GENETIC ALGORITHMS AND

GENETIC PROGRAMMING
 John R. Koza
Consulting Professor (Medical Informatics)
Department of Medicine
School of Medicine
Consulting Professor
Department of Electrical Engineering
School of Engineering
Stanford University
Stanford, California 94305

koza@stanford.edu
http://www.smi.stanford.edu/people/koza/
 DEFINITION OF THE GENETIC
ALGORITHM (GA)

The genetic algorithm is a probabalistic search

algorithm that iteratively transforms a set
(called a population) of mathematical objects
(typically fixed-length binary character
strings), each with an associated fitness value,
into a new population of offspring objects using
the Darwinian principle of natural selection
and using operations that are patterned after
naturally occurring genetic operations, such as
crossover (sexual recombination) and mutation.
 GENETIC ALGORITHM (GA)

Generation 0 Generation 1

Individuals Fitness Offspring

011 $3 111

001 $1 010

110 $6 110

010 $2 010
 HAMBURGER RESTAURANT
PROBLEM

• Price
1 = $ 0.50 price
0 = $10.00 price
• Drink
1 = Coca Cola
0 = Wine
• Ambiance
1 = Fast snappy service
0 = Leisurely service with tuxedoed waiter
CHROMOSOME (GENOME) OF THE
GLOBAL OPTIMUM

McDONALD's

1 1 1
 THE SEARCH SPACE
1 000
2 001
3 010
4 011
5 100
6 101
7 110
8 111

• Alphabet size K=2, Length L=3

• Size of search space: KL=2L=23=8
 IMPRACTICALITY OF RANDOM
OR ENUMERATIVE SEARCH

• 81-bit problems are very small for GA

• However, even if L is as small as 81, 281 ~
1027 = number of nanoseconds since the
beginning of the universe 15 billion years
ago
GA FLOWCHART
 GENERATION 0

Generation 0
1 011 3
2 001 1
3 110 6
4 010 2
Total
Worst
Average
Best
 DEFINITION OF THE GENETIC
ALGORITHM (GA)

The genetic algorithm is a probabalistic search

algorithm that iteratively transforms a set
(called a population) of mathematical objects
(typically fixed-length binary character
strings), each with an associated fitness value,
into a new population of offspring objects using
the Darwinian principle of natural selection
and using operations that are patterned after
naturally occurring genetic operations, such as
crossover (sexual recombination) and mutation.
 PROBABILISTIC SELECTION
BASED ON FITNESS

• Better individuals are preferred

• Best is not always picked
• Worst is not necessarily excluded
• Nothing is guaranteed
• Mixture of greedy exploitation and adventurous exploration
• Similarities to simulated annealing (SA)
PROBABILISTIC SELECTION
BASED ON FITNESS

0.17
0.25

0.08
0.5
 DARWINIAN FITNESS
PROPORTIONATE SELECTION

Generation 0 Mating pool

1 011 3 .25 011 3
2 001 1 .08 110 6
3 110 6 .50 110 6
4 010 2 .17 010 2
Total 12 17
Worst 1 2
Average 3.00 4.5
Best 6 6
 DEFINITION OF THE GENETIC
ALGORITHM (GA)

The genetic algorithm is a probabalistic search

algorithm that iteratively transforms a set
(called a population) of mathematical objects
(typically fixed-length binary character
strings), each with an associated fitness value,
into a new population of offspring objects using
the Darwinian principle of natural selection
and using operations that are patterned after
naturally occurring genetic operations, such as
crossover (sexual recombination) and mutation.
 MUTATION OPERATION
• Parent chosen probabilistically based on
fitness Parent
010
• Mutation point chosen at random
Parent
--0
• One offspring
Offspring
011
AFTER MUTATION OPERATION

Generation 0 Mating pool Generation 1

1 011 3 .25 011 3
2 001 1 .08 110 6
3 110 6 .50 110 6
4 010 2 .17 010 2 --- 011 3
Total 12 17
Worst 1 2
Average 3.00 4.5
Best 6 6
 CROSSOVER OPERATION

