NMF: nmf_update_euclidean – R documentation

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nmf_update_euclidean

NMF Multiplicative Updates for Euclidean Distance

Description

Multiplicative updates from Lee et al. (2001) for standard Nonnegative Matrix Factorization models V \approx W H, where the distance between the target matrix and its NMF estimate is measured by the – euclidean – Frobenius norm.

nmf_update.euclidean.w and nmf_update.euclidean.h compute the updated basis and coefficient matrices respectively. They use a C++ implementation which is optimised for speed and memory usage.

nmf_update.euclidean.w_R and nmf_update.euclidean.h_R implement the same updates in plain R.

Usage

nmf_update.euclidean.h(v, w, h, eps = 10^-9,
    nbterms = 0L, ncterms = 0L, copy = TRUE)

  nmf_update.euclidean.h_R(v, w, h, wh = NULL, eps = 10^-9)

  nmf_update.euclidean.w(v, w, h, eps = 10^-9,
    nbterms = 0L, ncterms = 0L, weight = NULL, copy = TRUE)

  nmf_update.euclidean.w_R(v, w, h, wh = NULL, eps = 10^-9)

Arguments

`eps`	small numeric value used to ensure numeric stability, by shifting up entries from zero to this fixed value.
`wh`	already computed NMF estimate used to compute the denominator term.
`weight`	numeric vector of sample weights, e.g., used to normalise samples coming from multiple datasets. It must be of the same length as the number of samples/columns in `v` – and `h`.
`v`	target matrix
`w`	current basis matrix
`h`	current coefficient matrix
`nbterms`	number of fixed basis terms
`ncterms`	number of fixed coefficient terms
`copy`	logical that indicates if the update should be made on the original matrix directly (`FALSE`) or on a copy (`TRUE` - default). With `copy=FALSE` the memory footprint is very small, and some speed-up may be achieved in the case of big matrices. However, greater care should be taken due the side effect. We recommend that only experienced users use `copy=TRUE`.

Details

The coefficient matrix (H) is updated as follows:

H_kj <- max(H_kj (W^T V)_kj, eps) / ( (W^T W H)_kj + eps )

These updates are used by the built-in NMF algorithms Frobenius and lee.

The basis matrix (W) is updated as follows:

W_ik <- max(W_ik (V H^T)_ik, eps) / ( (W H H^T)_ik + eps )

Value

a matrix of the same dimension as the input matrix to update (i.e. w or h). If copy=FALSE, the returned matrix uses the same memory as the input object.

Author(s)

Update definitions by Lee2001.

C++ optimised implementation by Renaud Gaujoux.

References

Lee DD and Seung H (2001). "Algorithms for non-negative matrix factorization." _Advances in neural information processing systems_. <URL: http://scholar.google.com/scholar?q=intitle:Algorithms+for+non-negative+matrix+factorization\#0>.

NMF

Algorithms and Framework for Nonnegative Matrix Factorization (NMF)

v0.23.0

GPL (>= 2)

Authors

Renaud Gaujoux, Cathal Seoighe

Initial release

2020-07-30