Conference2024 IEEE High Performance Extreme Computing Conference Hpec 2024 · January 1, 2024
In this work, we establish theoretical and practical connections between vertex indexing for sparse graph/network compression and matrix ordering for sparse matrix-vector multiplication and variable elimination. We present a fundamental analysis of adjacen ...
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Conference2023 IEEE High Performance Extreme Computing Conference Hpec 2023 · January 1, 2023
We introduce a novel approach for parallel data clustering with resolution variation. Conventional graph clustering is typically governed by a function defined over all possible cluster configurations but at a fixed value of the resolution hyperparameter d ...
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Journal ArticleIEEE J Biomed Health Inform · January 2022
In [1], the dose estimation accuracy using the alternative baseline method under modulated tube current was not correctly calculated due to an unintentional simulation error. ...
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Conference2022 IEEE High Performance Extreme Computing Conference Hpec 2022 · January 1, 2022
We introduce the novel graph-based algorithm SLAM (simultaneous local assortative mixing) for fast and high-quality superpixel segmentation of any large color image. Super-pixels are compact semantic image elements; superpixel segmen-tation is fundamental ...
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Journal ArticleIEEE J Biomed Health Inform · August 2021
OBJECTIVE: This study aims to develop and validate a novel framework, iPhantom, for automated creation of patient-specific phantoms or "digital-twins (DT)" using patient medical images. The framework is applied to assess radiation dose to radiosensitive or ...
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Conference2021 IEEE High Performance Extreme Computing Conference Hpec 2021 · January 1, 2021
We introduce a new method for vertex clustering or community detection on directed graphs (digraphs). The new method is an extension of the BlueRed method introduced initially for undirected graphs. Complementary to supervised or semisupervised classificat ...
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Journal Article2020 IEEE High Performance Extreme Computing Conference Hpec 2020 · September 22, 2020
We introduce the computational problem of graphlet transform of a sparse graph. Graphlets are fundamental topology elements of all graphs/networks. They can be used as coding elements to encode graph-topological information at multiple granularity levels, ...
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Journal ArticleArXiv · September 1, 2020
We introduce a new method for temporal pattern analysis of scientific collaboration networks. We investigate in particular virus research activities through five epidemic or pandemic outbreaks in the recent two decades and in the ongoing pandemic with COVI ...
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Journal Article2019 IEEE High Performance Extreme Computing Conference Hpec 2019 · September 1, 2019
We introduce SG-t-SNE, a nonlinear method for embedding stochastic graphs/networks into d-dimensional spaces, d = 1, 2, 3, without requiring vertex features to reside in, or be transformed into, a metric space. Graphs/networks are relational data, prevalen ...
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Conference2019 IEEE High Performance Extreme Computing Conference Hpec 2019 · September 1, 2019
We establish first a theoretical foundation for the use of Gromov-Hausdorff (GH) distance for point set registration with homeomorphic deformation maps perturbed by Gaussian noise. We then present a probabilistic, deformable registration framework. At the ...
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Conference2018 IEEE High Performance Extreme Computing Conference Hpec 2018 · November 26, 2018
The density peaks (DP) algorithm for cluster analysis, introduced by Rodriguez and Laio in 2014, has proven empirically competitive or superior in multiple aspects to other contemporary clustering algorithms. Yet, it suffers from certain drawbacks and limi ...
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Conference2018 IEEE High Performance Extreme Computing Conference Hpec 2018 · November 26, 2018
We extend the personalized PageRank model invented by Brin and Page to a model family, endowing each model with a characteristic damping scheme. On social bio-physical networks of today, actions, reactions and counteractions vary or unfold more than ever. ...
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Journal ArticleMed Phys · July 2018
PURPOSE: Often, the inverse deformation vector field (DVF) is needed together with the corresponding forward DVF in four-dimesional (4D) reconstruction and dose calculation, adaptive radiation therapy, and simultaneous deformable registration. This study a ...