• 2 parents chosen probabilistically based on

fitness
Parent 1 Parent 2
011 110
 CROSSOVER (CONTINUED)
• Interstitial point picked at random
Fragment 1 Fragment 2
01- 11-
• 2 remainders
Remainder 1 Remainder 2
--1 --0
• 2 offspring produced by crossover
Offspring 1 Offspring 2
111 010
AFTER CROSSOVER OPERATION

Generation 0 Mating pool Generation 1

1 011 3 .25 011 3 2 111 7
2 001 1 .08 110 6 2 010 2
3 110 6 .50 110 6
4 010 2 .17 010 2
Total 12 17
Worst 1 2
Average 3.00 4.5
Best 6 6
 AFTER REPRODUCTION
OPERATION
Generation 0 Mating pool Generation 1
1 011 3 .25
2 001 1 .08
3 110 6 .50 110 6 --- 110 6
4 010 2 .17
Total 12 17
Worst 1 2
Average 3.00 4.5
Best 6 6
 DEFINITION OF THE GENETIC
ALGORITHM (GA)

The genetic algorithm is a probabalistic search

algorithm that iteratively transforms a set
(called a population) of mathematical objects
(typically fixed-length binary character
strings), each with an associated fitness value,
into a new population of offspring objects using
the Darwinian principle of natural selection
and using operations that are patterned after
naturally occurring genetic operations, such as
crossover (sexual recombination) and mutation.
 GENERATION 1

Generation 0 Mating pool Generation 1

1 011 3 .25 011 3 2 111 7
2 001 1 .08 110 6 2 010 2
3 110 6 .50 110 6 --- 110 6
4 010 2 .17 010 2 --- 011 3
Total 12 17 18
Worst 1 2 2
Average 3.00 4.5 4.5
Best 6 6 7
 DEFINITION OF THE GENETIC
ALGORITHM (GA)

The genetic algorithm is a probabalistic search

algorithm that iteratively transforms a set
(called a population) of mathematical objects
(typically fixed-length binary character
strings), each with an associated fitness value,
into a new population of offspring objects using
the Darwinian principle of natural selection
and using operations that are patterned after
naturally occurring genetic operations, such as
crossover (sexual recombination) and mutation.
 DEFINITION OF THE GENETIC
ALGORITHM (GA)

The genetic algorithm is a probabalistic search

algorithm that iteratively transforms a set
(called a population) of mathematical objects
(typically fixed-length binary character
strings), each with an associated fitness value,
into a new population of offspring objects using
the Darwinian principle of natural selection
and using operations that are patterned after
naturally occurring genetic operations, such as
crossover (sexual recombination) and mutation.
 PROBABILISTIC STEPS

• The initial population is typically random

• Probabilistic selection based on fitness
- Best is not always picked
- Worst is not necessarily excluded
• Random picking of mutation and
crossover points
• Often, there is probabilistic scenario as
part of the fitness measure
ANTENNA DESIGN
 ANTENNA DESIGN

• The problem (Altshuler and Linden 1998) is to

determine the x-y-z coordinates of the 3-
dimensional position of the ends (X1, Y1, Z1, X2,
Y2, Z2,… , X7, Y7, Z7) of 7 straight wires so that
the resulting 7-wire antenna satisfies certain
performance requirements
• The first wire starts at feed point (0, 0, 0) in the
middle of the ground plane
• The antenna must fit inside the 0.5 cube
 ANTENNA GENOME

X1 Y1 Z1 X2 Y2 Z2 …
+0010 -1110 +0001 +0011 -1011 +0011 …

• 105-bit chromosome (genome)

• Each x-y-z coordinate is represented by 5 bits
(4-bit granularity for data plus a sign bit)
• Total chromosome is 3  7  5 = 105 bits
 ANTENNA FITNESS

• Antenna is for ground-to-satellite

communications for cars and handsets
• We desire near-uniform gain pattern 10
above the horizon
• Fitness is measured based on the
antenna's radiation pattern. The
radiation pattern is simulated by
National Electromagnetics Code (NEC)
 ANTENNA FITNESS

