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Particle Swarm Optimization for Microarray Data

V.Kumutha

Assistant Professor, Dept. of Computer Science

D. J. Academy for Managerial Excellence

Coimbatore, Tamil nadu, India

Email: kumuthav@gmail.com

S. Palaniammal

Professor and Head, Dept. of Science and Humanities

Sri Krishna College of Technology Coimbatore, Tamil

nadu, India

Email: splvlb@yahoo.com

AbstractDue to enormous growth in gene (gene function

and regulatory mechanisms) with the exposure in advanced

techniques, handling high dimensional data still becomes a

continuous research. Data mining plays a vital role for inferring

hidden information from voluminous data set to retrieve knowl-

edgeable information. Although fuzzy approaches are already

implemented in bio-inspirational concept, it lacks to process

efficiently in case of incomplete or inconsistent data set. This

leads to increased false alarm rate. In this proposed approach,

the degree of membership to indeterminacy is extended by

adopting the concept of generalization of fuzzy logic, which is

known as intuitionistic fuzzy logic. This paper proposes a hybrid

approach for clustering high dimensional data set using IFCM

and IFPSO to increase the detection accuracy and decrease the

false alarm ratio considerably. To find similarity among objects

and cluster centers intuitionistic based similarity measure is

used. Intuitionistic fuzzy particle swarm optimization optimizes

the working of the Intuitionistic FCM. Experimental results of

proposed approach shows better results when compared with the

existing methods.

Index TermsIntuitionistic fuzzy, FCM, IFPSO, gene expres-

sion data

I. INTRODUCTION

Clustering is termed as an unsupervised learning, applicable

in various fields [1]. Clustering methods tend to organize

data points into groups such that data points belong to one

cluster are similar whereas data points in different clusters are

distinct. These methods have applications in various areas such

as bioinformatics, taxonomy, image processing, information

retrieval, data mining etc. [2]. Hard (or crisp) clustering algo-

rithms have strict boundaries that require each data point of the

data set to one and only one cluster specifying the membership

value as 0 or 1. Several techniques have been developed

to cluster the input data in past decades [4, 5]. Hard, Soft,

Probabilistic and Possibilistic are the various classification of

clustering methods. Recent research is focused on Fuzzy c-

means (FCM), a soft clustering approach that generates fuzzy

partitions for a given data set.

Fuzzy clustering methods allows one data point to lie in more

than one cluster representing overlapping boundaries between

clusters by specifying the membership value between 0 and

1. The Fuzzy c-means (FCM) is one of the popular fuzzy

clustering methods which use fuzzy set theory [3]. FCM

cluster data according to an objective function and several

constraints. Fuzzy c-means is an effective algorithm, whereas

the random selections of center point make iterative process

falling into local optima solution hence different initializations

may lead to different results.

One of the major challenges posed by real-world clustering

applications is dealing with uncertainty in the localization of

the feature vectors. In gene expression data, the number of

samples is very limited while the volume of genes is very

large; such data sets are very sparse in high-dimensional gene

space. Also most of the genes collected may not necessarily

be of interest. A small percentage of genes which manifest

meaningful sample phenotype structure are buried in large

amount of noise. Intricacy arises in choosing informative genes

when there is uncertainty about which genes are relevant[16].

To handle this problem intuitionistic fuzzy approach is used.

Intuitionistic Fuzzy Sets (IFSs) [6] are generalized fuzzy sets,

which are useful in coping with the hesitancy originating

from imperfect or imprecise information. Membership and

non-membership value are elements involved in this sets. The

degree of membership denotes the validity or trueness of the

element to the set, whereas the non-validity of falseness of the

element to the set denotes the non-membership value. Apart

from validity and non-validity of the element, another element

named hesitancy or indeterminacy or uncertainty poses diffi-

culty in determining the validness of the membership of the

element to the group. Recent research indicates that applying

intuitionistic fuzzy sets to high dimensional data provides

optimal clustering results.

