Encoding Techniques in Genetic Algorithms

Debasis Samanta

Indian Institute of Technology Kharagpur

[email protected]

09.03.2018

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GA Operators

Following are the GA operators in Genetic Algorithms.

1 Encoding
2 Convergence test
3 Mating pool
4 Fitness Evaluation
5 Crossover
6 Mutation
7 Inversion

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Encoding Operation

1 Encoding
2 Convergence test
3 Mating pool
4 Fitness Evaluation
5 Crossover
6 Mutation
7 Inversion

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Different Encoding Schemes

Different GAs

Simple Genetic Algorithm (SGA)

Steady State Genetic Algorithm (SSGA)
Messy Genetic Algorithm (MGA)

Encoding Schemes

Binary encoding
Real value encoding
Order encoding
Tree encoding

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Different Encoding Schemes

Often, GAs are specified according to the encoding scheme it follows.

For example:
Encoding Scheme

Binary encoding –> Binary Coded GA or simply Binary GA

Real value encoding –> Real Coded GA or simply Real GA

Order encoding –> Order GA (also called as Permuted GA)

Tree encoding

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Encoding Schemes in GA

Genetic Algorithm uses metaphor consisting of two distinct elements :

1 Individual
2 Population

An individual is a single solution while a population is a set of

individuals at an instant of searching process.

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Individual Representation :Phenotype and
Genotype
An individual is defined by a chromosome. A chromosome stores
genetic information (called phenotype) for an individual.
Here, a chromosome is expressed in terms of factors defining a
problem.

Genotype

Factor 1 Factor 2 …. Factor n

Gene 1 Gene 2 …. Gene n

Phenotype

a b c 1 0 1 2 9 6 7 $ α β..................

Chromosome
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Individual Representation :Phenotype and
Genotype

Note :

A gene is the GA’s representation of a single factor (i.e. a design

parameter), which has a domain of values (continuous,
discontinuous, discrete etc.) symbol, numbering etc.

In GA, there is a mapping from genotype to phenotype. This

eventually decideds the performance (namely speed and
accuracy) of the problem solving.

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Encoding techniques

There are many ways of encoding:

1 Binary encoding: Representing a gene in terms of bits (0s and
1s).
2 Real value encoding: Representing a gene in terms of values or
symbols or string.
3 Permutation (or Order) encoding: Representing a sequence of
elements)
4 Tree encoding: Representing in the form of a tree of objects.

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Binary Encoding

In this encoding scheme, a gene or chromosome is represented by a

string (fixed or variable length) of binary bits (0’s and 1’s)

A: 0 1 1 0 0 1 0 1 0 1 0 1 0 1 1 1 1 0 Individual 1

B: 0 0 1 0 1 0 1 1 1 0 1 0 1 0 1 0 0 0 Individual 2

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Example: 0-1 Knapsack problem

There are n items, each item has its own cost (ci ) and weight (wi ).

There is a knapsack of total capacity w.

The problem is to take as much items as possible but not

exceeding the capacity of the knapsack.

This is an optimization problem and can be better described as follows.

Maximize :
P
i ci ∗ wi ∗ xi
Subject to
P
xi ∗ wi ≤ W
where xi ∈ [0 · · · 1]

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Example: 0-1 Knapsack problem
Consider the fallowing, an instance of the 0-1 Knapsack problem.
I3
I2
I1
Max. Weight
30 50
50
20
10

$60 $100 $120 Knapsack

Brute force approach to solve the above can be stated as follows:

Select at least one item
[10], [20], [30], [10, 20], [10, 30], [, 20, 30], [10, 20, 30]
So, for n-items, are there are 2n − 1 trials.
0 - means item not included and 1 - means item included
[100], [010], [011], [110], [101], [011], [111]
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Example: 0-1 Knapsack problem

The encoding for the 0-1 Knapsack, problem, in general, for n items
set would look as follows.

Genotype :
1 2 3 4 ..... n-1 n
.....

Phenotype :

0 1 0 1 1 0 1 0 1 0 1 0 1. . . . . .1 0 1
A binary string of n-bits

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Few more examples
Example 1 :
Minimize :
2
f (x) = x2 + 125
x
where 0 ≤ x ≤ 15 and x is any discrete integer value.