• Fitness is sum of the squares of the

difference between the average gain and
the antenna's gain
• Sum is taken for angles  between -90
and +90 and all azimuth angles  from
0 to 180
• The smaller the value of fitness, the
better
GRAPH OF ANTENNA FITNESS
U. S. PATENT 5,719,794
10-MEMBER TRUSS
 10-MEMBER TRUSS
• Prespecified topological arrangement of the 10
members, the load, and the wall (Goldberg and
Samtani 1986)
• Truss has 10 members (6 are length of 30 feet
and 4 are length 30√2 = 41 feet)
• The problem is to determine the cross-sectional
areas (A1, … , A10) of each of the 10 members
so as to minimize weight of the material for a
truss that supports the 2 loads
• The weight is based on volume (i.e., cross-
sectional area  length)
 TRUSS GENOME

A1 A2 A3 A4 A5 A6 A7 A8 A9 A10
0010 1110 0001 0011 1011 0011 1111 0011 0011 1010

• 40-bit chromosome (genome)

• 4-bit granularity for truss diameters
• 0000 = smallest diameter
• 1111 = largest diameter
• Total chromosome is 4  10 = 40 bits
 TRUSS FITNESS
• Two-part (multiobjective) fitness
measure
– First, fitness is computed by taking the sum,
over the 10 members, of the cross-sectional
area of each member times the length of each
member (30 feet or 30√2 = 41 feet).
– Second, a penalty (up to 10%) is imposed for
violating the stress constraints. Stresses are
computed using standard mechanical
engineering techniques.
• The smaller the total fitness, the better
CELLULAR AUTOMATA
 STATE TRANSITION TABLE

# WWW WW W X E EE EEE Rule

0 0 0 0 0 0 0 1 a0
1 0 0 0 0 0 1 0 a1
2 0 0 0 0 1 0 0 a2
3 0 0 0 0 1 1 0 a3
4 0 0 1 1 0 0 0 a4
… … … … … … … … …
127 1 1 1 1 1 1 1 a127
 CELLULAR AUTOMATA

A0 A1 A2 … A127
a0 a1 a2 … a127

• 128-bit chromosome (genome)

PROBLEM-SPECIFIC GENOMES

N  M GENOME

1 1 0 1 1 1 1
1 1 1 1 0 1 1
1 0 1 1 1 0 0
1 1 1 1 1 1 1
1 1 0 1 1 1 1
1 1 1 1 0 1 1
1 1 0 1 1 1 0
 GENETIC ALGORITHM USING
VARIABLE-LENGTH STRINGS

• 5-WIRE ANTENNA (5  15 = 75 bits)

X1 Y1 Z1 … X5 Y5 Z5
+0010 -1110 +0001 … +0010 -1110 +0001

• 4-WIRE ANTENNA (4  15 = 60 bits)

X1 Y1 Z1 … X4 Y4 Z4
+1010 -0110 +1101 … +1010 -0110 +1001
GENETIC PROGRAMMING
 THE CHALLENGE

"How can computers learn to solve problems without

being explicitly programmed? In other words, how
can computers be made to do what is needed to be
done, without being told exactly how to do it?"

 Attributed to Arthur Samuel (1959)

 CRITERION FOR SUCCESS

"The aim [is] ... to get machines to exhibit behavior,

which if done by humans, would be assumed to involve
the use of intelligence.“

 Arthur Samuel (1983)

 REPRESENTATIONS

• Decision trees • Binary decision

diagrams
• If-then production
• Formal grammars
rules
• Coefficients for
• Horn clauses polynomials
• Neural nets • Reinforcement
• Bayesian networks learning tables
• Frames • Conceptual clusters
• Propositional logic • Classifier systems
A COMPUTER PROGRAM
 GENETIC PROGRAMMING (GP)