The rest of this paper is organized as follows: Section 2

discusses the related works. Section 3 presents materials and

methods. Section 4 summarizes the experimental analysis

performed with benchmark data sets. The conclusion of the

proposed work is given in Section 5.

#319212013 IEEE

Proceedings of International Conference on Optical Imaging Sensor and Security, Coimbatore, Tamil Nadu, India, July 2-3, 2013

i=1

0 <

ij

ij

II. LITERATURE REVIEW degree of association or membership function of the i

th

object

th

There are many works in literature related to Intuitionistic

Fuzzy c-means. Hesam Izakian, et al.[7] presented a hybrid

fuzzy clustering method based on FCM and FPSO, which

makes use of the merits of both the algorithms. The FCM-

with the j cluster. The characters of are as follows:

ij

[0, 1] i = 1, 2, ....d (1)

ij

= 1, j = 1, 2, ...p (2)

FPSO algorithms applies FCM to the particles in the swarm

every number of iterations/generations such that the fitness

p

i=1

ij

< 1 ij = 1, 2, ...d (3)

value of each particle is improved. The hybrid FCM-FPSO

The objective function of FCM algorithm is to minimize the

obtained superior results than others and it can escape from

local optima. Also, the experimental results show that when

the size of data set (number of objects or clusters) is small,

the FPSO surpasses FCM but with increasing the size of data

set, the outcome of FCM was improved than FPSO.

Eq. 2:

where

J

m

=

p

m

d

2

1 > m < (4)

i=1 j=1 ij ij

d

ij

= |o

i

~ z

j

| (5)

E. Mehdizadeh, et al.[8] presented an efficient hybrid method

particularly for large data sets based on fuzzy particle swam

optimization (FPSO) and Fuzzy C-Means (FCM) algorithms,

meant to resolve the fuzzy clustering problem. The perfor-

where m(m > 1) is a scalar termed the weighting exponent

and controls the fuzziness of the resulting clusters and d

ij

is

the Euclidean distance from object o

i

to the cluster center z

j

.

The z

j

, centroid of the j

th

cluster, is acquired using Eq. (6).

mance was improved by seeding the initial swarm with the

result of the c-means algorithm. The experiment indicates that

Z

j

=

p

i=1

m

O

i

(6)

the computation times and solution quality of FPSO for large

data sets was better than FCM.

Algorithm 1.Fuzzy c-means

i=1

m

In M. Mir et al.[9], PSO algorithm and fuzzy methods were

combined to avoid local peaks and find global optimal solu-

tion,. This approach uses global search capacity to overcome

FCM deficits. It finds optimal location of clusters centers for

input data set and finally finds the member components of

each cluster.

Erol Egrioglu et al. [10] presented a hybrid approach, in

which fuzzy c-means clustering method and artificial neural

1.Select m (m>1) and initialize the membership function

values ,

ij

i=1,2,...p, j=1,2,..d

2.Compute the cluster centers Z

j

, j = 1,2,..., d by using Eq.

(6)

3.Compute Euclidian distance, d

ij

, i = 1,2,..., p; j=1,2,..., d

4.Update the membership function,

ij

i = 1, 2... p; j=1,2,...,

d by using below equation

1

networks were used in fuzzy time series to get more accurate

forecasts. Fuzzification step in FCM removes problems caused

ij

=

d

dij

2

m~

1

(7)

defined by artificial neural networks avoids use of difficult

matrix operations.

Runkler et al.[11] presented two methods for minimizing

the reformulated objective functions of the fuzzy c-means

clustering model by particle swarm optimization: PSO-V and

PSO-U. Every particle in PSO-V represents a component of a

cluster center, and in PSO-U each particle signifies an un-

scaled and unnormalized membership value. The approach

was compared with alternating optimization and ant colony

optimization methods.