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ConferenceOceans 2016 Mts IEEE Monterey Oce 2016 · November 28, 2016
Whale vocalizations can be modeled as polynomial-phase signals, which are widely used in radar and sonar applications. Such signals lie on a nonlinear manifold parameterized by polynomial phase coefficients. In this paper, we apply manifold learning method ...
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Journal ArticleCommunications in Computational Physics · August 1, 2016
We present RECFMM, a program representation and implementation of a recursive scheme for parallelizing the adaptive fast multipole method (FMM) on shared-memory computers. It achieves remarkable high performance while maintaining mathematical clarity and f ...
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Journal ArticleComputer Physics Communications · May 1, 2015
We present PAFMPB, an updated and parallel version of the AFMPB software package for fast calculation of molecular solvation-free energy. The new version has the following new features: (1) The adaptive fast multipole method and the boundary element method ...
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ConferenceInternational Conference for High Performance Computing Networking Storage and Analysis Sc · January 16, 2014
In this work, we provide energy-efficient architectural support for floating point accuracy. For each floating point addition performed, we "recycle" that operation's rounding error. We make this error architecturally visible such that it can be used, when ...
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Journal ArticleProceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition · November 15, 2013
We present a novel method for aligning images in an HDR (high-dynamic-range) image stack to produce a new exposure stack where all the images are aligned and appear as if they were taken simultaneously, even in the case of highly dynamic scenes. Our method ...
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Journal Article2013 IEEE High Performance Extreme Computing Conference Hpec 2013 · January 1, 2013
We address certain properties that arise in gigapixel-scale image stitching for snapshot images captured with a novel micro-camera array system, AWARE-2. This system features a greatly extended field of view and high optical resolution, offering unique sen ...
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Journal ArticleCommunications in Computational Physics · January 1, 2013
This paper summarizes the mathematical and numerical theories and computational elements of the adaptive fast multipole Poisson-Boltzmann (AFMPB) solver. We introduce and discuss the following components in order: the Poisson-Boltzmann model, boundary inte ...
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Journal Article2012 IEEE Conference on High Performance Extreme Computing Hpec 2012 · December 1, 2012
We present a new study of parallel algorithms for locating k-nearest neighbors (kNN) of each single query in a high dimensional (feature) space on a many-core processor or accelerator that favors synchronous operations, such as on a graphics processing uni ...
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Journal ArticleJournal of Circuits Systems and Computers · April 1, 2012
The nonuniform FFT (NuFFT) is widely used in many applications. Focusing on the most time-consuming part of the NuFFT computation, the data translation step, in this paper, we develop an automatic parallel code generation tool for data translation targetin ...
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Journal ArticleJournal of Computational Physics · January 1, 2011
We present in this paper a new kernel-independent fast multipole method (FMM), named as FKI-FMM, for pairwise particle interactions with translation-invariant kernel functions. FKI-FMM creates, using numerical techniques, sufficiently accurate and compress ...
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Journal ArticleComputer Physics Communications · December 1, 2010
FMM–YUKAWA is a mathematical software package primarily for rapid evaluation of the screened Coulomb interactions of N particles in three dimensional space. Since its release, we have revised and re-organized the data structure, software architecture, and ...
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Journal ArticleLecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics · November 19, 2010
The non-uniform FFT (NuFFT) has been widely used in many applications. In this paper, we propose two new scalable parallelization strategies to accelerate the data translation step of the NuFFT on multicore machines. Both schemes employ geometric tiling an ...
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Journal ArticleProceedings Design Automation and Test in Europe Date · June 9, 2010
Elementary functions are extensively used in computer graphics, signal and image processing, and communication systems. This paper presents a special-purpose compiler that automatically generates customized look-up tables and implementations for elementary ...
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Journal ArticleEmbedded Systems Week 2009 Proceedings of the 7th ACM International Conference on Embedded Software Emsoft 09 · December 24, 2009
This paper introduces parallelization strategies for the Non-Uniform FFT (NUFFT) data translation on multicore architectures. The NUFFT enables the use of the celebrated FFT with un-equally spaced data in numerous situations in signal and image processing ...