• GP applies the approach of the genetic

algorithm to the space of possible
computer programs
• Computer programs are the lingua
franca for expressing the solutions to a
wide variety of problems
• A wide variety of seemingly different
problems from many different fields can
be reformulated as a search for a
computer program to solve the problem.
 GP  MAIN POINTS
• Genetic programming now routinely delivers
high-return human-competitive machine
intelligence.
• Genetic programming is an automated
invention machine.
• Genetic programming has delivered a
progression of qualitatively more substantial
results in synchrony with five approximately
order-of-magnitude increases in the
expenditure of computer time.
 DEFINITION OF “HIGH-
RETURN”
The AI ratio (the “artificial-to-intelligence”
ratio) of a problem-solving method as the
ratio of that which is delivered by the
automated operation of the artificial
method to the amount of intelligence that
is supplied by the human applying the
method to a particular problem
 DEFINITION OF
“ROUTINE”
A problem solving method is routine if it is
general and relatively little human effort
is required to get the method to
successfully handle new problems within
a particular domain and to successfully
handle new problems from a different
domain.
 CRITERIA FOR
“HUMAN-COMPETITIVENESS”

• Previously patented, an improvement over a

patented invention, or patentable today
• Publishable in its own right as a new scientific
result independent of the fact that the result was
mechanically created
• Holds it own in regulated competition against
humans (or programs)
• 5 other similar criteria that are “arms-length”
from the fields of AI, ML, GP
PROGRESSION OF QUALITATIVELY MORE
SUBSTANTIAL RESULTS PRODUCED BY GP

• Toy problems
• Human-competitive non-patent results
• 20th-century patented inventions
• 21st-century patented inventions
• Patentable new inventions
GP FLOWCHART
 A COMPUTER PROGRAM IN C
int foo (int time)
{
int temp1, temp2;
if (time > 10)
temp1 = 3;
else
temp1 = 4;
temp2 = temp1 + 1 + 2;
return (temp2);
}
OUTPUT OF C PROGRAM
Time Output
0 6
1 6
2 6
3 6
4 6
5 6
6 6
7 6
8 6
9 6
10 6
11 7
12 7
 PROGRAM TREE

(+ 1 2 (IF (> TIME 10) 3 4))

CREATING RANDOM PROGRAMS
 CREATING RANDOM PROGRAMS

• Available functions
F = {+, -, *, %, IFLTE}
• Available terminals
T = {X, Y, Random-Constants}
• The random programs are:
– Of different sizes and shapes
– Syntactically valid
– Executable
 GP GENETIC OPERATIONS

• Reproduction
• Mutation
• Crossover (sexual recombination)
• Architecture-altering operations
MUTATION OPERATION
 MUTATION OPERATION

• Select 1 parent probabilistically based on fitness

• Pick point from 1 to NUMBER-OF-POINTS
• Delete subtree at the picked point
• Grow new subtree at the mutation point in same
way as generated trees for initial random
population (generation 0)
• The result is a syntactically valid executable
program
• Put the offspring into the next generation of the
population
CROSSOVER OPERATION
 CROSSOVER OPERATION

• Select 2 parents probabilistically based on fitness

• Randomly pick a number from 1 to NUMBER-OF-
POINTS for 1st parent
• Independently randomly pick a number for 2nd parent
• The result is a syntactically valid executable program
• Put the offspring into the next generation of the
population
• Identify the subtrees rooted at the two picked points
 REPRODUCTION OPERATION

• Select parent probabilistically based on

fitness
• Copy it (unchanged) into the next
generation of the population
 FIVE MAJOR PREPARATORY STEPS FOR
GP

• Determining the set of terminals

• Determining the set of functions
• Determining the fitness measure
• Determining the parameters for the run
• Determining the method for designating a result and the
criterion for terminating a run
ILLUSTRATIVE GP RUN
SYMBOLIC REGRESSION

Independent Dependent
variable X variable Y
-1.00 1.00
-0.80 0.84
-0.60 0.76
-0.40 0.76
-0.20 0.84
0.00 1.00
0.20 1.24
0.40 1.56
0.60 1.96
0.80 2.44
1.00 3.00
 PREPARATORY STEPS

Objective: Find a computer program with one input

(independent variable X) whose output
equals the given data
1 Terminal set: T = {X, Random-Constants}

