space of A _____ Linear Algebra: define the rank of matrix dimension of the row ( or column ) space of a matrix A is called the rank of Arank( A ) Linear Algebra: how to determine the row put matrix in row echelon form and the space of a matrix non-zero rows form the basis of row space of A Linear Algebra: if A is an m x n matrix of rank n x r r, then the dimension of the solution space of Ax=0 is _____ Linear Algebra: define the coordinate Let B = {v1, v2, ..