Skip to main content

Table 1 Algorithms of NMF variants

From: The non-negative matrix factorization toolbox for biological data mining

Function Description
nmfrule The standard NMF optimized by gradient-descent-based multiplicative rules.
nmfnnls The standard NMF optimized by NNLS active-set algorithm.
seminmfrule Semi-NMF optimized by multiplicative rules.
seminmfnnls Semi-NMF optimized by NNLS.
sparsenmfnnls Sparse-NMF optimized by NNLS.
sparsenmfNNQP Sparse-NMF optimized by NNQP.
sparseseminmfnnls Sparse semi-NMF optimized by NNLS.
kernelnmfdecom Kernel NMF through decomposing the kernel matrix of input data.
kernelseminmfrule Kernel semi-NMF optimized by multiplicative rule.
kernelseminmfnnls Kernel semi-NMF optimized by NNLS.
kernelsparseseminmfnnls Kernel sparse semi-NMF optimized by NNLS.
kernelSparseNMFNNQP Kernel sparse semi-NMF optimized by NNQP.
convexnmfrule Convex-NMF optimized by multiplicative rules.
kernelconvexnmf Kernel convex-NMF optimized by multiplicative rules.
orthnmfrule Orth-NMF optimized by multiplicative rules.
wnmfrule Weighted-NMF optimized by multiplicative rules.
sparsenmf2rule Sparse-NMF on both factors optimized by multiplicative rules.
sparsenmf2nnqp Sparse-NMF on both factors optimized by NNQP.
vsmf Versatile sparse matrix factorization optimized by NNQP and l1QP.
nmf The omnibus of the above algorithms.
computeKernelMatrix Compute the kernel matrix k(A,B) given a kernel function.