2 Function set: F = {+, -, *, %}

3 Fitness: The sum of the absolute value of the

differences between the candidate
program’s output and the given data
(computed over numerous values of the
independent variable x from –1.0 to +1.0)
4 Parameters: Population size M = 4

5 Termination: An individual emerges whose sum of

absolute errors is less than 0.1
 SYMBOLIC REGRESSION

POPULATION OF 4 RANDOMLY CREATED

INDIVIDUALS FOR GENERATION 0
 SYMBOLIC REGRESSION x2 + x + 1

FITNESS OF THE 4 INDIVIDUALS IN GEN 0

x+1 x2 + 1 2 x

0.67 1.00 1.70 2.67

 SYMBOLIC REGRESSION x2 + x + 1

GENERATION 1

Second offspring
First offspring of of crossover of
Mutant of (c) crossover of (a)
  (a) and (b)
and (b)   picking “+” of
Copy of (a) picking “2” picking “+” of parent (a) and
as mutation parent (a) and
point left-most “x” of
left-most “x” of parent (b) as
parent (b) as crossover points
crossover points
CLASSIFICATION
 GP TABLEAU – INTERTWINED
SPIRALS
Objective: Create a program to classify a given
point in the x-y plane to the red or
blue spiral
1 Terminal set: T = {X,Y,Random-Constants}
2 Function set: F = {+,-,*,%,IFLTE,SIN,COS}
3 Fitness: The number of correctly classified
points (0 – 194)
4 Parameters: M = 10,000. G = 51
5 Termination: An individual program scores 194
WALL-FOLLOWER
FITNESS
BEST OF GENERATION 57
BOX MOVER – BEST OF GEN 0
 BOX MOVER
GEN 45 – FITNESS CASE 1
TRUCK BACKER UPPER
 TRUCK BACKER UPPER
• 4-Dimensional control problem
– horizontal position, x
– vertical position, y
– angle between trailer and horizontal, t
– angle between trailer and cab, d
• One control variable (steering wheel turn angle)
• State transition equations map the 4 state
variables into 1 output (the control variable)
• Simulation run over many initial conditions and
over hundreds of time steps
GENETIC PROGRAMMING: ON THE
PROGRAMMING OF COMPUTERS BY
MEANS OF NATURAL SELECTION
(Koza 1992)
 2 MAIN POINTS FROM 1992 BOOK

• Virtually all problems in artificial intelligence,

machine learning, adaptive systems, and
automated learning can be recast as a search
for a computer program.
• Genetic programming provides a way to
successfully conduct the search for a computer
program in the space of computer programs.
 SOME RESULTS FROM 1992 BOOK

• Intertwined Spirals • Randomizer

• Truck Backer Upper • Cellular Automata
• Broom Balancer • Task Prioritization
• Wall Follower • Image Compression
• Box Mover
• Econometric Equation
• Artificial Ant
• Optimization
• Differential Games
• • Boolean Function Learning
Inverse Kinematics
• Central Place Foraging • Co-Evolution of Game-
• Block Stacking Playing Strategies
PROGRESSION OF QUALITATIVELY MORE
SUBSTANTIAL RESULTS PRODUCED BY GP

• Toy problems
• Human-competitive non-patent results
• 20th-century patented inventions
• 21st-century patented inventions
• Patentable new inventions
 COMPUTER PROGRAMS

• Subroutines provide one way to REUSE code  possibly

with different instantiations of the dummy variables
(formal parameters)
• Loops (and iterations) provide a 2nd way to REUSE code
• Recursion provide a 3rd way to REUSE code
• Memory provides a 4th way to REUSE the results of
executing code
 SYMBOLIC REGRESSION

Fitness case L0 W0 H0 L1 W1 H1 Dependent variable D

1 3 4 7 2 5 3 54
2 7 10 9 10 3 1 600
3 10 9 4 8 1 6 312
4 3 9 5 1 6 4 111
5 4 3 2 7 6 1 -18
6 3 3 1 9 5 4 -171
7 5 9 9 1 7 6 363
8 1 2 9 3 9 2 -36
9 2 6 8 2 6 10 -24
10 8 1 10 7 5 1 45
EVOLVED SOLUTION

