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Background

Nonnegative Matrix Factorization (NMF) is an unsupervised learning technique that has been applied successfully in several fields, including signal processing, face recognition and text mining. Recent applications of NMF in bioinformatics have demonstrated its ability to extract meaningful information from high-dimensional data such as gene expression microarrays. Developments in NMF theory and applications have resulted in a variety of algorithms and methods. However, most NMF implementations have been on commercial platforms, while those that are freely available typically require programming skills. This limits their use by the wider research community.

Results

Our objective is to provide the bioinformatics community with an open-source, easy-to-use and unified interface to standard NMF algorithms, as well as with a simple framework to help implement and test new NMF methods. For that purpose, we have developed a package for the R/BioConductor platform. The package ports public code to R, and is structured to enable users to easily modify and/or add algorithms. It includes a number of published NMF algorithms and initialization methods and facilitates the combination of these to produce new NMF strategies. Commonly used benchmark data and visualization methods are provided to help in the comparison and interpretation of the results.

Conclusions

The NMF package helps realize the potential of Nonnegative Matrix Factorization, especially in bioinformatics, providing easy access to methods that have already yielded new insights in many applications.


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Version

Install

install.packages('NMF')

Monthly Downloads

8,611

Version

0.21.0

License

GPL (>= 2)

Maintainer

Nicolas Sauwen

Last Published

March 6th, 2018

Functions in NMF (0.21.0)

nmf_update.lee_R

NMF Algorithm/Updates for Frobenius Norm
basiscor

Correlations in NMF Models
cophcor

Cophenetic Correlation Coefficient
bioc-NMF

Specific NMF Layer for Bioconductor
cutdendro

Fade Out the Upper Branches from a Dendrogram
heatmap-NMF

Heatmaps of NMF Factors
pmax.inplace

Updating Objects In Place
nmf

Running NMF algorithms
nmf.equal

Testing Equality of NMF Models
nmfFormals

Showing Arguments of NMF Algorithms
nmfModel

Factory Methods NMF Models
parse_formula

Simple Parsing of Formula
methods-NMF

Registry for NMF Algorithms
plot,NMFfit,missing-method

Plots the residual track computed at regular interval during the fit of the NMF model x.
residuals

Residuals in NMF Models
seed

Interface for NMF Seeding Methods
setNMFMethod

Registering NMF Algorithms
silhouette.NMF

Silhouette of NMF Clustering
smoothing

Smoothing Matrix in Nonsmooth NMF Models
ibterms

Fixed Terms in NMF Models
bterms<-

Fixed Terms in NMF Models
NMF-defunct

Defunct Functions and Classes in the NMF Package
NMF-class

Generic Interface for Nonnegative Matrix Factorisation Models
NMFns-class

NMF Model - Nonsmooth Nonnegative Matrix Factorization
NMFstd-class

NMF Model - Standard model
.atrack

Annotation Tracks
checkErrors

Error Checks in NMF Runs
basis

Accessing NMF Factors
deviance

Distances and Objective Functions
cluster_mat

Cluster Matrix Rows in Annotated Heatmaps
basisnames

Dimension names for NMF objects
NMFSeed-class

Base class that defines the interface for NMF seeding methods.
.fcnnls

Internal Routine for Fast Combinatorial Nonnegative Least-Squares
NMFStrategy-class

Virtual Interface for NMF Algorithms
esGolub

Golub ExpressionSet
match_atrack

Extending Annotation Vectors
NMFStrategyFunction-class

Interface for Single Function NMF Strategies
NMFStrategy

Factory Method for NMFStrategy Objects
compare-NMF

Comparing Results from Different NMF Runs
aheatmap

Annotated Heatmaps
nneg

Transforming from Mixed-sign to Nonnegative Data
nmf_update.ns

NMF Multiplicative Update for Nonsmooth Nonnegative Matrix Factorization (nsNMF).
algorithm,NMFList-method

Returns the method names used to compute the NMF fits in the list. It returns NULL if the list is empty.
NMF-deprecated

Deprecated Functions in the Package NMF
NMF-package

Algorithms and framework for Nonnegative Matrix Factorization (NMF).
NMFfitX-class

Virtual Class to Handle Results from Multiple Runs of NMF Algorithms
options-NMF

NMF Package Specific Options
c,NMF-method

Concatenating NMF Models
canFit

Testing Compatibility of Algorithm and Models
consensus,NMFfitXn-method

Computes the consensus matrix of the set of fits stored in object, as the mean connectivity matrix across runs.
consensushc

