NMF Multiplicative Update for NMF with Offset Models

V \approx W H + I

nmf_update.offset_R implements a complete single
  update step, using plain R updates.
nmf_update.offset implements a complete single
  update step, using C++-optimised updates.
Algorithms ‘offset’ and ‘.R#offset’ provide
  the complete NMF-with-offset algorithm from Badea
  (2008), using the C++-optimised and pure R updates
  nmf_update.offset and
  nmf_update.offset_R respectively.

  
    

Usage

nmf_update.euclidean_offset.h(v, w, h, offset, eps = 10^-9, copy = TRUE)

nmf_update.euclidean_offset.w(v, w, h, offset, eps = 10^-9, copy = TRUE)

nmf_update.offset_R(i, v, x, eps = 10^-9, ...)

nmf_update.offset(i, v, x, copy = FALSE, eps = 10^-9, ...)

nmfAlgorithm.offset_R(..., .stop = NULL, maxIter = 2000, eps = 10^-9, stopconv = 40, 
  check.interval = 10)

nmfAlgorithm.offset(..., .stop = NULL, maxIter = 2000, copy = FALSE, eps = 10^-9, 
      stopconv = 40, check.interval = 10)

Arguments

offset

current value of the offset/intercept vector. It must be of length equal to the number of rows in the target matrix.

v

target matrix.

eps

small numeric value used to ensure numeric stability, by shifting up entries from zero to this fixed value.

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.

i

current iteration number.

x

current NMF model, as an NMF-class object.

...

extra arguments. These are generally not used and present only to allow other arguments from the main call to be passed to the initialisation and stopping criterion functions (slots onInit and Stop respectively).

.stop

specification of a stopping criterion, that is used instead of the one associated to the NMF algorithm. It may be specified as:

• the access key of a registered stopping criterion;
• a single integer that specifies the exact number of iterations to perform, which will be honoured unless a lower value is explicitly passed in argument maxIter.
• a single numeric value that specifies the stationnarity threshold for the objective function, used in with nmf.stop.stationary;
• a function with signature (object="NMFStrategy", i="integer", y="matrix", x="NMF", ...), where object is the NMFStrategy object that describes the algorithm being run, i is the current iteration, y is the target matrix and x is the current value of the NMF model.

maxIter

maximum number of iterations to perform.

stopconv

number of iterations intervals over which the connectivity matrix must not change for stationarity to be achieved.

check.interval

interval (in number of iterations) on which the stopping criterion is computed.

w

current basis matrix

h

current coefficient matrix

Author