NMF: scale.NMF – R documentation

Pricing

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

Get Started for Free

Documentation

NMF

scale.NMF

Rescaling NMF Models

Description

Rescales an NMF model keeping the fitted target matrix identical.

Usage

## S3 method for class 'NMF'
 scale(x, center = c("basis", "coef"),
    scale = 1)

Arguments

`x`	an NMF object
`center`	either a numeric normalising vector delta, or either `'basis'` or `'coef'`, which respectively correspond to using the column sums of the basis matrix or the inverse of the row sums of the coefficient matrix as a normalising vector. If numeric, `center` should be a single value or a vector of length the rank of the NMF model, i.e. the number of columns in the basis matrix.
`scale`	scaling coefficient applied to D, i.e. the value of alpha, or, if `center='coef'`, the value of 1/alpha (see section Details).

Details

Standard NMF models are identifiable modulo a scaling factor, meaning that the basis components and basis profiles can be rescaled without changing the fitted values:

X = W H = (W D) (D^-1 H)

with D= alpha * diag(1/delta_1, ..., 1/delta_r)

The default call scale(object) rescales the basis NMF object so that each column of the basis matrix sums up to one.

Value

an NMF object

Examples

# random 3-rank 10x5 NMF model
x <- rnmf(3, 10, 5)

# rescale based on basis
colSums(basis(x))
colSums(basis(scale(x)))

rx <- scale(x, 'basis', 10)
colSums(basis(rx))
rowSums(coef(rx))

# rescale based on coef
rowSums(coef(x))
rowSums(coef(scale(x, 'coef')))
rx <- scale(x, 'coef', 10)
rowSums(coef(rx))
colSums(basis(rx))

# fitted target matrix is identical but the factors have been rescaled
rx <- scale(x, 'basis')
all.equal(fitted(x), fitted(rx))
all.equal(basis(x), basis(rx))

NMF

Algorithms and Framework for Nonnegative Matrix Factorization (NMF)

v0.23.0

GPL (>= 2)

Authors

Renaud Gaujoux, Cathal Seoighe

Initial release

2020-07-30