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Recursive Approach in Sparse Matrix LU Factorization
51 Recursive approach in sparse matrix LU factorization Jack Dongarra, Victor Eijkhout and the resulting matrix is often guaranteed to be positive Piotr Łuszczek∗ definite or close to it. However, when the linear sys- University of Tennessee, Department of Computer tem matrix is strongly unsymmetric or indefinite, as Science, Knoxville, TN 37996-3450, USA is the case with matrices originating from systems of Tel.: +865 974 8295; Fax: +865 974 8296 ordinary differential equations or the indefinite matri- ces arising from shift-invert techniques in eigenvalue methods, one has to revert to direct methods which are This paper describes a recursive method for the LU factoriza- the focus of this paper. tion of sparse matrices. The recursive formulation of com- In direct methods, Gaussian elimination with partial mon linear algebra codes has been proven very successful in pivoting is performed to find a solution of Eq. (1). Most dense matrix computations. An extension of the recursive commonly, the factored form of A is given by means technique for sparse matrices is presented. Performance re- L U P Q sults given here show that the recursive approach may per- of matrices , , and such that: form comparable to leading software packages for sparse ma- LU = PAQ, (2) trix factorization in terms of execution time, memory usage, and error estimates of the solution. where: – L is a lower triangular matrix with unitary diago- nal, 1. Introduction – U is an upper triangular matrix with arbitrary di- agonal, Typically, a system of linear equations has the form: – P and Q are row and column permutation matri- Ax = b, (1) ces, respectively (each row and column of these matrices contains single a non-zero entry which is A n n A ∈ n×n x where is by real matrix ( R ), and 1, and the following holds: PPT = QQT = I, b n b, x ∈ n and are -dimensional real vectors ( R ). -
Accelerating Matching Pursuit for Multiple Time-Frequency Dictionaries
Proceedings of the 23rd International Conference on Digital Audio Effects (DAFx-20), Vienna, Austria, September 8–12, 2020 ACCELERATING MATCHING PURSUIT FOR MULTIPLE TIME-FREQUENCY DICTIONARIES ZdenˇekPr˚uša,Nicki Holighaus and Peter Balazs ∗ Acoustics Research Institute Austrian Academy of Sciences Vienna, Austria [email protected],[email protected],[email protected] ABSTRACT An overview of greedy algorithms, a class of algorithms MP Matching pursuit (MP) algorithms are widely used greedy meth- falls under, can be found in [10, 11] and in the context of audio ods to find K-sparse signal approximations in redundant dictionar- and music processing in [12, 13, 14]. Notable applications of MP ies. We present an acceleration technique and an implementation algorithms in the audio domain include analysis [15], [16], coding of the matching pursuit algorithm acting on a multi-Gabor dictio- [17, 18, 19], time scaling/pitch shifting [20] [21], source separation nary, i.e., a concatenation of several Gabor-type time-frequency [22], denoising [23], partial and harmonic detection and tracking dictionaries, consisting of translations and modulations of possi- [24]. bly different windows, time- and frequency-shift parameters. The We present a method for accelerating MP-based algorithms proposed acceleration is based on pre-computing and thresholding acting on a single Gabor-type time-frequency dictionary or on a inner products between atoms and on updating the residual directly concatenation of several Gabor dictionaries with possibly different in the coefficient domain, i.e., without the round-trip to thesig- windows and parameters. The main idea of the present accelera- nal domain. -
A Survey of Direct Methods for Sparse Linear Systems