Genotype :

Phenotype :

01101
A binary string of 5-bits

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Few more examples
Example 2 :
Maximize :
f (x, y ) = x 3 − x 2 y + xy 2 + y 3
Subject to :
x + y ≤ 10
and
1 ≤ x ≤ 10
−10 ≤ y ≤ 10

Genotype :

x y

Phenotype :

01101 11001
Two binary string of 5-bits each
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Pros and cons of Binary encoding scheme

Limitations:
1 Needs an effort to convert into binary from
2 Accuarcy depends on the binary reprresentation

Advantages:
1 Since operations with binary represntation is faster, it provide a
faster implementations of all GA operators and hence the execution
of GAs.
2 Any optimization problem has it binary-coded GA implementation

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Real value encoding

The real-coded GA is most suitable for optimization in a

continuous search space.
Uses the direct representations of the design paparmeters.
Thus, avoids any intermediate encoding and decoding steps.

Genotype :

x y

Phenotype :

5.28 -475.36
Real-value representation

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Real value encoding with binary codes

Methodology: Step 1 [Deciding the precision]

For any continuous design variable x such that XL ≤ x ≤ XU , and if ε is

the precision required, then string length n should be equal to
 
n = log2 XU −Xε
L

where XL ≤ x ≤ XU

Equivalently,  
ε = XU2−Xn
L

In general, ε = [0 · · · 1]. It is also called, Obtaianable accuracy

Note:If ε = 0.5, then 4.05 or 4.49 ≡ 4 and 4.50 or 4.99 ≡ 4.5 and so
on.

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Real value encoding: Illustration 1

1 Example 1:
1 ≤ x ≤ 16, n = 6. What is the accuracy?

16−1 15
ε= 26
= 64 = 0.249 ≈ 0.25

2 Example 2:
What is the obtainable accuracy, for the binary representation for a
variable X in the range range 20.1 ≤ X ≤ 45.6 with 8-bits?

3 Example 3:
In the above case, what is the binary representation of X = 34.35?

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Real value encoding with binary codes

Methodology: Step 2[Obtaining the binary representation]

Once, we know the length of binary string for an obtainable accuracy

(i.e precision), then we can have the following mapping relation from a
real value X to its binary equivalent decoded value XB ,which is given
by
X = XL + X2Un−X
−1 × XB
L

where XB = Decoded value of a binary string,

n is the number of bits in the representation,
XL → 0 0 0 0 · · · 0 and
XU → 1 1 1 1 · · · 1
are the decoded values of the binary representation of the lower and
upper values of X .

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Real value encoding: Illustration 2

Example:

Suppose, XL = 2 and XU = 17 are the two extreme decoded values of

a variable x.

n = 4 is the number of binary bits in the representation for x.

XB = 10(= 1 0 1 0) is a decoded value for a given x.

What is the value of x =? and its binary representation??

17−2
Here, x = 2 + 24 −1
× 10 = 12
Binary representation of x = 1 1 0 0

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Order Encoding

Let us have a look into the following instance of the Traveling

Salesman Problem (TSP).

All cities are to be visited A possible tour

TSP
- Visit all the cities
- One city once only
- Starting and ending city is the same

How we can formally define the TSP?

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Order Encoding for TSP
Understanding the TSP:
There is a cost of visiting a city from another city and hence the total
cost of visiting all the cities but exactly once (except the starting city).
Objective function: To find a tour (i.e. a simple cycle covering all the
cities) with a minimum cost involved.
Constraints:
All cities must be visited.
There will be only one occurrence of each city (except the starting
city).
Design parameters:
Euclidean distance may be taken as the measurement of the cost,
otherwise, if it is specified explicitly.
The above stated information are the design variables in this case.
We are to search for the best path out of n! possible paths.
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A small instance of the TSP

d A B C D E 6
2 4
A 0 2  6 4

B 2 0 7  5
5 D
C  7 0 3 1 B
E
D 6  3 0  3
7
E 4 5 1  0

d= Distance matrix C

Connectivity among cities

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Defining the TSP

Minimizing

Pn−2
cost = i=0 d(ci , ci+1 ) + d(cn−1 , c0 )

Subject to
P = [c0 , c1 , c2 , · · · , cn−1 , c0 ]
where ci ∈ X ;
Here, P is an ordered collection of cities and ci 6= cj such that
∀i, j = 0, 1, · · · , n − 1
Note: P represents a possible tour with the starting cities as c0 .
and
X = x1 , x2 , · · · , xn , set of n number of cities,
d(xi , xj ) is the distance between any two cities xi and xj .
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Tree encoding

In this encoding scheme, a solution is encoded in the form of a binary

tree.

