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“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?