R: Residual Sum of Squares and Explained Variance

rss {NMF} | R Documentation

## Residual Sum of Squares and Explained Variance

### Description

`rss` and `evar` are S4 generic functions that respectively computes the Residual Sum of Squares (RSS) and explained variance achieved by a model.

The explained variance for a target V is computed as:

evar = 1 - RSS/sum v_{ij}^2

,

### Usage

      rss(object, ...)

      ## S4 method for signature 'matrix'
    rss(object, target)

      evar(object, ...)

      ## S4 method for signature 'ANY'
    evar(object, target, ...)

### Arguments

`object` | an R object with a suitable `fitted`, `rss` or `evar` method.
`...` | extra arguments to allow extension, e.g. passed to `rss` in `evar` calls.
`target` | target matrix

### Details

where RSS is the residual sum of squares.

The explained variance is usefull to compare the performance of different models and their ability to accurately reproduce the original target matrix. Note, however, that a possible caveat is that some models explicitly aim at minimizing the RSS (i.e. maximizing the explained variance), while others do not.

### Value

a single numeric value

### Methods

evar

  `signature(object = "ANY")`: Default method for `evar`.

  It requires a suitable `rss` method to be defined for `object`, as it internally calls `rss(object, target, ...)`.

rss

  `signature(object = "matrix")`: Computes the RSS between a target matrix and its estimate `object`, which must be a matrix of the same dimensions as `target`.

  The RSS between a target matrix V and its estimate v is computed as:

  RSS = ∑_{i,j} (v_{ij} - V_{ij})^2

  Internally, the computation is performed using an optimised C++ implementation, that is light in memory usage.

rss

  `signature(object = "ANY")`: Residual sum of square between a given target matrix and a model that has a suitable `fitted` method. It is equivalent to `rss(fitted(object), ...)`

  In the context of NMF, Hutchins et al. (2008) used the variation of the RSS in combination with the algorithm from Lee et al. (1999) to estimate the correct number of basis vectors. The optimal rank is chosen where the graph of the RSS first shows an inflexion point, i.e. using a screeplot-type criterium. See section Rank estimation in `nmf`.

  Note that this way of estimation may not be suitable for all models. Indeed, if the NMF optimisation problem is not based on the Frobenius norm, the RSS is not directly linked to the quality of approximation of the NMF model. However, it is often the case that it still decreases with the rank.

### References

Hutchins LN, Murphy SM, Singh P and Graber JH (2008). "Position-dependent motif characterization using non-negative matrix factorization." _Bioinformatics (Oxford, England)_, *24*(23), pp. 2684-90. ISSN 1367-4811, <URL: http://dx.doi.org/10.1093/bioinformatics/btn526>, <URL: http://www.ncbi.nlm.nih.gov/pubmed/18852176>.

Lee DD and Seung HS (1999). "Learning the parts of objects by non-negative matrix factorization." _Nature_, *401*(6755), pp. 788-91. ISSN 0028-0836, <URL: http://dx.doi.org/10.1038/44565>, <URL: http://www.ncbi.nlm.nih.gov/pubmed/10548103>.

### Examples

    #----------
    # rss,matrix-method
    #----------
    # RSS bewteeen random matrices
    x <- rmatrix(20,10, max=50)
    y <- rmatrix(20,10, max=50)
    rss(x, y)
    rss(x, x + rmatrix(x, max=0.1))

    #----------
    # rss,ANY-method
    #----------
    # RSS between an NMF model and a target matrix
    x <- rmatrix(20, 10)
    y <- rnmf(3, x) # random compatible model
    rss(y, x)

    # fit a model with nmf(): one should do better
    y2 <- nmf(x, 3) # default minimizes the KL-divergence
    rss(y2, x)
    y2 <- nmf(x, 3, 'lee') # 'lee' minimizes the RSS
    rss(y2, x)

[Package NMF version 0.21.0 Index]