The Living Thing / Notebooks : Matrix factorisation, approximate

Forget QR and LU decompositions, there are now so many ways of factorising matrices that there are not enough acronyms in the alphabet to hold them, especially if you suspect your matrix is sparse, or could be made sparse because of some underlying constraint, or probably could, if squinted at in the right fashion, be such as a graph transition matrix, or Laplacian, or noisy transform of some smooth object, or at least would be very close to sparse or…

Your big matrix is the product (or sum, or…) of two matrices that are in some way simple (small-rank, small dimension, sparse), possibly with additional constraints. Can you find these simple matrices?

Here’s an example. Godec —- A decomposition into low-rank and sparse components. (looks combined multidimensional factorisation and outlier detection). Implementations for MATLAB and R exist.

A hip one from last decade is Non Negative Matrix factorisation (NMF), which I think is a classic. I should explain why.

There are so many of these things, depending on your preferred choice of loss function, free variable and whatever.

Keywords: Matrix sketching, matrix sparsification. Deterministic and randomized methods. There seems to be little contact with the related area of \(\mathcal{H}\)-matrix methods, as seen in, e.g. covariance matrices. Why is that?

(See for one lab’s backgrounder and their implementation, h2lib, hlibpro for a black-box closed-source one.)

Matrix concentration inequalities turn out to be crucial in making this work.

I would like to learn more about

Igor Carron’s Matrix Factorization Jungle classifies the following problems as matrix-factorisation type.

Kernel Factorizations
Spectral clustering
\(A = DX\) with unknown D and X, solve for sparse X and X_i = 0 or 1
K-Means / K-Median clustering
\(A = DX\) with unknown D and X, solve for XX^T = I and X_i = 0 or 1
Subspace clustering
\(A = AX\) with unknown X, solve for sparse/other conditions on X
Graph Matching
\(A = XBX^T\) with unknown X, B solve for B and X as a permutation
\(A = DX\) with unknown D and X, solve for elements of D,X positive
Generalized Matrix Factorization
\(W.*L - W.*UV'\) with W a known mask, U,V unknowns solve for U,V and L lowest rank possible
Matrix Completion
\(A = H.*L\) with H a known mask, L unknown solve for L lowest rank possible
Stable Principle Component Pursuit (SPCP)/ Noisy Robust PCA
\(A = L + S + N\) with L, S, N unknown, solve for L low rank, S sparse, N noise
Robust PCA
\(A = L + S\) with L, S unknown, solve for L low rank, S sparse
Sparse PCA
\(A = DX\) with unknown D and X, solve for sparse D
Dictionary Learning
\(A = DX\) with unknown D and X, solve for sparse X
Archetypal Analysis
\(A = DX\) with unknown D and X, solve for D = AB with D, B positive
Matrix Compressive Sensing (MCS)
find a rank-r matrix L such that \(A(L) ~= b\) / or \(A(L+S) = b\)
Multiple Measurement Vector (MMV)
\(Y = A X\) with unknown X and rows of X are sparse.
compressed sensing
\(Y = A X\) with unknown X and rows of X are sparse, X is one column.
Blind Source Separation (BSS)
\(Y = A X\) with unknown A and X and statistical independence between columns of X or subspaces of columns of X
Partial and Online SVD/PCA
Tensor Decomposition

Truncated Classic PCA is clearly also an example of this, but is excluded from the list for some reason. Boringness? the fact it’s a special case of Sparse PCA?

See also compressed sensing, deconvolution, optimisation, random features and clustering, sparse regression, generic solvers



Sketching” is what I am going to use to describe the subset of factorisations which reduce the dimensionality of the matrices in question in a way I will make clear shortly.

Mart16 mentions CUR and interpolative decompositions. Does preconditioning fit here?

Randomized methods

Most of these algorithms have multiple optima and use a greedy search to find solutions; that is, they are deterministic up to choice of starting parameters.

There are also randomised versions,


Enough theory! Plug the hip new toy into my algorithm!”


Vowpal Wabbit does this:

HPC for matlab, R, python, c++: libpmf:

LIBPMF implements the CCD++ algorithm, which aims to solve large-scale matrix factorization problems such as the low-rank factorization problems for recommender systems.


Julia: laplacians.jl:

Laplacians is a package containing graph algorithms, with an emphsasis on tasks related to spectral and algebraic graph theory. It contains (and will contain more) code for solving systems of linear equations in graph Laplacians, low stretch spanning trees, sparsifiation, clustering, local clustering, and optimization on graphs.

All graphs are represented by sparse adjacency matrices. This is both for speed, and because our main concerns are algebraic tasks. It does not handle dynamic graphs. It would be very slow to implement dynamic graphs this way.

Laplacians.jl was started by Daniel A. Spielman. Other contributors include Rasmus Kyng, Xiao Shi, Sushant Sachdeva, Serban Stan and Jackson Thea.

Matlab: Chih-Jen Lin’s nmf.m - “This tool solves NMF by alternative non-negative least squares using projected gradients. It converges faster than the popular multiplicative update approach. “

c++: distributed nmf: In this repository, we offer both MPI and OPENMP implementation for MU, HALS and ANLS/BPP based NMF algorithms. This can run off the shelf as well easy to integrate in other source code. These are very highly tuned NMF algorithms to work on super computers. We have tested this software in NERSC as well OLCF cluster. The openmp implementation is tested on many different linux variants with intel processors. The library works well for both sparse and dense matrix. (KaBP16, Kann16, FKPB15)

C++/MATLAB/python: Spams includes some matrix factorisations in its sparse approx toolbox. (see optimisation)

python: scikit-learn does a few matrix factorisation of course, in its inimitable batteries-in-the-kitchen-sink way.

python: nimfa - “Nimfa is a Python library for nonnegative matrix factorization. It includes implementations of several factorization methods, initialization approaches, and quality scoring. Both dense and sparse matrix representation are supported.”

C++: Tapkee. Pro-tip —- even without coding, tapkee does a long list of nice dimensionality reduction from the CLI, some of which are explicitly manifold learners (and the rest are manifold learning which is not so different)

  • PCA and randomized PCA
  • Kernel PCA (kPCA)
  • Random projection
  • Factor analysis


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