(- (* (* W0 L0) H0)
(* (* W1 L1) H1))
DIFFERENCE IN VOLUMES

D = L0W0H0 – L1W1H1
AUTOMATICALLY DEFINED
FUNCTION volume
 AUTOMATICALLY DEFINED
FUNCTION volume

(progn
(defun volume (arg0 arg1 arg2)
(values
(* arg0 (* arg1 arg2))))
(values
(- (volume L0 W0 H0)
(volume L1 W1 H1))))
 AUTOMATICALLY DEFINED
FUNCTIONS

• ADFs provide a way to REUSE code

• Code is typically reused with different
instantiations of the dummy variables
(formal parameters)
 ADDITION OF V0 AND V1

Fitness case L0 W0 H0 L1 W1 H1 V0 V1 D
1 3 4 7 2 5 3 84 30 54
2 7 10 9 10 3 1 630 30 600
3 10 9 4 8 1 6 360 48 312
4 3 9 5 1 6 4 135 24 111
5 4 3 2 7 6 1 24 42 -18
6 3 3 1 9 5 4 9 180 -171
7 5 9 9 1 7 6 405 42 363
8 1 2 9 3 9 2 18 54 -36
9 2 6 8 2 6 10 96 120 -24
10 8 1 10 7 5 1 80 35 45
DIVIDE AND CONQUER
 DIVIDE AND CONQUER

• Decompose a problem into sub-problems

• Solve the sub-problems
• Assemble the solutions of the sub-
problems into a solution for the overall
problem
CHANGE OF REPRESENTATION
 CHANGE OF REPRESENTATION

• Identify regularities
• Change the representation
• Solve the overall problem
 ADF IMPLEMENTATION
• Each overall program in population includes
– a main result-producing branch (RPB) and
– function-defining branch (i.e., automatically defined
function, ADF)
• In generation 0, create random programs with
different ingredients for the RPB and the ADF
– Terminal set for ADF typically contains dummy
arguments (formal parameters), such as ARG0,
ARG1, …
– Function set of the RPB contains ADF0
– ADFs are private and associated with a particular
individual program in the population
 ADF MUTATION

• Select parent probabilistically on the basis

of fitness
• Pick a mutation point from either RPB or
an ADF
• Delete sub-tree rooted at the picked point
• Grow a new sub-tree at the picked point
composed of the allowable ingredients
appropriate for the picked point
• The offspring is a syntactically valid
executable program
 ADF CROSSOVER

• Select parent probabilistically on the basis of

fitness
• Pick a crossover point from either RPB or an
ADF of the FIRST patent
• The choice of crossover point in the SECOND
parent is RESTRICTED to the picked RPB or
to the picked ADF
• The sub-trees are swapped
• The offspring are syntactically valid executable
programs
GENETIC PROGRAMMING II: AUTOMATIC
DISCOVERY OF REUSABLE PROGRAMS
(Koza 1994)
 MAIN POINTS OF 1994 BOOK

• Scalability is essential for solving non-trivial

problems in artificial intelligence, machine
learning, adaptive systems, and automated
learning
• Scalability can be achieved by reuse
• Genetic programming provides a way to
automatically discover and reuse subprograms
in the course of automatically creating computer
programs to solve problems
 COMPUTER PROGRAMS

• Subroutines provide one way to REUSE code  possibly

with different instantiations of the dummy variables
(formal parameters)
• Loops (and iterations) provide a 2nd way to REUSE code
• Recursion provide a 3rd way to REUSE code
• Memory provides a 4th way to REUSE the results of
executing code
 MEMORY