Hierarchical Clustering of a Consensus Matrix
NMFfitX

Factory Method for Multiple NMF Run Objects
algorithmic-NMF

Generic Interface for Algorithms
gfile

Open a File Graphic Device
tryViewport

Internal Grid Extension
summary

Assessing and Comparing NMF Models
parallel-NMF

Utilities for Parallel Computations
ccBreaks

Generate Break Intervals from Numeric Variables
nmf_update.lsnmf

Multiplicative Updates for LS-NMF
ccPalette

Builds a Color Palette from Compact Color Specification
nbasis

Dimension of NMF Objects
lverbose

Internal verbosity option
NMFList-class

Class for Storing Heterogeneous NMF fits
randomize

Randomizing Data
purity

Purity and Entropy of a Clustering
NMFOffset-class

NMF Model - Nonnegative Matrix Factorization with Offset
NMFStrategyIterative-class

Interface for Algorithms: Implementation for Iterative NMF Algorithms
scale.NMF

Rescaling NMF Models
nmfSeed

Seeding Strategies for NMF Algorithms
NMFfit-class

Base Class for to store Nonnegative Matrix Factorisation results
nmfWrapper

Wrapping NMF Algorithms
objective,NMFfit-method

Returns the objective function associated with the algorithm that computed the fitted NMF model object, or the objective value with respect to a given target matrix y if it is supplied.
offset,NMFOffset-method

Offsets in NMF Models with Offset
getRNG1

Extracting RNG Data from NMF Objects
revPalette

Flags a Color Palette Specification for Reversion
nmfAlgorithm.SNMF_R

NMF Algorithm - Sparse NMF via Alternating NNLS
dispersion

Dispersion of a Matrix
rmatrix

Generating Random Matrices
ccRamp

Builds a Color Ramp from Compact Color Specification
fitted

Fitted Matrix in NMF Models
registerDoBackend

Utilities and Extensions for Foreach Loops
nmfAlgorithm

Listing and Retrieving NMF Algorithms
show,NMFOffset-method

Show method for objects of class NMFOffset
featureScore

Feature Selection in NMF Models
show,NMFSeed-method

Show method for objects of class NMFSeed
nmfApply

Apply Function for NMF Objects
ccSpec

Extract Colour Palette Specification
show,NMFfitX-method

Show method for objects of class NMFfitX
consensus,NMFfitX1-method

Returns the consensus matrix computed while performing all NMF runs, amongst which object was selected as the best fit.
is.nmf

Testing NMF Objects
connectivity

Clustering Connectivity and Consensus Matrices
show,NMFfitX1-method

Show method for objects of class NMFfitX1
txtProgressBar

Simple Progress Bar
show,NMFfitXn-method

Show method for objects of class NMFfitXn
show,NMFns-method

Show method for objects of class NMFns
fcnnls

Fast Combinatorial Nonnegative Least-Square
syntheticNMF

Simulating Datasets
t.NMF

Transformation NMF Model Objects
fit

Extracting Fitted Models
nmfCheck

Checking NMF Algorithm
nmfEstimateRank

Estimate Rank for NMF Models
nmf_update.KL.h

NMF Multiplicative Updates for Kullback-Leibler Divergence
nmfObject

Updating NMF Objects
nmf_update.euclidean.h

NMF Multiplicative Updates for Euclidean Distance
nmfReport

Run NMF Methods and Generate a Report
offset,NMFfit-method

Returns the offset from the fitted model.
nmf_update.euclidean_offset.h

NMF Multiplicative Update for NMF with Offset Models
profplot

Plotting Expression Profiles
predict

Clustering and Prediction
runtime,NMFList-method

Returns the CPU time required to compute all NMF fits in the list. It returns NULL if the list is empty. If no timing data are available, the sequential time is returned.
rnmf

Generating Random NMF Models
runtime.all,NMFfitXn-method

Returns the CPU time used to perform all the NMF fits stored in object.
rss

Residual Sum of Squares and Explained Variance
show,NMFList-method

Show method for objects of class NMFList
show,NMF-method

Show method for objects of class NMF
show,NMFStrategyIterative-method

Show method for objects of class NMFStrategyIterative
show,NMFfit-method

Show method for objects of class NMFfit
utils-NMF

Utility Function in the NMF Package
NMFSeed

setupBackend

Computational Setup Functions
staticVar

Get/Set a Static Variable in NMF Algorithms
sparseness

Sparseness
NMFStop

Stopping Criteria for NMF Iterative Strategies
[,NMF-method

Sub-setting NMF Objects
nmf_update.brunet_R

NMF Algorithm/Updates for Kullback-Leibler Divergence
NMFfitXn-class

Structure for Storing All Fits from Multiple NMF Runs
NMFfitX1-class

Structure for Storing the Best Fit Amongst Multiple NMF Runs
Strategy-class

Generic Strategy Class
advanced-NMF

Advanced Usage of the Package NMF