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Journal ArticleIEEE Transactions on Computers · December 1, 2009
This paper describes TANOR, an automated framework for designing hardware accelerators for numerical computation on reconfigurable platforms. Applications utilizing numerical algorithms on large-size data sets require high-throughput computation platforms. ...
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Journal ArticleProceedings of SPIE the International Society for Optical Engineering · November 11, 2009
This paper presents a systematic approach for automatic generation of look-up-table (LUT) for function evaluations and minimization in hardware resource on field programmable gate arrays (FPGAs). The class of functions supported by this approach includes s ...
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Journal ArticleProceedings of SPIE the International Society for Optical Engineering · November 11, 2009
This paper presents an acceleration method, using both algorithmic and architectural means, for fast calculation of local correlation coefficients, which is a basic image-based information processing step for template or pattern matching, image registratio ...
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Journal ArticleApplied optics · April 2009
We describe a multiple-aperture long-wave infrared camera built on an uncooled microbolometer array with the objective of decreasing camera thickness. The 5 mm thick optical system is an f/1.2 design with a 6.15 mm effective focal length. An integrated ima ...
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Journal ArticleOptics express · April 2009
We have previously reported on coded aperture snapshot spectral imagers (CASSI) that can capture a full frame spectral image in a snapshot. Here we describe the use of CASSI for spectral imaging of a dynamic scene at video rate. We describe significant adv ...
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Journal ArticleProceedings of SPIE the International Society for Optical Engineering · December 18, 2008
This paper presents an acceleration method, using both algorithmic and architectural means, for fast calculation of local correlation coefficients , which is a basic image-based information processing step for template or pattern matching, image registrati ...
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Journal ArticleProceedings of SPIE the International Society for Optical Engineering · December 17, 2008
This paper describes numerical estimation techniques for coded aperture snapshot spectral imagers (CASSI). In a snapshot, a CASSI captures a two-dimensional (2D) array of measurements that is an encoded representation of both spectral information and 2D sp ...
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Journal ArticleProceedings of SPIE the International Society for Optical Engineering · December 17, 2008
We address the discrepancy that existed between the low arithmetic complexity of nonuniform Fast Fourier Transform (NUFFT) algorithms and high latency in practical use of NUFFTs with large data sets, especially, in multi-dimensional domains. The execution ...
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Journal ArticleProceedings of SPIE the International Society for Optical Engineering · December 17, 2008
This paper introduces the theoretical development of a numerical method, named NeAREst, for solving non-negative linear inverse problems, which arise often from physical or probabilistic models, especially, in image estimation with limited and indirect mea ...
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Journal ArticleApplied optics · April 2008
We introduce a framework of focal-plane coding schemes for multichannel sampling in optical systems. A particular objective is to develop an ultrathin imager without compromising image resolution. We present a complete f/2.1 optical system with a thickness ...
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Journal ArticleElectronic Transactions on Numerical Analysis · January 1, 2008
This contribution proposes a decompositional iterative method with low memory requirements for the steadystate analysis ofKronecker structured Markov chains. The Markovian system is formed by a composition of subsystems using the Kronecker sum operator for ...
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Journal ArticleProceedings 2007 International Conference on Field Programmable Logic and Applications Fpl · December 1, 2007
Algorithm-architecture co-exploration is hindered by the lack of efficient tools. As a consequence, designers are currently able to explore only a limited set of points in the whole design space. There-fore, a tool that can allow fast exploration of algori ...
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Journal ArticleIEEE Workshop on Signal Processing Systems Sips Design and Implementation · December 1, 2007
A hardware efficient approach is introduced for elementary function evaluations in certain structured matrix computations. It is a comprehensive approach that utilizes lookup tables for compactness, employs interpolations with adders and multipliers for th ...