III. MATERIALS AND METHODS

1) Fuzzy C-Means algorithm: The Fuzzy C-Means algo-

rithm (FCM) is an iterative algorithm that finds clusters in data

and which uses the concept of fuzzy membership, instead of

assigning an object to a single cluster, each object will have

different membership values on each cluster. It partitions set

of n objects in R

d

dimensional [12] space into d (1 d p)

O=o

1

,o

2

,...,o

p

fuzzy clusters with Z=z

1]

,z

2

,...,z

p

cluster

centers or centroids. A fuzzy matrix with p rows and d

columns is defined for fuzzy clustering of objects in which

p is the number of data objects and d is the number of

clusters,

ij

, the element in the i

th

row and j

th

column in ,

point out the

k=1

(

dik

)

5.If not converged, go to step 2.

2) Intuitionistic Fuzzy c-means Clustering(IFCMC): The

Intuitionistic Fuzzy Set (IFS) was defined as an extension of

the ordinary Fuzzy Set [12],[13]. As opposed to a fuzzy set

in X, given by:

A = {(x,

A

(x))|x X } (8)

where

A

(x) [0,1] is the membership function of the fuzzy

set A, an intuitionistic fuzzy set B is given by:

B = {(x,

B

(x)),

B

(x)x X } (9)

where

B

(x) [0,1] and

B

(x) [0,1] are such that:

0 >

B

(x),

B

(x) > 1 (10)

and

B

(x),

B

(x) [0,1] denote degrees of membership and

non-membership of x B, respectively.

For each intuitionistic fuzzy set B in X, hesitation margin

(or intuitionistic fuzzy index) of x B is given by:

B

(x) = 1 ~ (x) ~

B

(x) (11)

which expresses a hesitation degree of whether x belongs to

B or not. It is obvious that 0>

B

(x)> 1 , for each x X.

To describe an intuitionistic fuzzy set completely, it is

necessary to use any two functions from the triplet:

membership func- tion; non-membership function; and

hesitation margin.

The fuzzy membership value and the cluster center are updated

using (12) and (13).

U

ik

= U

ik

+

ik

(12)

1~

m

j=1

.

X (t + 1) = X (t) + V (t + 1) (19)

where, X and V are position and velocity of particle respec-

tively. w is inertia weight, c1 and c2 are positive constants,

called acceleration coefficients which control the influence of

pbest and gbest on the search process, P is the number of

particles in the swarm, r1 and r2 are random values in range

k=1

U

ik

x

ik

i

=

k=1

U

ik

(13)

[0, 1].

4) Fuzzy PSO Algorithm: A particle swarm optimization

The objective function for IFCMC is

with fuzzy set theory is called fuzzy particle swarm opti-

J =

c

n

u

m

d(x

k

, v

2

)x +

e

1~

i

(14)

mization (FPSO) [15]. Using fuzzy relation between variables,

with m=2

i=1 k=1 ik i i=1 i

FPSO redefines the position and velocity of particles and its

also applied for clustering problem. In this method X is the

Algorithm 2. Intuitionistic FCM

1.Select m > 1

2.Initialize membership and non-membership degree of data

position of particle, the fuzzy relation for the set of data

objects O=o

1

,o

2

,o

n

, to set of clusters centers Z=z

1

,z

2

,.z

n

can be expressed as follows:

objects.

3.Detect initial centroids by selecting c random intuitionistic

11

...

1c

(20)

fuzzy object.

4.Fuzzy matrix

ij

=

S

1

(x

j

~

i

)

1

(15)

X =

... ... ...

n1

...

nc

Here,

ij

is the membership function of the i

th

object with

c 1

i=1

(S

1

(x

i

~

i

)

1~ m

5.Calculate centroid

the j

th

cluster with constraints

i

[0, 1] i = 1, 2, ..n j = 1, 2, ..c (21)

S(A, B) =

n

c

j=1

ij

= 1 i = 1, 2, ..c (22)

P

A

(x

j

)

B

(x

j

) +

A

(x

j

)

B

(x

j

) +

A

(x

j

)

B

(x

j

)

j=1

therefore it is known that the position matrix of each particle

n

max(

P

2

(x

j

) +

2

(x

j

) +

2

x

j

)

(16)

is the same as fuzzy matrix in FCM algorithm. Also the

velocity of each particle is stated using a matrix with the size

A

j=1

6.Update the centroid

A A

x

ik

n rows and c columns, the elements of which are in range

between -1 and 1.

