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**Analysis of Hyperspectral Data with Diffusion Maps and Fuzzy ART
**

Rui Xu, Louis du Plessis, Steven Damelin, Michael Sears, and Donald C. Wunsch II

Abstract-The presence of large amounts of data in

hyperspectral images makes it very difficult to perform further

tractable analyses. Here, we present a method of analyzing real

hyperspectral data by dimensionality reduction using diffusion

maps. Diffusion maps interpret the eigenfunctions of Markov

matrices as a system of coordinates on the original data set in

order to obtain an efficient representation of data geometric

descriptions. A neural network clustering theory, Fuzzy ART, is

further applied to the reduced data to form clusters of the

potential minerals. Experimental results on a subset of

hyperspectral core imager data show that the proposed methods

are promising in addressing the complicated hyperspectral data

and identifying the minerals in core samples.

1. INTRODUCTION

T

HE advent of new spectral imaging techniques makes

hyperspectral data more commonly accessible in recent

decades. Spectral imaging refers to the process of

sampling an image at several different frequencies [1]. Digital

color photography is a form of spectral imaging. The picture

is sampled at three different frequencies , one in the blue range

of the spectrum and the other two in red and green

respectively. Every sample gives a matrix of intensity values,

which could be plotted to give a gray-scale image. When all

three matrices are blended together a color image is produced.

Multispectral imaging refers to the process of sampling an

image at more frequencies. Images are commonly sampled in

the frequency range between 400 and 2,500 nm, since this is

the range of the optical spectrum where the sun provides

useful illumination [1]. In hyperspectral imaging the image is

sampled at hundreds of frequencies, compared to only a few

for multispectral imaging. Furthermore, the different

frequencies in multispectral imaging are usually distributed in

an irregular fashion, whereas the bands in hyperspectraI

imaging are regularly spaced [1].

Manuscript received January 5, 2009.

R. Xu is with the Applied Computational Intelligence Laboratory,

Department of Electrical & Computer Engineering, Missouri University of

Science and Technology, MO 65409 USA (phone: 573-341-6811 ; fax:

573·341-4521 ; e-mail: rxu@mst.edu) .

L. du Plessis is with the School of Computat ional and Applied

Mathemat ics, University of the Witwater srand, Johannesburg, South Africa

(email: Laduplessis@gmai l.com).

S. Damelin is with the Department of Mathematical Sciences, Georgia

Southern University, Statesboro, GA 30460 USA, and the School of

Computational and Applied Mathemat ics, University of the Witwatersrand ,

Johanne sburg, South Africa (e-mail: damelin@georgiasouthem.edu).

M. Sears is with the School of Computer Science, University of the

Witwat ersrand, Johannesburg, South Africa (email:

michael.sears @wits.ac. za).

D. C. Wunsch [[ is with the Department of Electrical & Computer

Engineering, Missouri University of Science & Technol ogy, Rolla, MO

65409 USA (e-mail: dwunsch@mst.edu) .

978-1-4244-3553-1/09/$25.00 ©2009 IEEE

q

Fig. 1. The hyperspectral data cube. For every one of the m frequencies

sampled, there is an image of p x q of intensity values. Similarly, for

every one of the pixels in the image, there is a compl ete spectrum of

values. This cube image is generated with the data used in our studies.

Because of the regular spacing of narrow bands, a

continuous spectrum can be drawn for every pixel in the

image. Instead of ending up with a flat two-dimensional

matrix of values, we obtain a "hypercube" of data, as shown

in Fig. 1. This is where the problem in analyzing and storing

hyperspectral data comes in. Having more than a hundred

bands for every pixel means having enormous amounts of

data. If the hyperspectraI imager scans in m bands, then every

pixel of the hyperspectral image can be seen as an m

dimensional vector.

Currently, hyperspectral imaging is mainly used In

airborne surveillance techniques [2]. Some uses for

hyperspectral imaging include crop assessment ,

environmental applications, and mineral exploit ation [3].

