“Non-negative Matrix Factorization (NMF) for Pattern Recognition” T. Ensari, J. Chorowski, J. M....

“Non-negative Matrix Factorization (NMF)for Pattern Recognition”

T. Ensari, J. Chorowski, J. M. ZuradaUniversity of Louisville, USA

Outline

Definition Why NMF? NMF Algorithms Clustering with NMF Applications Areas:

- Gene/Protein, Image, Audio and Text Data Analysis NMF for Document Clustering Several Types of NMF Conclusion

Definition of NMF

‘A’ is given data matrix, A: (m x n) We are looking for W: (m x k) ≥ 0 and H: (k x n) ≥ 0 where k << min(m,n) for the best approximation on:

A ≈ W . H min

W basis matrix

H coefficient matrix

(nonnegative lower dimensional representation)

k low rank value (Choosing k is still open problem !)

Definition of NMF

Definition of NMF

History: Proposed by Lee and Seung, Nature,

1999.

NMF can be used as an Unsupervised

Dimension Reduction / Clustering Method

Why NMF?

Nonnegative constraints are physically meaningful.- Pixels in digital image Biomedical Image Processing- Molecule concentration in bioinformatics (e.g. mRNA,

protein, miRNA, etc.) Microarray Analysis- Signal intentisities in mass spectrometry Computational

Proteomics Speed: Fast convergence It can be applied for several tasks ( Gene/Protein Microarray Data Analysis, Digital Image, Processing, Text Data Mining, etc.). Hard and soft clustering are possible.

NMF Algorithms

Multiplicative Update Rule (Lee&Seung, 2000). Gradient Descent (Hoyer, 2004). Alternating Least Squares (Paatero, 1994).

NMF is algorithm dependent, so W and H are

not unique !

NMF Algorithms

COST FUNCTIONS:

Square of the Euclidean distance between A and B:

Generalized Kullback-Leibler divergence of A and B:

NMF Algorithms

Multiplicative Update Rule for W and H matrices:

- Lee&Seung, 1999.- Iteratively update until the error is below

some threshold. - Guaranteed convergence to a local minimum.

( ε is sufficiently small positive number to avoid zero division).

Clustering with NMF

NMF is one of the Dimension Reduction/Clustering

Method and these are other methods in the literature:

- k-Means Clustering

- Singular Value Decomposition (SVD)- Self Organizing Maps (SOM)- Hierarchical Clustering- Principal Component Analysis (PCA)- Mixture of Gaussian

Clustering with NMF

What is clustering? Finding groups of objects such that the objects in a group will be similar (or related) to one another and different from (or unrelated to) the objects in other groups.

Inter-cluster distances are maximized

Intra-cluster distances are

minimized

Clustering with NMF

Document Clustering: Grouping of text documents into meaningful clusters in an unsupervised manner.

Government

Science

Arts

Clustering with NMF

It is unsupervised clustering example.

For low-dimensional data sets, our eyes are excellent at clustering.

Cluster analysis becomes much more challenging (and much more interesting) if the data

set is both large and high-dimensional.

The goal of cluster analysis is to find hidden structure in a data set.

Applications on Gene/Protein Data

Goal: Discover hidden patterns in large quantities of data produced from microarray experiments.

Explore data to identify structure without supervision.

Data can be represented in non-negative matrix (gene × samples).

Applications on Gene/Protein Data

Applications on Gene/Protein Data

Applications on Gene/Protein Data

Applications on Image Processing

Data Compression Clustering Images Finding Similar Images

Applications on Image Processing

Reconstructed images:

Applications on Audio Data

Audio demonstration: We can separate the sounds.

Applications on Audio Data

Amplitude spectrogram: Audio represented as a non-negative matrix.

Applications on Text Data

a) Typical document matrix before clustering

b) Document clustering with NMF (k=2)

c) Document clustering with NMF (k=5)

Applications on Text Data

Data Compression

Finding Similar Terms

Finding Similar Documents

Cluster Documents

Topic Detection and Tracking

NMF for Document Clustering

20 News articles dataset:

Dataset Number of Documents

Number ofClasses

Newsgroups 20,000 20

NMF for Document Clustering

Synonyms Noise in A data matrix For example: Century, Symbol,…

NMF for Document Clustering Matlab Outputs after using NMF (k = 10):

religion christian peopl god line detail valu moral server scienc talk object jesus saw mac built arab frank dwyer configur RELIGION

name uk mathew shall folk tree righteous pin speed ram ps mb meg isa centri slot ns simm

mail drive help pleas info anybodi video manufactur monitor vga COMPUTER

name com server file help sandvik newton appl kent ignor spread windowstein brad kill guess imagin final water org reveal river sourc israel isra arab civilian ncsu mb alan norton lebanon hasan nysernet hernlem lebanes

net know object option thank summar advanc compil righteous anybodi driver latest site ftp ati window bio

avail price street charg card uk mathew cost sorri plus display fix driver super vga ati ultra mb ship diamond beast armenian

atheism version atheist exist god stein edu answer cs keith ve ac charley wingat mango umd contradictori imag ultb isc rit mozumd il

version word god rather man brad keep shall said hear turkish org tree heart righteous receiv luke bless davidian ps isa turkey armenian sdpa armenia urartu POLITICS

card file po cwru hear format mous summar compil islam convert job email muslim luke bless bus diamond slot

Several Types of NMF

There are several types of NMF proposed in the literature, some of them are:

- Sparse NMF- Quadratic NMF- Probabilistic NMF- Orthogonal NMF- Nonsmooth NMF- Weighted NMF- Convex NMF- Bayesian NMF- Gaussian NMF- Projective NMF

Conclusion

We can use NMF for

- Dimensionality Reduction (Data Mining)

- Clustering Analysis (Pattern Analysis)

Current NMF Research:

- Algorithms

- Alternative Objective Functions

- Convergence Criterion

- Updating NMF

- Initializing NMF

- Choosing k

Thank you…

and Questions?