The equations (18) and (19) are used for updating the positions

Z

j

=

n ik

(17)

and velocities of the particles based on the matrix.

k=1

n

k=1

ik

7.Update the membership, non-membership and hesitation

value

3) Particle Swarm Optimization PSO: Particle swarm opti-

mization (PSO) is a population-based stochastic optimization

technique inspired by bird flocking and fish schooling [14]

which is based on iterations or generations. The algorithmic

flow in PSO starts with a population of particles whose

After updating the position matrix, it may violate the con-

straints given in (1) and (2) since it is compulsory to normalize

the position matrix. First all the negative elements in matrix are

set to zero. If all elements in a row of the matrix are zero, they

need to be reevaluated using series of random numbers within

the interval between 0 and 1, and then the matrix undergoes

the following transformation without violating the following

constraints:

positions represent the potential solutions for the intentionl

11

1c

problem, and search space are randomly initialized by the

velocity. The search for optimal position is performed by

X normal =

c

j=1

1j

c

.

1j

.

.

(23)

.

. .

updating the particle velocities and positions for each iteration.

n1

nc

In each iteration, the fitness value of each particles position is

j=1

1j

j=1

1j

c c

determined using a fitness function. Using two best positions,

personal best position and global best position the velocity

of each particle is updated. The personal best position, pbest,

This technique uses the following equation as fitness function

for evaluating the solutions

K

is the best position the particle has visited and gbest is the

best position the swarm has visited since the first time step.

f (X ) =

J

m

(24)

A particles velocity and position are updated as follows.

V (t + 1) = wV (t) + c1r1(pbest(t) ~ X (t))

+c2r2(gbest(t) ~ X (t)); k = 2, 3, .P (18)

Here, K is a constant and J

m

is the objective function of FCM

algorithm. The smaller is Jm, the better is the clustering effect

and the higher is the individual fitness f(X). The termination

condition in this method is the maximum number of iterations

ij

or no improvement in gbest in a number of iterations. The

FCM algorithm is quicker than the FPSO algorithm because

it need not as much of function evaluations, but it normally

go down into local optima. FCM algorithm incorporated with

the particles using hesitation degree which is also known as

indeterministic degree.

11

...

1c

... ... ... (26)

FPSO algorithm to form a hybrid clustering algorithm called

FCM-FPSO which maintains the merits of both FCM and PSO

X =

n1

...

nc

algorithms.

Algorithm 3. Fuzzy PSO

Input : Dataset

Output : Objective Values

Step 1. Initialize the parameters including population size P,

c

1

, c

2

, w and the maximum iterative count.

Step 2. Create a swarm with P particles (X, pbest, gbest and

V are n c matrices).

Step 3. Initialize X, V, pbest for each particle and gbest for

the swarm.

Step 4. Calculate the cluster centers for each particle using

Algorithm 4. IFPSO algorithm

Input : Dataset

Output : Objective Values

Step 1. Initialize the parameters including population size P,

c1, c2, w and the maximum iterative count.

Step 2. Create a swarm with P particles (X, pbest, gbest and

V are n c matrices).

Step 3. Initialize X, V, pbest for each particle and gbest for

the swarm.

Step 4. Calculate the cluster centers for each particle using by

Eq. (17)

Z

j

=

n

i=1

m

O

i

m

(25)

Step 5. Calculate the fitness value of each particle using

i=1

ij

Step 5. Calculate the fitness value of each particle using Eq.

K

f (X ) =

J

m

(27)

(24)

Step 6. Calculate pbest for each particle.

Step 7. Calculate gbest for the swarm.

Step 8. Update the velocity matrix for each particle using Eq.

