bksvd -- Block Krylov Singular Value Decomposition

Simple MATLAB code for iterative computing an SVD or PCA via the randomized block Krylov method analyzed in Randomized Block Krylov Methods for Stronger and Faster Approximate Singular Value Decomposition

Installation

Download bksvd.m, add to MATLAB path, or include directly in project directory.

Documentation

bksvd can be used as a drop-in replacement for MATLAB's svds function for computing the Singular Value Decomposition (SVD). It can also be used for Principal Component Analysis (PCA) which performs an SVD on the after mean-centering the data matrix.

Usage

Input: bksvd(A, k, iter, bsize, center)

• A : matrix to decompose
• k : number of singular vectors to compute, default = 6
• iter : number of iterations, default = 3, increase for higher accuracy
• bsize : block size, must be >= k, default = k
• center : set to true if A's rows should be mean-centered before the singular value decomposition (e.g. when performing PCA), default = false

Output: k singular vector/value pairs

• U : an orthogonal matrix whose columns are approximate top k left singular vectors for A
• S : a diagonal matrix whose entries are A's approximate top k singular values
• V : an orthogonal matrix whose columns are approximate top k right singular vectors for A

U*S*V' is a near optimal low-rank approximation for A

Example

Standard Singular Values Decomposition:

% generate test matrix
s = 1.5.^[-40:.5:40];
A = randn(10000,161)*diag(s)*randn(161,161);

% compute SVD
[U,S,V] = bksvd(A,10);

bksvd is typically as accurate as svds and often faster:

tic; [U,S,V] = svds(A,30); toc;
Elapsed time is 1.380471 seconds.
norm(A- U*S*V')/norm(A)
0.0018

tic; [U,S,V] = bksvd(A,30); toc;
Elapsed time is 0.062798 seconds.
norm(A- U*S*V')/norm(A)
0.0018

Principal Component Analysis:

For PCA, A's rows (data points) should be mean-centered before computing the SVD. If the center flag is set to true, bksvd can do this implicitly, without densifying A:

[U,S,V] = bksvd(A,10,4,10,true);

Here V contains loading vector for the top 10 principal components. U*S can be taken as a dimensionality reduction for the data to 10 components.

Parameter Tuning

For higher accuracy (at the cost of slower runtime), the number of iterations can be increased from the default of 3, although for many matrices this is unecessary. Increasing the block size, bsize, so that it is > k also increases accuracy. For matrices with quickly decaying singular values, increasing block size can be more effective than increasing iterations. For details, see the NIPS paper.

Other Implementations

An implementation of bksvd is available through MLPACK. We plan to upload a Python implementation soon.