Description Usage Arguments Details Value References
These update rules, defined for the
NMFns
model V \approx W S H
from PascualMontano et al. (2006), that
introduces an intermediate smoothing matrix to enhance
sparsity of the factors.
nmf_update.ns
computes the updated nsNMF model. It
uses the optimized C++ implementations
nmf_update.KL.w
and
nmf_update.KL.h
to update W and
H respectively.
nmf_update.ns_R
implements the same updates in
plain R.
Algorithms ‘nsNMF’ and ‘.R#nsNMF’ provide
the complete NMF algorithm from PascualMontano et
al. (2006), using the C++optimised and plain R updates
nmf_update.brunet
and
nmf_update.brunet_R
respectively. The
stopping criterion is based on the stationarity of the
connectivity matrix.
1 2 3 4 5 6 7 8 9 10 11  nmf_update.ns(i, v, x, copy = FALSE, ...)
nmf_update.ns_R(i, v, x, ...)
nmfAlgorithm.nsNMF_R(..., .stop = NULL,
maxIter = nmf.getOption("maxIter") %% 2000,
stopconv = 40, check.interval = 10)
nmfAlgorithm.nsNMF(..., .stop = NULL,
maxIter = nmf.getOption("maxIter") %% 2000,
copy = FALSE, stopconv = 40, check.interval = 10)

i 
current iteration number. 
v 
target matrix. 
x 
current NMF model, as an

copy 
logical that indicates if the update should
be made on the original matrix directly ( 
... 
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 
.stop 
specification of a stopping criterion, that is used instead of the one associated to the NMF algorithm. It may be specified as:

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. 
The multiplicative updates are based on the updates proposed by Brunet et al. (2004), except that the NMF estimate W H is replaced by W S H and W (resp. H) is replaced by W S (resp. S H) in the update of H (resp. W).
See nmf_update.KL
for more details on the
update formula.
an NMFns
model object.
PascualMontano A, Carazo JM, Kochi K, Lehmann D and Pascualmarqui RD (2006). "Nonsmooth nonnegative matrix factorization (nsNMF)." _IEEE Trans. Pattern Anal. Mach. Intell_, *28*, pp. 403415.
Brunet J, Tamayo P, Golub TR and Mesirov JP (2004). "Metagenes and molecular pattern discovery using matrix factorization." _Proceedings of the National Academy of Sciences of the United States of America_, *101*(12), pp. 41649. ISSN 00278424, <URL: http://dx.doi.org/10.1073/pnas.0308531101>, <URL: http://www.ncbi.nlm.nih.gov/pubmed/15016911>.
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