Here, we are interested in the identification of minerals in

core samples. Core samples are long pieces of rock that was

drilled in areas suspected of being rich in minerals . Sites for

new mines are identified using data collected from core

samples. It would be advantageous to automatically identify

the different minerals resident in a piece of core. AngIoGold

Ashanti has constructed the Hyperspectral Core Imager (HC!)

that scans in core samples. The HCI scans in 5 meters of core

every hour, at 400 bands, producing 2 gigabytes of data every

hour [2]. With this amount of data being produced every hour,

3390

(1)

be the degree of Xi; the Markov or transition matrix P is then

constructed by calculating each entry as

w(x

j

, Xj)

p(X.,X.) =. (3)

1 ) d(x

j

)

From the definition of the weight function, P(Xi' Xj) can be

interpreted as the transition probability from Xi to Xj in one

time step. From the definition of the Gaussian kernel it can be

seen that the transition probability will be high for similar

elements. This idea can be further extended by considering

pt(Xi' Xj) in the lhpower p

t

ofP as the probability of transition

from Xi to Xj in t time steps [4]. Therefore, the parameter t

defines the granularity of the analysis. With the increase of

the value of t, local geometric information of data is also

integrated. The change in direction of t makes it possible to

control the generation of more specific or broader clusters.

Because of the symmetry property of the kernel function,

for each t 1, we may obtain a sequence ofN eigenvalues of

P, 1=AO Al ... AN, with the corresponding eigenvectors

{<pj, j = 1,... ,N}, satisfying,

p

t

<P j =.,1/ <P j • (4)

Using the eigenvectors as a new set of coordinates on the data

set, the mapping from the original data space to an

L-dimensional (L < m) Euclidean space 9l

L

can be defined as

'1', : Xi (Ar'CPl (x.), ..., ;L;,cpt. (xJr. (5)

Correspondingly, the diffusion distance between a pair of

points Xi and Xj

D,(Xi,X) =IIp'(Xi' .)- p'(X

j

' -)IL'l-b' (6)

where qJo is the unique stationary distribution

m (x) = d(x) X E 9l

n1

(7)

'1'"0 Ld(x;)' ,

XjEX

is approximated with the Euclidean distance in 9l

L

, written as

Dt(xj,x

j

) =II'Pt(x

j

) - 'Pt(xj)ll. (8)

It can be seen that the more paths that connect two points in

the graph, the smaller the diffusion distance is.

The kernel width parameter (J represents the rate at which

the similarity between two points decays. There is no good

theory to guide the choice of (J. Several heuristics have been

proposed, and they boil down to trading off sparseness of the

kernel matrix (small (J) with adequate characterization of the

true affinity of two points. One of the main reasons for using

spectral clustering methods is that, with sparse kernel

matrices, long range affinities are accommodated through the

chaining of many local interactions as opposed to standard

Euclidean distance methods - e.g. correlation - that impute

global influence into each pair-wise affinity metric, making

long range interactions dominate local interactions.

It is apparent from the previous introductions that the most

costly part of the diffusion map is the construction of the

affinity matrix, as we square the amount of data. However,

this matrix is symmetric, and all the diagonal entries are equal

to one. This means that only (N

2

- N) / 2 entries of the matrix

storage and analysis becomes a major problem. The sheer

amount of data produced motivates the need for an automated

analysis technique.

Here, we address high-dimensional hyperspectral data

using diffusion maps, which consider the eigenfunctions of

Markov matrices as a system of coordinates on the original

data set in order to obtain efficient representation of data

geometric descriptions [4-6]. The major difference between

diffusion maps and methods like principle component

analysis (PCA) is that in diffusion maps, a kernel is chosen

before the procedure. This kernel is chosen by our prior

defmition of the geometry of the data [4]. In PCA, all

correlations between values are considered, while only high

correlation values are considered in diffusion maps.

Diffusion maps have already been applied in the analyses of

protein data [7], gene expression data [8], video sequences

[9], and so on, and have achieved attractive performances.

The assumption is that every core sample contains only a few

different kinds of minerals so that there is a lot of redundant

data. It should therefore be sufficient to have only a few key

values per pixel to identify different materials. The reduced

data obtained are then clustered with a neural network cluster

theory, Fuzzy ART (FA) [10], to generate clusters of the

potential minerals. FA is based on Adaptive Resonance

Theory (ART) [11-12], which was inspired by neural

modeling research and was developed as a solution to the

plasticity-stability dilemma: how adaptable (plastic) should a

learning system be so that it does not suffer from catastrophic

forgetting of previously-learned rules (stability)? ART can

learn arbitrary input patterns in a stable, fast, and

self-organizing way, thus overcoming the effect of learning

instability that plagues many other competitive networks.

Experimental results on a subset of hyperspectral data show

that the proposed methods are promising in addressing the

complicated hyperspectral data and identifying the minerals

in core samples.

The remainder of this paper is organized as follows.

Section II and III briefly introduce diffusion maps and FA.

The experimental results are presented and discussed in

section IV, and section V concludes the paper.