A D A B E G C F (In-order)

(TL R TR)
B C
A B D C E G F (Pre-order)

D E F (R TL TR)

D B G E E C A (Post-order)
G
(TL TR R)

A binary tree Three compact representation

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Floor Planning : An example of tree encoding
Floor planning is a standard problem in VLSI design. Here, given n
circuits of different area requirements, we are to arrange them into a
floor of chip layout, so that all circuits are placed in a minimum layout
possible.

C2
C1
C3
C1

C2
C9 C5

C5

C6
C7 C4
C4 C8
C6 C8

C7
C9
C10 C3

10 circuits A floor plan

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Formulation of floor planning problem

A possible formulation of Floor planning problem of VLSI circuit is as

follows.
Given :

1 A set of n rectangular blocks B = b1 , b2 , · · · , bi , · · · , bn

2 For each bi ∈ B, we have the following specification:

the width wi and height hi (which are constant for rigid blocks and
variable for flexible blocks)
1 hi
ρi , the desirable aspect ratio about where ρi ≤ wi ≤ ρi , where
ρi = 1, if the block bi is rigid.
ai = wi × hi , the area of each block bi .

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Formulation of floor planning problem

3 A set of nets N = {n1 , n2 , · · · , nk } describing the connectivity

information.

Wire = f1 (B, N)
4 Desirable floor plan aspect ratio ρ such that 1ρ ≤ W
H
≤ ρ, where H
and W are the height and width of the floor plan, respectively.

Area = f2 (B, N, ρ)
5 Timing information.
Delay = f3 (B, N, ρ)

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Formulation of Floor planning problem
A legal floor plan is a floor plan that satisfies the following constraints.
Constraints :

3 Each block bi is assigned to a location say (xi , yi ).

4 No two blocks overlap
5 For each flexible block say bi , ai = wi × hi and should meet aspect
ratio constraint.

Objectives :
We are to find a floor plan, which would
1 Minimize floor plan area.
2 Minimize wire length.
3 Minimize circuit delay.
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Tree encoding for Floor planning problem

3 4 5
1 1

4 5 6 7

2 2
6 7 3

Floor Plan I Floor Plan II

1 How many floor plans are possible?

2 Can we find a binary tree representation of a floor plan??

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Binary tree representation for floor planning

A floor plan can be modeled by a binary tree with n leaves and n − 1

nodes where

each node represents a vertical cut-line or horizontal cut-line, and

Letter V and H refer to vertical and horizontal cut-operators.

each leaf node represents a rectangle blocks.

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Example : Floor plane I

H H
3
1
2 1 H 3
4 5

2 V V
6 7

6 7 4 5

Floor Plan I Binary tree representation of the floor plan I

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Example : Floor plane I

Note 1:
The operators H and V expressed in polish notation carry the following
meanings:
ijH → Block bj is on top of the block bi .
ijV → Block bi is on the left of block bj .

Note 2: A tree can be represented in a compact form using Polish

notation
Note 3: Polish notation
a + b ÷ c = a + (b ÷ c) = abc ÷ +
a + b − c = ab + c−

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Example : Floor plane I

Note 4:
Post order traversal of a binary tree is equivalent to polish notation

+ -

abc÷+ ab+c-
a ÷ + c

b c
a b

Note 5:
There is only one way to performing a post order traversal of a binary
tree.

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Example : Floor Plane I (with Polish notation

H H
3
1
2 1 H 3
4 5

2 V V
6 7

6 7 4 5

Floor Plan I Binary tree representation of the floor plan I

Polish notation : 2 1 H 6 7 V 4 5 V H 3 H V

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Example : H and V operators

H
V2
2
3 1 V
H3 2
V4
3
4 5
2
H1 H 2

1 4
V 3
Floor Plan
4 5

Binary tree

Polish notation : 4 5 V 3 H 2 V 1 H

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Example :Floor plan II

H H

2 1 V
H
?
6 7
V 3

4 5

2 1 H 6 7 V 4 5 V 3 H H V

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Example :Floor plan II

H H 3
1

2 1 V
H 4 5

6 7 2
V 3 6 7

4 5

2 1 H 6 7 V 4 5 V 3 H H V

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Problem

Problem :

How many number of solutions possible with n blocks in a floor

planning problem?

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Problem

Problem :

How many number of solutions with n blocks in a floor planning

problem?
1 2n


N= n+1 n

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Any question??

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