A survey of direct methods for sparse linear systems Timothy A. Davis, Sivasankaran Rajamanickam, and Wissam M. Sid-Lakhdar Technical Report, Department of Computer Science and Engineering, Texas A&M Univ, April 2016, http://faculty.cse.tamu.edu/davis/publications.html To appear in Acta Numerica Wilkinson defined a sparse matrix as one with enough zeros that it pays to take advantage of them.1 This informal yet practical definition captures the essence of the goal of direct methods for solving sparse matrix problems. They exploit the sparsity of a matrix to solve problems economically: much faster and using far less memory than if all the entries of a matrix were stored and took part in explicit computations. These methods form the backbone of a wide range of problems in computational science. A glimpse of the breadth of applications relying on sparse solvers can be seen in the origins of matrices in published matrix benchmark collections (Duff and Reid 1979a) (Duff, Grimes and Lewis 1989a) (Davis and Hu 2011). The goal of this survey article is to impart a working knowledge of the underlying theory and practice of sparse direct methods for solving linear systems and least-squares problems, and to provide an overview of the algorithms, data structures, and software available to solve these problems, so that the reader can both understand the methods and know how best to use them. 1 Wilkinson actually defined it in the negation: \The matrix may be sparse, either with the non-zero elements concentrated ... or distributed in a less systematic manner. We shall refer to a matrix as dense if the percentage of zero elements or its distribution is such as to make it uneconomic to take advantage of their presence." (Wilkinson and Reinsch 1971), page 191, emphasis in the original. -
Paper, We Present Data Fusion Across Multiple Signal Sources
68 IEEE JOURNAL OF SOLID-STATE CIRCUITS, VOL. 51, NO. 1, JANUARY 2016 A Configurable 12–237 kS/s 12.8 mW Sparse-Approximation Engine for Mobile Data Aggregation of Compressively Sampled Physiological Signals Fengbo Ren, Member, IEEE, and Dejan Markovic,´ Member, IEEE Abstract—Compressive sensing (CS) is a promising technology framework, the CS framework has several intrinsic advantages. for realizing low-power and cost-effective wireless sensor nodes First, random encoding is a universal compression method that (WSNs) in pervasive health systems for 24/7 health monitoring. can effectively apply to all compressible signals regardless of Due to the high computational complexity (CC) of the recon- struction algorithms, software solutions cannot fulfill the energy what their sparse domain is. This is a desirable merit for the efficiency needs for real-time processing. In this paper, we present data fusion across multiple signal sources. Second, sampling a 12—237 kS/s 12.8 mW sparse-approximation (SA) engine chip and compression can be performed at the same stage in CS, that enables the energy-efficient data aggregation of compressively allowing for a sampling rate that is significantly lower than the sampled physiological signals on mobile platforms. The SA engine Nyquist rate. Therefore, CS has a potential to greatly impact chip integrated in 40 nm CMOS can support the simultaneous reconstruction of over 200 channels of physiological signals while the data acquisition devices that are sensitive to cost, energy consuming <1% of a smartphone’s power budget. Such energy- consumption, and portability, such as wireless sensor nodes efficient reconstruction enables two-to-three times energy saving (WSNs) in mobile and wearable applications [5]. -
A Fast Implementation of the Minimum Degree Algorithm Using Quotient Graphs
A Fast Implementation of the Minimum Degree Algorithm Using Quotient Graphs ALAN GEORGE University of Waterloo and JOSEPH W. H. LIU Systems Dimensions Ltd. This paper describes a very fast implementation of the m~n~mum degree algorithm, which is an effective heuristm scheme for fmding low-fill ordermgs for sparse positive definite matrices. This implementation has two important features: first, in terms of speed, it is competitive with other unplementations known to the authors, and, second, its storage requirements are independent of the amount of fill suffered by the matrix during its symbolic factorization. Some numerical experiments which compare the performance of this new scheme to some existing minimum degree programs are provided. Key Words and Phrases: sparse linear equations, quotient graphs, ordering algoritl~ms, graph algo- rithms, mathematical software CR Categories: 4.0, 5.14 1. INTRODUCTION Consider the symmetric positive definite system of linear equations Ax = b, (1.1) where A is N by N and sparse. It is well known that ifA is factored by Cholesky's method, it normally suffers some fill-in. Thus, if we intend to solve eq. (1.1) by this method, it is usual first to find a permutation matrix P and solve the reordered system (pApT)(px) = Pb, (1.2) where P is chosen such that PAP T suffers low fill-in when it is factored into LL T. There are four distinct and independent phases that can be identified in the entire computational process: Permmsion to copy without fee all or part of this material m granted provided that the copies are not made or distributed for direct commercial advantage, the ACM copyright notice and the titleof the publication and its date appear, and notice is given that copying ts by permission of the Association for Computing Machinery. -
