Fast sparse matrixvector multiplication by exploiting. For a m x ndimensional sparse matrix and 0 sparse matrix with space for 3n nonzeros. An important feature of this concept is that if asatis es the rip of order 2mwith a parameter small enough, then every msparse vector can be reconstructed by the 1minimization method. Import from sparse matrix external format matlab spconvert. The dbcsr distributed block compressed sparse row library described in this article is a wellperforming library for scalable parallel sparse matrixmatrix multiplication with defined and demonstrable scaling bounds. This format seeks to minimize the memory footprint of the column index array of the typical compressed sparse row csr format by exploiting dense substructures inside the sparse matrix.
We consider p data points in rn, in a data matrix x. You can store the matrix as usual, in rowcompressed sparse format. Specifically, if i already have 4999 of the matrix slices calculated, will the following be very slow operations. Interactions between compressed sensing random matrices.
Taha bahadori, zemin zheng, yan liu and jinchi lv march 1. Implementing sparse matrix vector multiplication on throughputoriented processors nathan bell and michael garland proceedings of supercomputing 09 efficient sparse matrix vector multiplication on cuda nathan bell and michael garland nvidia technical report nvr2008004, december 2008 iterative methods for sparse linear systems yousef saad. Because sparse matrices are stored in compressed sparse column format, there are different costs associated with indexing into a sparse matrix than there are with indexing into a full matrix. The index structure is stored in three sparse vectors in coo. Assuming we have a nonsymmetric sparse matrix, we create vectors. I cant create a singleprecision sparse matrix on the gpu. Sparse principal component analysis stanford university. The toolbox has been developed at the department of informatics at the technical university of denmark.
Ucbcsd031297 november 25, 2003 computer science division eecs university of california berkeley, california 94720. Random sparse matrices random sparse matrix i a random sparse matrix a can be obtained by determining, randomly and independently, for each element a ij whether it is 0 or not. Spmm is a generalization of spmv in which a sparse nbym matrix a is multiplied by a tall and narrow dense nbyk matrix b k sparse matrix data structures example. Fast sparse matrix vector multiplication by exploiting variable block structure richard w.
In addition,fspak incorporates other nonstandard procedures in commercial packages such as sparse vector methods tinney et al. We improve the performance of sparse matrix vector mul. Spmm is a generalization of spmv in which a sparse nbym matrix a is multiplied by a tall and narrow dense nbyk matrix b k sparse matrix stores only nonzero elements to save space 9. M and n, the number of rows and columns of the matrix well often assume assume the matrix is square, in which case mn. Sparse precision matrix estimation 105 semidefinite. As prior information, we either assume that x itself is sparse, i. Suppose that we want to use a from sp to estimate 0. To decide if this is a worthwhile change, can someone tell me how the sparse memory access works in matlab.
We consider the spmv operation y is the base container adaptor for sparse matrices. Data access in sparse matrix matlab answers matlab central. Given a sparse x, how to verify whether it is actually the sparsest one. If d is already a sparse matrix, then spconvert returns d. Since the matrix is sparse, you only need to store the cells that are filled in. A sparse matrix obtained when solving a finite element problem in two dimensions. We consider the spmv operation y sparse regression, classification and principal component analysis. Dimensionality reduction svd or pca on a large, sparse. The above sparse matrix contains only 9 nonzero elements, with 26 zero elements. The most obvious, as you pointed out, is that sparse elements must be indexed for a general sparse matrix, i believe matlab uses a compressed row storage scheme another, less apparent slowdown, is due to vectorization and pipelining data into the processor. Because this system is underdetermined, the recovery problem of the vector x from the measurement vector y is an illposed problem. The simplest sparse matrix storage structure is coo. The authors show that a sparse signal can be reconstructed. Taha bahadori, zemin zheng, yan liu and jinchi lv march 1, 2018 abstract sparse reducedrank regression is an important tool to uncover meaningful dependence structure between large numbers of predictors and responses in many big data applications such as genomewide association studies and social media analysis.
There are a few reasons for an almost full sparse matrix being more computationally expensive than just using a full matrix. Dimensionality reduction svd or pca on a large, sparse matrix. If not, the geometric interpretation of pca shows that the first principal component will be close to the vector of means and all subsequent pcs will be orthogonal to it, which will prevent them from approximating any pcs that happen to be close to that first vector. Follow 33 views last 30 days tungduong on 15 mar 2017. Then for each column, you store which entries exist in the sparsity pattern.