(18)

Step 9. Update the position matrix for each particle using Eq.

(19)

Step 10. If terminating condition is not met, go to step 4.

IV. PROPOSED APPROACH

Dataset Preprocessing Applying IFPSO

Applying IFCM Generating cluster patterns

Fig. 1. Framework of Proposed Work

A. Intuitionistic Fuzzy Particle Swarm Optimization (IFPSO)

Existing approaches works fine for the data-sets which are

not corrupted with noise but if the data set is noisy or distorted

then it wrongly classifies noisy pixels because of its abnormal

feature data and results in an incorrect membership and

improper clustering. The above said problem was also faced by

the fuzzy particle swarm optimization approach. To overcome

the problem of abnormal features that exist among the particle

clustering can be overwhelmed by introducing the concept of

intuitionistic fuzzy based particle swarm optimization which is

the generalization of fuzzy based particle swarm optimization.

In this approach each particle is concerned not only with the

membership function but the indeterministic degree also taken

into consideration for handling the abnormality problem. The

abnormality problem arises due to the inconsistency of the

particles position information.

This proposed approach IFPSO introduces another degree into

the consideration for handling the uncertainty problem among

Step 6. Calculate pbest for each particle.

Step 7. Calculate gbest for the swarm.

Step 8. Update the velocity matrix for each particle using Eq.

(18)

Step 9. Update the position matrix for each particle using Eq.

(19)

Step 10. If terminating condition is not met, go to step 4.

B. Hybrid Intuitionistic Fuzzy C Means and Intuitionistic

Fuzzy Particle Swarm Optimization

The IFCM algorithm is quicker than the IFPSO algorithms

because it uses few function evaluations, but it normally go

down into local optima. Rather, IFCM algorithm incorporated

with IFPSO algorithm to form a hybrid clustering algorithm

called IFCM-IFPSO which maintains the merits of both IFCM

and IPSO algorithms. In IFCM-IFPSO algorithm, IFCM is

applied to the particles in the swarm every number of itera-

tions/generations such that the fitness value of each particle is

improved. The algorithm 5 illustrate hybrid IFCM-IFPSO.

Algorithm 5. IFCM-IFPSO algorithm

Input : Dataset

Output : Objective Values

Step 1. Initialize the parameters of IFPSO and IFCM including

population size P, c1, c2, w, and m.

Step 2. Create a swarm with P particles (X, pbest, gbest and

V are n c matrices).

Step 3. Initialize X, V, pbest for each particle and gbest for

the swarm

Step 4. IFPSO algorithm

4.1 Calculate the cluster centers for each particle using by (17)

4.2 Calculate the fitness value of each particle using by (24)

4.3 Calculate pbest for each particle.

4.4 Calculate gbest for the swarm.

4.5 Update the velocity matrix for each particle using by (18)

4.6 Update the position matrix for each particle using by (19)

Fig. 1. Results for Iris data set

4.7 If terminating condition is not met, go to step

Step 5. IFCM algorithm

5.1 Compute the cluster centers j z , j = 1,2,..., c , by using

(13)

5.2 Compute Intuitionistic based Similarity measurement pro-

posed by (x, y)

Fig. 2. Results for Yeast data set

r

1

D(A, B) = 1 ~

2

n

X

i=1

(

A

(x

i

) +

B

(x

i

))

2

Fig. 3. Results for Colon cancer data set

+(

A

(x

i

) +

B

(x

i

))

2

+ (

A

(x

i

) +

B

(x

i

))

2

(28)

In this A refers to the object and B refers to the centroid of

the ith cluster.

5.3 Update the membership function

ij

, i = 1,2n j=1,2,..., c

by using (15)

5.4 Calculate pbest for each particle.

5.5 Calculate gbest for the swarm.

5.6. If IFCM terminating condition is not met, go to step 5.

Step 6. If IFCM-IFPSO terminating condition is not met, go

to Step 4.