State-Of-The-Art Sparse Direct Solvers
State-of-The-Art Sparse Direct Solvers Matthias Bollhöfer, Olaf Schenk, Radim Janalík, Steve Hamm, and Kiran Gullapalli Abstract In this chapter we will give an insight into modern sparse elimination meth- ods. These are driven by a preprocessing phase based on combinatorial algorithms which improve diagonal dominance, reduce fill–in and improve concurrency to allow for parallel treatment. Moreover, these methods detect dense submatrices which can be handled by dense matrix kernels based on multi-threaded level–3 BLAS. We will demonstrate for problems arising from circuit simulation how the improvement in recent years have advanced direct solution methods significantly. 1 Introduction Solving large sparse linear systems is at the heart of many application problems arising from engineering problems. Advances in combinatorial methods in combi- nation with modern computer architectures have massively influenced the design of state-of-the-art direct solvers that are feasible for solving larger systems efficiently in a computational environment with rapidly increasing memory resources and cores. Matthias Bollhöfer Institute for Computational Mathematics, TU Braunschweig, Germany, e-mail: m.bollhoefer@tu- bs.de Olaf Schenk Institute of Computational Science, Faculty of Informatics, Università della Svizzera italiana, Switzerland, e-mail: [email protected] arXiv:1907.05309v1 [cs.DS] 11 Jul 2019 Radim Janalík Institute of Computational Science, Faculty of Informatics, Università della Svizzera italiana, Switzerland, e-mail: [email protected] Steve Hamm NXP, United States of America, e-mail: [email protected] Kiran Gullapalli NXP, United States of America, e-mail: [email protected] 1 2 M. Bollhöfer, O. Schenk, R. Janalík, Steve Hamm, and K. -
On the Performance of Minimum Degree and Minimum Local Fill
1 On the performance of minimum degree and minimum local fill heuristics in circuit simulation Gunther Reißig Before you cite this report, please check whether it has already appeared as a journal paper (http://www.reiszig.de/gunther, or e-mail to [email protected]). Thank you. The author is with Massachusetts Institute of Technology, Room 66-363, Dept. of Chemical Engineering, 77 Mas- sachusetts Avenue, Cambridge, MA 02139, U.S.A.. E-Mail: [email protected]. Work supported by Deutsche Forschungs- gemeinschaft. Part of the results of this paper have been obtained while the author was with Infineon Technologies, M¨unchen, Germany. February 1, 2001 DRAFT 2 Abstract Data structures underlying local algorithms for obtaining pivoting orders for sparse symmetric ma- trices are reviewed together with their theoretical background. Recently proposed heuristics as well as improvements to them are discussed and their performance, mainly in terms of the resulting number of factorization operations, is compared with that of the Minimum Degree and the Minimum Local Fill al- gorithms. It is shown that a combination of Markowitz' algorithm with these symmetric methods applied to the unsymmetric matrices arising in circuit simulation yields orderings significantly better than those obtained from Markowitz' algorithm alone, in some cases at virtually no extra computational cost. I. Introduction When the behavior of an electrical circuit is to be simulated, numerical integration techniques are usually applied to its equations of modified nodal analysis. This requires the solution of systems of nonlinear equations, and, in turn, the solution of numerous linear equations of the form Ax = b; (1) where A is a real n × n matrix, typically nonsingular, and x; b ∈ Rn [1–3]. -
Improved Greedy Algorithms for Sparse Approximation of a Matrix in Terms of Another Matrix