II. DIFFUSION MAPS

Given a data set X = {Xi, i = 1,.. . ,N} on am-dimensional

data space, a finite graph with N nodes corresponding to N

data points can be constructed on X as follows. Every two

nodes in the graph are connected by an edge weighted

through a non-negative, symmetric, and positive definite

kernel w: X x X (0, 00). Typically, a Gaussian kernel is

defined as

W(Xi,X) =exp[ Ilx

i

,

where (J is the kernel width parameter. The kernel reflects the

degree of similarity between Xi and Xj, and 11·11 is the Euclidean

norm in 9l

m

. The resulting symmetric semi-positive definite

matrix W = {W(Xi' Xj)}NxN is called the affinity matrix.

Let

d(xj) = L w(xj,X

j

)

XjEX

(2)

3391

(9)

(11)

Reset

Input Pattern I

Layer F

1

Layer F2 0 0 0 ... 0 0 0

Fig. 3. The original ROB image of the data (left) and the ROB image of

the masked hyperspectral image (right) . The core tray and the blurred

edges have been cut out for the masked image.

uncommitted neuron is selected for coding, a new

uncommitted neuron is created to represent a potential new

cluster.

FA displays many attractive characteristics that are also

inherent and general in the ART family. FA is capable of both

on-line (incremental) and off-line (batch) learning. The

computational cost of FA is O(N1ogN) or O(N) for one-pass

variant [13], and it can cope with large amounts of

multidimensional data, maintaining efficiency. In comparison,

the commonly used standard agglomerative hierarchical

clustering algorithms run at least O(N

2

) [14]. FA dynamically

generates clusters without the requirement of specifying the

number of clusters in advance as in the classical K-means

algorithm. Another important feature of FA is the capability

Fig. 2. Topological structure of Fuzzy ART. Layers F

1

and F

2

arc

connected via adaptive weights W. The orienting subsystem is

controlled by the vigilance parameter p.

The winning neuron J then becomes activated, and an

expectation is reflected in layer F] and compared with the

input pattern. The orienting subsystem with the pre-specified

vigilance parameter p (0 :s p :s 1) determines whether the

expectation and the input pattern are closely matched. If the

match meets the vigilance criterion,

IXI\ w

J

!

P"';'-lxl-' (12)

weight adaptation occurs, where learning starts and the

weights are updated using the following learning rule,

w . ui cw) = p( x 1\ WJ(old)) +(1- P)wJ(old) , (13)

where fJ E [0,1] is the learning rate parameter. This procedure

is called resonance, which suggests the name of ART. On the

other hand, if the vigilance criterion is not met, a reset signal

is sent back to layer F

2

to shut off the current winning neuron,

which will remain disabled for the entire duration of the

presentation of this input pattern, and a new competition is

performed among the rest of the neurons. This new

expectation is then projected into layer F], and this process

repeats until the vigilance criterion is met. In the case that an

need to be calculated. Calculating this matrix could be very

easily parallelized however , since any two entries are

completely independent of each other. The transition matrix

can be obtained from W by dividing every row element-wise

with d(xD. This could also be done in parallel. Experimental

results show that the resulting matrix is sparse, and since we

only need to find the first couple of eigenvectors and

eigenvalues, this should not pose too much of a problem.

III. FuzzyART

Fuzzy ART (FA) incorporates fuzzy set theory into ART

and extends the ART family by allowing stable recognition of

clusters in response to both binary and real-valued input

patterns with either fast or slow learning [10]. The basic FA

architecture consists of two-layer nodes or neurons, the

feature representation field Flo and the category

representation field F

2

, as illustrated in Fig. 2. The neurons in

layer F] are activated by the input pattern, while the

prototypes of the formed clusters are stored in layer F

2

• The

neurons in layer F

2

that are already being used as

representations of input patterns are said to be committed.

Correspondingly, the uncommitted neuron encodes no input

patterns. The two layers are connected via adaptive weights

Wj , emanating from nodej in layer F

2

. After an input pattern is

presented, the neurons (including a certain number of

committed neurons and one uncommitted neuron) in layer F

2

compete by calculating the category choice function

T _IXI\Wj [

J - a+lwjl

where 1\ is the fuzzy AND operator defined by

(XI\Y), =min(x"y,) , (10)

and a > 0 is the choice parameter to break the tie when more

than one prototype vector is a fuzzy subset of the input pattern,

based on the winner-take-all rule,

TJ

3392

Component 1 Component 2

120 120

100 100

80 80

60 60

40 40

20 20

-40 -20 20 40 60 80 100 -40 -20 20 40 60 80 100

Component 3 Component 4

120 120

100 100

80 80

60 60

40 40

20 20

-40 -20 20 40 60 80 100 -40 -20 20 40 60 80 100

Fig. 4. The first four components obtained in the diffusion map for the middl e image. These component s interpret the major clusters in the image.

of detecting atypical patters or outliers during its learning.