V. EXPERIM ENTAL RESULTS

The algorithms discussed in the previous section have been

implemented using MATLAB. For evaluating the performance

of the proposed work, four different benchmark data sets are

taken into consideration.

A. Parameter settings

The optimized performance of the IFPSO and IFCM-IFPSO,

fine tuning has been executed and best values for their

parameters are chosen. The experimental results based on

these algorithms achieve best under the following settings:

c1,c2, the value is 2.0 - population is 10, and weight values

are: the minimum of weight value is 0.1 and maximum of

value is 0.9 and weighting exponent component m value is 2

which is common to all the algorithms. The FCM and IFCM

terminating condition is: if the previous iteration of centroid

values and current iteration of centroid values are same,

terminate the algorithm. The FPSO and IFPSO terminating

condition is till it reaches the maximum iteration value when

the algorithm cannot improve the gbest in 1000 consecutive

iterations. Also the IFCM-IFPSO terminating condition is met,

when the algorithm cannot improve the gbest in 2 consecutive

iterations.

The experimental results of over 100 independent runs for

Fig. 4. Results for Leukemia data set

TABLE I

GE N E EX P R E S S I O N DATA S E

T

Data set No. of samples No. of genes

Yeast 79 2467

Colon cancer 62 2000

Leukemia 72 7129

TABLE II

BE N C H M A R K DATA S E T

Data set No. of attributes No. of instances

Iris 4 150

IFCM and 10 independent runs for IFPSO and IFCM-IFPSO

are shown in the figures 2,3,4 and 5. The figures shows the

objective function values. As shown in the figures 2 to 7, the

hybrid IFCM-IFPSO acquires better quality results than others

in all of data sets and it can flee from local optima. The below

figure shows the various generation runs of proposed IFCM-

IFPSO algorithm with the mean and best score value (Figures

6,8 & 10).

The figure 6 shows Average cumulative change in value of

the fitness function over 50 generations less than 1e-006 and

Fig. 5. Average cumulative change for 129 generations

Fig. 6. Mean and best score value for 129 generations

constraint violation less than 1e-006, after 129 generations.

Final best point: [0.99999 0.99998]

Figure 8 shows Average cumulative change in value of the

fitness function over 50 generations less than 1e-006 and

constraint violation less than 1e-006, after 120 generations.

Final best point: [1.0004 1.0009]

Figure 10 shows Average cumulative change in value of the

fitness function over 50 generations less than 1e-006 and

constraint violation less than 1e-006, after 116 generations.

Final best point: [0.99997 0.9999]

VI. CONCLUSION

The clustering of high dimensional gene expression is a

very important problem in data mining. Many algorithms have

been proposed for clustering. The fuzzy c-means algorithm is

sensitive to initialization and is easily trapped in local optima.

On the other hand, the fuzzy particle swarm algorithm is a

global stochastic tool which could be implemented and applied

easily to solve various function optimization problems, or the

complications that can be converted to optimization problem

Fig. 7. Average cumulative change for 116 generations

Fig. 8. Mean and best score value for 116 generations

tasks. Both of them fail to handle the uncertainty condition

and they left the concept of indeterminacy when there is a

presence of vagueness or incompleteness in clustering dataset.

In this paper, in order to overcome the shortcomings of

the fuzzy c-means and fuzzy particle swarm optimization an

algorithm is proposed to overcome the indeterminacy, which

leads to a noticeable improvement in the performance of

clustering objects. Instead of just considering the membership

value of each object in the cluster, the proposed approach

takes into account the indeterministic value as an important

factor in the case of incompleteness in the data set clustering.

Experimental results over six well-known data sets, Iris, Glass,

Cancer, and Wine, indicates that the suggested hybrid method

is efficient and can reveal very encouraging results in term of

quality of solution found. A new hybrid method combining

Intuitionistic fuzzy c-means and Intuitionistic fuzzy Particle

swarm optimization algorithm have been applied successfully

for real world data sets. The computational results show that

the performance of the proposed algorithm is better than the

other existing algorithms.

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