For this reason, using sparse matrices can significantly reduce the amount of memory required for data storage. Performance optimizations and bounds for sparse symmetric matrix multiple vector multiply benjamin c. Cc is a data directory which contains examples of files in the compressed column cc format for storing sparse matrices the sparse compressed column data structure involves. We use vecxto denote the p2vector formed by stacking the columns of x,and x,y means trxyt throughout the paper. Spmm is a generalization of spmv in which a sparse nbym matrix a is multiplied by a tall and narrow dense nbyk matrix b. Sparse recovery using sparse matrices people mit csail. We remark that the provided hism description assumes that the dimension of the matrix is sq sq. The original matrix %% the svds v component gives the principle components. I sparse matrix computations have alarger integer overhead associated with each oatingpoint operation. P rincipal component anal ysis pca for sparse h igh. Even if this rip condition is di cult to check on a given matrix, it actually holds true with high.
Input matrix, specified as a matrix with either three or four columns. The matrix computation language and environment matlab is extended to include sparse matrix storage and operations. Implementing sparse matrixvector multiplication on throughputoriented processors nathan bell and michael garland proceedings of supercomputing 09 efficient sparse matrixvector multiplication on cuda nathan bell and michael garland nvidia technical report nvr2008004, december 2008 iterative methods for sparse linear systems yousef saad. The only change to the outward appearance of the matlab language is a pair of com. The sparse compressed column data structure involves.
There is a multiplication timer in the test file, it comes out with. In other applications, sparsity can be useful for computational reasons. Fast sparse matrixvector multiplication by exploiting variable block structure richard w. So the sparse matrix takes up about 1% plus pointers and stuff of the space required for the dense matrix array. Introduction this package is a proofofconcept release of the compressed sparse extended format for sparse matrices. In both cases, the first two columns of d are subscripts and the third column is composed of data values. Optimal solutions for sparse principal component analysis. Design and implementation article pdf available in siam journal on matrix analysis and applications 1 may 1997 with 1,215 reads how we measure reads. Performance of sparse matrixmultiple vectors multiplication. For a m x ndimensional sparse matrix and 0 s parse p rincipal. By contrast, if most of the elements are nonzero, then the matrix is considered dense. I still, using sparsity can save large amounts of cpu time and also memory space. The number of zerovalued elements divided by the total number of elements e. Basically, ive been doing svd without bothering to center or scale first, because ive never found a good way to do this without converting my sparse matrix to a dense matrix.
A sparse matrix stores only nonzero elements to save space 9. While full or dense matrices store every single element in memory regardless of value, sparse matrices store only the nonzero elements and their row indices. The first vector nonzero vector stores nonzero elements of the sparse matrix. Optimization of sparse matrixvector multiplication on emerging multicore platforms.
A four column matrix specifies the real third column and imaginary fourth column parts of complex numbers. Note that sparse is smart enough to accumulate values that happen to lie at the same index. Sparse matrix linear algebra is requisite for enabling such simulations. First of all, you really do want to center the data. The result is a tridiagonal matrix with about 50% band density. Block compressed row format bsr scipy lecture notes. In order to store the new matrix with 42 at 3,1, matlab inserts an additional row into the nonzero values vector and subscript vectors, then shifts all matrix values after 3,1 using linear indexing to access or assign an element in a large sparse matrix will fail if the linear index exceeds 2481, which is the current upper bound for the number of elements allowed in a matrix. Thus if p and q are identical for two cases, then the corresponding values will be summed up.
Optimized filling of sparse matrix using spalloc matlab. In numerical analysis and scientific computing, a sparse matrix or sparse array is a matrix in. We can hope that most of the later pcs will be approximately correct, but. We use a loss function l, 0 for this estimation problem, and we require it to satisfy the following two conditions. Then use a forloop to fill in the columns of s one at a time. Optimization of sparse matrixvector multiplication on. Pdf on jan 1, 1984, sergio pissanetzky and others published sparse matrix technology find, read and cite all the research you need on researchgate. Deterministic sensing matrices in compressive sensing. Sparse precision matrix estimation via lasso penalized d. Cc is a data directory which contains examples of files in the compressed column cc format for storing sparse matrices. We improve the performance of sparse matrixvector mul.