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Journal ArticleProceedings of SPIE the International Society for Optical Engineering · September 18, 2006
This paper describes a compressive sensing strategy developed under the Compressive Optical MONTAGE Photography Initiative. Multiplex and multi-channel measurements are generally necessary for compressive sensing. In a compressive imaging system described ...
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Journal ArticleProceedings of SPIE - The International Society for Optical Engineering · 2006
We consider compressive sensing in the context of optical spectroscopy. With compressive sensing, the ratio between the number of measurements and the number of estimated values is less than one, without compromising the fidelity in estimation. A compressi ...
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Journal Article2006 IEEE International Systems on Chip Conference Soc · January 1, 2006
This work focuses on reducing power consumption while maintaining the efficiency and accuracy of matrix computations using both algorithmic and architectural means. We transform the algorithms, in adaptation to application specifics, to translate the matri ...
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Journal ArticleProceedings of SPIE the International Society for Optical Engineering · November 15, 2005
We introduce a novel approach for compressive coding at the sensor layer for an integrated imaging system. Compression at the physical layer reduces the measurements-to-pixels ratio and the data volume for storage and transmission, without confounding imag ...
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Journal ArticleIEEE Transactions on Reliability · September 1, 2005
We present a hierarchical model for the analysis of proactive fault management in the presence of system resource leaks. At the low level of the model hierarchy is a degradation model in which we use a nonhomogeneous Markov chain to establish an explicit c ...
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Journal ArticleMathematics of Computation · October 1, 2004
We provide a different perspective of the spectral division methods for block generalized Schur decompositions of matrix pairs. The new approach exposes more algebraic structures of the successive matrix pairs in the spectral division iterations and reveal ...
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Journal ArticleJournal of the Optical Society of America. A, Optics, image science, and vision · July 2004
Reference structure tomography (RST) uses multidimensional modulations to encode mappings between radiating objects and measurements. RST may be used to image source-density distributions, estimate source parameters, or classify sources. The RST paradigm p ...
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Journal ArticleProceedings of the International Conference on Dependable Systems and Networks · December 1, 2003
We present a framework of adaptive estimation and rejuvenation of software system performance in the presence of aging sources. The framework specifies that a degradation model not only describe an aging process but also enable the adaptation of model-base ...
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Journal ArticleSIAM Journal on Matrix Analysis and Applications · January 1, 2003
We present a matrix representation for the fast Gauss transform (FGT) originally proposed by Greengard and Strain. With the matrix representation we reveal the matrix structures explored and exploited in the FGT, relate the multidimensional FGT to the one- ...
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Journal ArticleSIAM Journal on Scientific Computing · January 1, 2003
In this paper we present modified algorithms for computing deflating subspaces of matrix pairs using the matrix sign function. Our new algorithms achieve a considerable reduction of the computational cost of the generalized Newton iteration for the matrix ...
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Journal ArticleApplied Numerical Mathematics · January 1, 2002
We propose a methodology aimed at automating the software development of fast discrete transforms for N-body problems. The methodology starts with a representation of the transform matrix in compact form. Then, two translation phases are applied. One trans ...
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Journal ArticleACM Transactions on Modeling and Computer Simulation · April 1, 2001
Trace-driven simulation is a valuable tool for evaluating I/O systems. This article presents a new algorithm, called FASTSLIM, that reduces the size of I/O traces and improves simulation performance without compromising simulation accuracy. FASTSLIM is mor ...
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Journal ArticleSIAM Review · January 1, 2001
We present a matrix interpretation of the three-dimensional fast multipole method (FMM). The FMM is for efficient computation of gravitational/electrostatic potentials and fields. It has found various applications and inspired the design of many efficient ...
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Journal ArticleSIAM Journal on Scientific Computing · January 1, 2001
We present one-sweep parallel algorithms for the inversion of general and symmetric positive definite matrices. The algorithms feature simple programming and performance optimization while maintaining the same arithmetic cost and numerical properties of co ...