The detection of such patterns is accomplished via the

employment of a match-based criterion that decides to which

degre e a particular pattern matches the characteristics of an

already formed category in layer F

2

• Finally, FA is far simpler

to implement, for example, than kernel-based clustering or

clustering algorithms based on mixture densities. More

discussions on the properti es of FA in terms of prototype,

access, reset, and the number of learning epochs required for

weight stabilization can also be found in [15].

IV. EXPERIMENTAL RESULTS A ND DISCUSSIONS

We applied the proposed method to the hyperspectral dat a

from AngloGold Ashanti. The or iginal image (Fig. 3) is of a

core sample on the imaging tray of the Hel, which is further

split into thr ee overlapping subimages, denot ed as upper,

middl e, and lower image, due to the large size of the image.

For these images, the sides have been trimmed to remove

almost all traces of the core tray. The original image contains

640 bands that are produced by thre e spectrometers that

measure overlapping parts of the spectrum, whi ch is then

reduced to 400 unique bands. Among the 400 bands, we only

used 100 bands from the middle of the third spectrometer, the

part that is most sensitive to mineral features, in our further

analyses. It is impossible to use spectral values from all three

spectrometers because the spectrometers are not perfectly

Fig. 5. Clustering result of FA on the middle image, with the

dimensionality reduced to 20. Four maj or clusters are observed.

3393

Component 2

Component 4

80 100

100 80 60

-:

40 20

Component 1

120 120

100 100

80 80

60 60

40 40

20 20

-40 -20 80 100 -40 -20

Component 3

120 120

100 100

80 80

60 60

40

.-

40

20 20

-40 -20 20 40 60 80 100 -40 -20

Fig. 6. The first four principal components obtained in the PCA for the middl e image.

spatially aligned. Furthermore, the extremes of the ranges of

each spectrometer are particularly noisy and not of much use.

The Gaussian kernel was applied in our further analyses ,

with the kernel width parameter (J set to 10

3

. The time step

parameter was set to 1. All values in P less than 10.

3

were set

to O. According to our experiments, we find that the

clustering results are not sensitive to the category choice

parameter a, which was then set as 10-

3

for all analyses. We

also fixed the learning rate fJ at 1 for fast learning. It is clear

from previous discussions that the vigilance parameter p

plays an important role in determining the number of

categories formed in Layer F

2

• The larger the value of p, the

fewer mismatches will be tolerated ; therefore, more clusters

are likely to be generated. In our study, we start with a

relatively small value ofp and gradually increase it to observe

its effect on the formed clusters.

Fig. 4 shows the first four components of the diffusion map

on the middle image. The /hcomponent corresponds to the /h

dimension of the diffusion map. Compared to the resulting

clusters by FA with the dimensionality reduced to 20

dimensions (Fig. 5), it can be seen that the first four

components represent the major clusters (top right) existing

in the data. In comparison, the first four principal components

of PCA on the middle image are depicted in Fig. 6, where

clusters are not clearly shown as the case when diffusion

maps are used. As discussed in [3], a major concern on the

Fig. 7. Clustering result of FA on the lower image, before (left) and

after (right) the dimensionality reduced from 100 to 20. The vigilance

parameter is set at 0.8.

3394

(c) (d)

Fig. 8. Effect of the vigilance parameter p on the resulting clusters.

Clusters ofthe lower image when (a) p = 0.6, (b) p = 0.7, (c) p = 0.8, and

(d) p = 0.9. More clusters are generated with the increase ofp.

F2 layer of FA is 5, 9, 15, and 21, respectively. Clusters have

become clearer as p gradually increases. There is an obvious

spatial correlation between bands ofthe unprocessed data and

the clustering results. The results are also consistent with the

analyses using the K-means algorithm [2]; however, it is not a

trivial task for K-means to determine the number ofclusters in

advance.

Fig. 9 displays the cluster ing result ofthe upper image with

20 dimensions. The clusters formed at the lower right of the

image, which are shown in amber, correspond to the part of

the tray that is not removed. Hence, these clusters should not

occur anywhere else on the image, as the figure shows. The

composite image of the clustering result is obtained by

merging the three subimages based on the overlapping parts,

as shown in Fig. 10, although a representative spectrum for

each cluster could be used to decide the merge of the clusters.

