Table 2 NMF-based data mining approaches
From: The non-negative matrix factorization toolbox for biological data mining
Function | Description |
|---|---|
NMFCluster | Take the coefficient matrix produced by a NMF algorithm, and output the clustering result. |
chooseBestk | Search the best number of clusters based on dispersion Coefficients. |
biCluster | The biclustering method using one of the NMF algorithms. |
featureExtractionTrain | General interface. Using training data, generate the bases of the NMF feature space. |
featureExtractionTest | General interface. Map the test/unknown data into the feature space. |
featureFilterNMF | On training data, select features by various NMFs. |
featSel | Feature selection methods. |
nnlsClassifier | The NNLS classifier. |
perform | Evaluate the classifier performance. |
changeClassLabels01 | Change the class labels to be in {0,1,2,⋯,C−1} for C-class problem. |
gridSearchUniverse | A framework to do line or grid search. |
classificationTrain | Train a classifier, many classifiers are included. |
classificationPredict | Predict the class labels of unknown samples via the model learned by classificationTrain. |
multiClassifiers | Run multiple classifiers on the same training data. |
cvExperiment | Conduct experiment of k-fold cross-validation on a data set. |
significantAcc | Check if the given data size can obtain significant accuracy. |
learnCurve | Fit the learning curve. |
FriedmanTest | Friedman test with post-hoc Nemenyi test to compare multiple classifiers on multiple data sets. |
plotNemenyiTest | Plot the CD diagram of Nemenyi test. |
NMFHeatMap | Draw and save the heat maps of NMF clustering. |
NMFBicHeatMap | Draw and save the heat maps of NMF biclustering. |
plotBarError | Plot Bars with STD. |
writeGeneList | Write the gene list into a.txt file. |
normmean0std1 | Normalization to have mean 0 and STD 1. |
sparsity | Calculate the sparsity of a matrix. |
MAT2DAT | Write a data set from MATLAB into.dat format in order to be readable by other languages. |