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Transactions on Computational Biology and Bioinformatics
3
II. PRELIMINARIES
A. Canonical Particle Swarm Optimization
As a famous swarm intelligence algorithm, PSO was first
proposed by Kennedy and Eberhart in 1995 [22]. This algorith-
m was initially inspired from the behaviors of birds flocking to
build a dynamic model that can be employed in optimization.
In PSO, each particle has two variables that are position and
velocity respectively. Over the course of optimization, particles
update their positions and velocities based on the updating
equations shown in (1):
V
i
(t + 1) = ωV
i
(t) + c
1
R
1
(t)(pbest
i
(t) − X
i
(t))
+ c
2
R
2
(t)(gbest(t) − X
i
(t))
X
i
(t + 1) = X
i
(t) + V
i
(t + 1)
(1)
where t is the iteration (generation) number, V
i
(t) and X
i
(t)
represent the velocity and position of the i
th
particle at gener-
ation t respectively; ω is termed inertia weight, c
1
and c
2
are
the acceleration coefficients, R
1
(t) and R
2
(t) are two vectors
randomly generated within [0, 1]
d
and d is the dimension of
the problem; pbest i(t) is the personal historical best position
of the i
th
particle and g
best
(t) is the current best particle found
so far. Kennedy has referred c
1
R
1
(t)(pbest
i
(t) − X
i
(t)) and
c
2
R
2
(t)(gbest
i
(t) − X
i
(t)) as the cognitive component and
social component, respectively [22].
According to (1), each particle will learn from its own
historical best position p
best
, so p
best
guides the direction for
individual particle. Besides, all particles will learn from g
best
,
so g
best
plays the role to guide the whole swarm. If g
best
is a
local optima, it is hard for the whole swarm to get rid of it.
In current years, many researches are conducted to weaken
the influence of g
best
to the whole swarm. In [17], the author
proposed a variant of PSO, where particles will learn from
p
best
only. However, in the algorithm the parameter setting,
which heavily affects algorithms’ performance, is on the
basis of empirical experiments. In [18], the authors divided
the whole swarm into pairs and employed a competitive
mechanism in pair comparison. The loser particle will learn
from the winner one. However, since in one generation only
half of particles, say loser particles, are involved in update,
while the winner particles do not update, so the whole swarm
has a low efficiency in convergence. In this paper, we propose
a novel particle swarm optimizer by employing grouping
strategy with p
best
guidance. We split the whole swarm into
several groups. In each group, the worse particles will learn
from the group best one. In addition, every particle has a
probability to learn from p
best
of other particles. In this
way, both convergence and diversity maintenance can be
considered simultaneously.
B. Measures of Population Diversity
There are mainly two ways to measure population diversity.
The first one is distance-based measurement (DBM) which
calculates the Euclidian distances among individuals. There
are several different forms of DBMs, such as the mean spatial
distance among all individuals, the mean distance between
individuals and the center position of the swarm, the maximum
distance between individuals, etc [23], [24], [25]. Normally, a
large distance means an abundant population diversity, while
a small distance implies a poor population diversity.
The second way is frequency-based measurement (FBM). In
FBM, the frequency of representative individuals is counted to
evaluate the population diversity [26], [27]. In [28], mean gene
frequency is employed to determine the population diversity.
Besides, entropy measurement is another way belonging to
FBM, since entropy uses the probability of appearance of
genes/fitness. A detail investigation of FBM for swarm in-
telligence can be found in [29], [30].
In [31], Wineberg and Oppacher draw the conclusion that,
although the two measurements have different forms, both of
them use the distance-based idea between all possible pairs
of chromosomes and organisms in a swarm. For FBM, it is
usually to count the frequency of each individuals. Especially
for continuous problems, it rarely appears two same individu-
als. Hence, the we do not use FBM to measure the population
diversity in this paper, but only use DBM. According to [30],
many types of DBM are proposed. In this paper, we employ
the sum of variance of each dimension as the measurement.
The diversity D for a swarm is given in (2).
D =
v
u
u
t
n
X
j=1
D
2
j
(2)
where D is the diversity of a swarm, n is the dimension and
D
j
=
1
m
m
X
i=1
[x
ij
− ¯x
j
]
2
(3)
¯x
j
=
1
m
m
X
i=1
x
ij
(4)
and x
ij
is the j
th
dimension of the i
th
particle, m is the
population size.
III. GROUPING PARTICLE SWARM OPTIMIZER WITH P
best
S
GUIDANCE (GPSO-PG)
A. Design of GPSO-PG
To weaken the effects of one solution, such as g
best
, to
PSO’s performance, we design a novel variant of PSO, termed
Grouping Particle Swarm Optimization with P
best
Guidance
(GPSO-PG). The motivation is to reduce the effects of any
individual particle to the whole swarm. First, at the beginning
of each generation, we divide the whole swarm into several
groups in a random way. The size of each group is equal.
In each group, we compare the particles and select a local
best particle called a winner for the rest particles. Besides, all
loser particles will be involved in the velocity update by the
equations shown in (5). In (5), we employ the set of p
best
s
provided by all particles, but not g
best
, to guide the swarm’s
direction.
V
i
(t + 1) = ωV
i
(t) + c
1
R
1
(t)(X
lb
(t) − X
i
(t))
+ c
2
R
2
(t)(pbest
s
(t) − X
i
(t))
X
i
(t + 1) = X
i
(t) + V
i
(t + 1)
(5)