Improved Greedy Algorithms for Sparse Approximation of a Matrix in terms of Another Matrix Crystal Maung Haim Schweitzer Department of Computer Science Department of Computer Science The University of Texas at Dallas The University of Texas at Dallas Abstract We consider simultaneously approximating all the columns of a data matrix in terms of few selected columns of another matrix that is sometimes called “the dic- tionary”. The challenge is to determine a small subset of the dictionary columns that can be used to obtain an accurate prediction of the entire data matrix. Previ- ously proposed greedy algorithms for this task compare each data column with all dictionary columns, resulting in algorithms that may be too slow when both the data matrix and the dictionary matrix are large. A previously proposed approach for accelerating the run time requires large amounts of memory to keep temporary values during the run of the algorithm. We propose two new algorithms that can be used even when both the data matrix and the dictionary matrix are large. The first algorithm is exact, with output identical to some previously proposed greedy algorithms. It takes significantly less memory when compared to the current state- of-the-art, and runs much faster when the dictionary matrix is sparse. The second algorithm uses a low rank approximation to the data matrix to further improve the run time. The algorithms are based on new recursive formulas for computing the greedy selection criterion. The formulas enable decoupling most of the compu- tations related to the data matrix from the computations related to the dictionary matrix. -
Tiebreaking the Minimum Degree Algorithm For
TIEBREAKING THE MINIMUM DEGREE ALGORITHM FOR ORDERING SPARSE SYMMETRIC POSITIVE DEFINITE MATRICES by IAN ALFRED CAVERS B.Sc. The University of British Columbia, 1984 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in THE FACULTY OF GRADUATE STUDIES DEPARTMENT OF COMPUTER SCIENCE We accept this thesis as conforming to the required standard THE UNIVERSITY OF BRITISH COLUMBIA December 1987 © Ian Alfred Cavers, 1987 In presenting this thesis in partial fulfilment of the requirements for an advanced degree at the University of British Columbia, I agree that the Library shall make it freely available for reference and study. I further agree that permission for extensive copying of this thesis for scholarly purposes may be granted by the head of my department or by his or her representatives. It is understood that copying or publication of this thesis for financial gain shall not be allowed without my written permission. Department of Computer Science The University of British Columbia 1956 Main Mall Vancouver, Canada V6T 1Y3 Date December 16, 1987 DE-6(3/81) Abstract The minimum degree algorithm is known as an effective scheme for identifying a fill reduced ordering for symmetric, positive definite, sparse linear systems, to be solved using a Cholesky factorization. Although the original algorithm has been enhanced to improve the efficiency of its implementation, ties between minimum degree elimination candidates are still arbitrarily broken. For many systems, the fill levels of orderings produced by the minimum degree algorithm are very sensitive to the precise manner in which these ties are resolved. -
Privacy Preserving Identification Using Sparse Approximation With
Privacy Preserving Identification Using Sparse Approximation with Ambiguization Behrooz Razeghi, Slava Voloshynovskiy, Dimche Kostadinov and Olga Taran Stochastic Information Processing Group, Department of Computer Science, University of Geneva, Switzerland behrooz.razeghi, svolos, dimche.kostadinov, olga.taran @unige.ch f g Abstract—In this paper, we consider a privacy preserving en- Owner Encoder Public Storage coding framework for identification applications covering biomet- +1 N M λx λx L M rics, physical object security and the Internet of Things (IoT). The X × − A × ∈ X 1 ∈ A proposed framework is based on a sparsifying transform, which − X = x (1) , ..., x (m) , ..., x (M) a (m) = T (Wx (m)) n A = a (1) , ..., a (m) , ..., a (M) consists of a trained linear map, an element-wise nonlinearity, { } λx { } and privacy amplification. The sparsifying transform and privacy L p(y (m) x (m)) Encoder | amplification