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Journal ArticleInternational Journal of High Speed Computing · December 1, 2000
In this paper we demonstrate the parallelism of the spectral division using the matrix sign function for the generalized nonsymmetric eigenproblem. We employ the so-called generalized Newton iterative scheme in order to compute the sign function of the mat ...
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Journal ArticleLinear Algebra and Its Applications · September 1, 2000
We derive efficient approaches for two-parameter Hankel transforms. Such transforms arise, for example, in covariance matrix computations for performance modeling and evaluation of adaptive optics (AO) systems. Fast transforms are highly desirable since th ...
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Journal ArticleLinear Algebra and Its Applications · September 1, 2000
The wave front field aberrations induced by atmospheric turbulence can severely degrade the performance of an optical imaging system. Adaptive optics refers to the process of removing unwanted wave front distortions in real time, i.e., before the image is ...
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Journal ArticlePhysical Review A Atomic Molecular and Optical Physics · January 1, 2000
A constructive procedure for generating a prescribed unitary transform via the optically driven evolution of a multilevel atom is described. Assuming a clean separation of the coupled levels, the procedure employs the rotating wave approximation together w ...
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Journal ArticleACM Transactions on Mathematical Software · January 1, 2000
We develop an algorithmic framework for reducing the bandwidth of symmetric matrices via orthogonal similarity transformations. This framework includes the reduction of full matrices to banded or tridiagonal form and the reduction of banded matrices to nar ...
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Journal ArticleACM Transactions on Mathematical Software · January 1, 2000
We present a software toolbox for symmetric band reduction via orthogonal transformations, together with a testing and timing program. The toolbox contains drivers and computational routines for the reduction of full symmetric matrices to banded form and t ...
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Journal ArticlePhysical Review A Atomic Molecular and Optical Physics · January 1, 2000
A constructive procedure for generating a prescribed unitary transform via the optically driven evolution of a multilevel atom is described. Assuming a clean separation of the coupled levels, the procedure employs the rotating wave approximation together w ...
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Journal ArticleProceedings of SPIE the International Society for Optical Engineering · December 1, 1998
Real-time adaptive-optics is a means for enhancing the resolution of ground based, optical telescopes beyond the limits previously imposed by the turbulent atmosphere. One approach for linear performance modeling of closed-loop adaptive-optics systems invo ...
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Journal ArticleSIAM Journal on Scientific Computing · January 1, 1998
The QR factorization with column pivoting (QRP), originally suggested by Golub [Numer. Math., 7 (1965), 206-216], is a popular approach to computing rank-revealing factorizations. Using Level 1 BLAS, it was implemented in LINPACK, and, using Level 2 BLAS, ...
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Journal ArticleSIAM Journal on Matrix Analysis and Applications · January 1, 1996
We describe a divide-and-conquer tridiagonalization approach for matrices with repeated eigenvalues. Our algorithm hinges on the fact that, under easily constructively verifiable conditions, a symmetric matrix with band width b and k distinct eigenvalues m ...
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Journal ArticleProceedings of the Scalable High Performance Computing Conference · December 1, 1994
In this paper, we discuss work in progress on a complete eigensolver based on the Invariant Subspace Decomposition Algorithm for dense symmetric matrices (SYISDA). We describe a recently developed acceleration technique that substantially reduces the overa ...
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Journal ArticleProceedings of the Scalable High Performance Computing Conference · December 1, 1994
We present a two-step variant of the `successive band reduction' paradigm for the tridiagonalization of symmetric matrices. Here we first reduce a full matrix to narrow-banded form, and from there to tridiagonal form. The first step allows easy exploitatio ...
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ConferenceProceedings of Scalable Parallel Libraries Conference Splc 1993 · January 1, 1993
The goal of the PRISM project is the development of infrastructure and algorithms for the parallel solution of eigenvalue problems. We are currently investigating a complete eigensolver based on the invariant Subspace Decomposition Algorithm for dense symm ...
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