It is encouraging that the overlaps between the pictures are

consistent with each other.

As we discuss in Section 11, one way to speed-up the

process of the diffusion maps is parallelization. However, a

major bottleneck in the performance of parallel computing is

communication. The speed of communication mediums is not

currently comparable to that of processors [16]. In our

particular case most of the overhead stems from having to

distribute data to the different processors and then

reassembling the results efficiently. We believe that one of

the most efficient algorithms is to simply send the complete

set ofdata points to every processor and use each processor to

calculate (N

2

- N) / 2r weights, where r is the number of

processors. A possible approach to implementing such an

Fig. 9. Clustering results of the upper image with FA. The clusters in

amber are the part ofthe tray.

(b) (a)

application of PCA to hyperspectral data is the number and

shape of the principal eigenvectors. The transform has a

blurring effect and the eigenvectors would most likely only

describe the most common characteristics of the data. The

existence of rare spectra in the data could go unnoticed

because of this. Whether such a weakness is carried over into

diffusion maps is worthy of further investigation.

The clustering results of FA on the lower image before and

after the dimension is reduced from 100 to 20 are shown in

Fig. 7, respectively. It is obvious that before the diffusion

map is applied, it is very difficult to observe any clear

clusters. However, when the dimension is reduced to 20,

major clusters become much clearer and could be easily

identified.

Fig. 8 depicts the effect of the vigilance parameter p on the

number of clusters generated. The value of p varies from 0.6

to 0.9 with a step of 0.1. The number of clusters created in the

3395

Fig. 10. Clustering results of the composite image with FA. The

vigilance parameter was set at 0.8.

algorithm would be to use Google's MapReduce function,

which is specifically designed to make it easy to implement

concurrent programs that use large sets of data [17]. The data

is mapped to many computers, and after processing, the

results are reduced to a manageable scale. Speed-up can also

be achieved in terms of graphics processing units (GPUs).

Although GPUs are mostly familiar to us from computer

games and 3-D graphics processors , they are increasingly

becoming a complementary platform for general-purpose

computation, as in computational intelligence, which is

usually involved with highly expensive computation. The

stream processing capability of GPUs, where the same

instruction is performed on different data streams, makes

them ideally suited to the computation of the transition

matrix. An implementation of GPU in accelerating ART can

produce a speed-up 22 times greater than the CPU

implementation [18]. However, it is necessary to understand

the limitations of the graphics processing hardware and to

take these limitations into account in developing algorithms

targeted at the GPU. Further investigation of the speed-up of

the diffusion maps and FA, based on the above discussions

and some possible pre-processing steps for noise reduction

are important topics for further research.

V. CONCLUSIONS

The occurrence of large amounts of hyperspectral data

brings important challenges to store and process. Here, we

investigate the performance ofdiffusion maps and fuzzy ART

to real hyperspectral image data, from core samples provided

by AngloGold Ashanti. The experimental results are very

encouraging and promising, with clearly defined clusters

found in the data, which correlate well with features of the

original image.

ACKNOWLEDGMENT

Partial support for this research from the National Science

Foundation, the Missouri University of Science &

Technology Intelligent Systems Center, and the M.K. Finley

Missouri endowment, is gratefully acknowledged.

We are grateful to Anglo Technical Division Geosciences

Resource Group and AngloGold Ashanti for allowing us

access to the Hcr data.

R EFERENC ES

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Chang, Editor, Hyperspectral Data Exploitation: Theory and

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(2) K. Cawse, S. Damelin, L. du Plessis, R. McIntyre, M. Mitchley, and M.

Sears, "An investigation of data compression techniques for

hyperspectral core imager data, " In Proceedings ofthe Mathematics in

Industry Study Group - MISG2008, South Africa , to appear, 2008.

(3) J. Bowles and D. Gillis, "An optical real-time adaptive spectral

identification systems(ORASIS)," In C. Chang, Editor, Hyperspectral

Data Exploitation: Theory and Applications, pp. 77- I06, Wiley, 2007.

(4) R. Coifman and S. Lafon, " Diffusion maps ," Applied and

Computat ional Harmonic Analysis , vol. 21, pp. 5-30,2006.

[5] S. Lafon and A. Lee, " Diffusion maps and coarse-graining: A unified

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[10] G. Carpenter, S. Grossberg, and D. Rosen, "Fuzzy ART: fast stable

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[15] 1. Huang, M. Georgiopoulos, and G. Heileman, "Fuzzy ART

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