are not symmetric for the data owner and data user. b Schematic Decoding List Probe +1 We demonstrate that the proposed approach is closely related (Private Decoding) y = x (m) + z d (a (m) , b) γL λy λy ≤ − to sparse ternary codes (STC), a recent information-theoretic 1 p (positions) − ´x y = ´x (Pubic Decoding) 1 m M (y) concept proposed for fast approximate nearest neighbor (ANN) ≤ ≤ L Data User b = Tλy (Wy) search in high dimensional feature spaces that being machine learning in nature also offers significant benefits in comparison Fig. 1: Block diagram of the proposed model. to sparse approximation and binary embedding approaches. We demonstrate that the privacy of the database outsourced to a for example biometrics, which being disclosed once, do not server as well as the privacy of the data user are preserved at a represent any more a value for the related security applications. -
Column Subset Selection Via Sparse Approximation of SVD
Column Subset Selection via Sparse Approximation of SVD A.C¸ivrila,∗, M.Magdon-Ismailb aMeliksah University, Computer Engineering Department, Talas, Kayseri 38280 Turkey bRensselaer Polytechnic Institute, Computer Science Department, 110 8th Street Troy, NY 12180-3590 USA Abstract Given a real matrix A 2 Rm×n of rank r, and an integer k < r, the sum of the outer products of top k singular vectors scaled by the corresponding singular values provide the best rank-k approximation Ak to A. When the columns of A have specific meaning, it might be desirable to find good approximations to Ak which use a small number of columns of A. This paper provides a simple greedy algorithm for this problem in Frobenius norm, with guarantees on( the performance) and the number of columns chosen. The algorithm ~ k log k 2 selects c columns from A with c = O ϵ2 η (A) such that k − k ≤ k − k A ΠC A F (1 + ϵ) A Ak F ; where C is the matrix composed of the c columns, ΠC is the matrix projecting the columns of A onto the space spanned by C and η(A) is a measure related to the coherence in the normalized columns of A. The algorithm is quite intuitive and is obtained by combining a greedy solution to the generalization of the well known sparse approximation problem and an existence result on the possibility of sparse approximation. We provide empirical results on various specially constructed matrices comparing our algorithm with the previous deterministic approaches based on QR factorizations and a recently proposed randomized algorithm. -
Modified Sparse Approximate Inverses (MSPAI) for Parallel
Technische Universit¨atM¨unchen Zentrum Mathematik Modified Sparse Approximate Inverses (MSPAI) for Parallel Preconditioning Alexander Kallischko Vollst¨andiger Abdruck der von der Fakult¨atf¨ur Mathematik der Technischen Universit¨at M¨unchen zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigten Dissertation. Vorsitzender: Univ.-Prof. Dr. Peter Rentrop Pr¨ufer der Dissertation: 1. Univ.-Prof. Dr. Thomas Huckle 2. Univ.-Prof. Dr. Bernd Simeon 3. Prof. Dr. Matthias Bollh¨ofer, Technische Universit¨atCarolo-Wilhelmina zu Braunschweig (schriftliche Beurteilung) Die Dissertation wurde am 15.11.2007 bei der Technischen Universit¨ateingereicht und durch die Fakult¨atf¨urMathematik am 18.2.2008 angenommen. ii iii Abstract The solution of large sparse and ill-conditioned systems of linear equations is a central task in numerical linear algebra. Such systems arise from many applications like the discretiza- tion of partial differential equations or image restoration. Herefore, Gaussian elimination or other classical direct solvers can not be used since the dimension of the underlying co- 3 efficient matrices is too large and Gaussian elimination is an O n algorithm. Iterative solvers techniques are an effective remedy for this problem. They allow to exploit sparsity, bandedness, or block structures, and they can be parallelized much easier. However, due to the matrix being ill-conditioned, convergence becomes very slow or even not be guaranteed at all. Therefore, we have to employ a preconditioner. The sparse approximate inverse (SPAI) preconditioner is based on Frobenius norm mini- mization. It is a well-established preconditioner, since it is robust, flexible, and inherently parallel. Moreover, SPAI captures meaningful sparsity patterns automatically.