Settable Indexed Matrix Relational memory

(named) vector memory
variables memory
 LANGDON'S DATA STRUCTURES

• Stacks
• Queues
• Lists
• Rings
 COMPUTER PROGRAMS

• Subroutines provide one way to REUSE code  possibly

with different instantiations of the dummy variables
(formal parameters)
• Loops (and iterations) provide a 2nd way to REUSE code
• Recursion provide a 3rd way to REUSE code
• Memory provides a 4th way to REUSE the results of
executing code
 AUTOMATICALLY DEFINED
ITERATION (ADI)
• The overall program includes an iteration-
performing branch (IPB) in addition to a
result-producing branch (RPB) and function-
defining branches (ADF)
• There are no infinite loops because the iteration
is performed over a known, fixed set
– protein or DNA sequence (of varying length)
– time-series data
– two-dimensional array of pixels
• Memory is usually involved and is used to
communicate between IPB, RPB, and ADF
 TRANSMEMBRANE SEGMENT
IDENTIFICATION PROBLEM

Goal is to classify a given protein segment

as being a transmembrane domain or
non-transmembrane area of the protein
 TRANSMEMBRANE SEGMENT
IDENTIFICATION PROBLEM
(progn
(defun ADF0 ()
(ORN (ORN (ORN (I?) (H?)) (ORN (P?) (G?))) (ORN (ORN (ORN (Y?)
(N?)) (ORN (T?) (Q?))) (ORN (A?) (H?))))))
(defun ADF1 ()
(values (ORN (ORN (ORN (A?) (I?)) (ORN (L?) (W?))) (ORN (ORN
(T?) (L?)) (ORN (T?) (W?))))))
(defun ADF2 ()
(values (ORN (ORN (ORN (ORN (ORN (D?) (E?)) (ORN (ORN (ORN
(D?) (E?)) (ORN (ORN (T?) (W?)) (ORN (Q?) (D?)))) (ORN (K?)
(P?)))) (ORN (K?) (P?))) (ORN (T?) (W?))) (ORN (ORN (E?)
(A?)) (ORN (N?) (R?))))))
(progn (loop-over-residues
(SETM0 (+ (- (ADF1) (ADF2)) (SETM3 M0))))
(values (% (% M3 M0) (% (% (% (- L -0.53) (* M0 M0)) (+ (% (%
M3 M0) (% (+ M0 M3) (% M1 M2))) M2)) (% M3 M0))))))
 TRANSMEMBRANE SEGMENT
IDENTIFICATION PROBLEM

• in-sample correlation of 0.976

• out-of-sample correlation of 0.968
• out-of-sample error rate 1.6%
 AUTOMATICALLY DEFINED
LOOP (ADL)

• loop initialization branch, LIB

• loop condition branch, LCB
• loop body branch, LBB
• loop update branch, LUB
ADL
 COMPUTER PROGRAMS

• Subroutines provide one way to REUSE code  possibly

with different instantiations of the dummy variables
(formal parameters)
• Loops (and iterations) provide a 2nd way to REUSE code
• Recursion provide a 3rd way to REUSE code
• Memory provides a 4th way to REUSE the results of
executing code
 AUTOMATICALLY DEFINED
RECURSION (ADR)

• recursion condition branch, RCB

• recursion body branch, RBB
• recursion update branch, RUB
• recursion ground branch, RGB
ADR
 HUMAN-COMPETITIVE RESULTS
(NOT RELATED TO PATENTS)

Transmembrane segment identification problem for proteins

Motifs for D–E–A–D box family and manganese superoxide dismutase family of proteins
Cellular automata rule for Gacs-Kurdyumov-Levin (GKL) problem
Quantum algorithm for the Deutsch-Jozsa “early promise” problem
Quantum algorithm for Grover’s database search problem
Quantum algorithm for the depth-two AND/OR query problem
Quantum algorithm for the depth-one OR query problem
Protocol for communicating information through a quantum gate
Quantum dense coding
Soccer-playing program that won its first two games in the 1997 Robo Cup competition
Soccer-playing program that ranked in the middle of field in 1998 Robo Cup competition
Antenna designed by NASA for use on spacecraft
Sallen-Key filter
PROGRESSION OF QUALITATIVELY MORE
SUBSTANTIAL RESULTS PRODUCED BY GP

• Toy problems
• Human-competitive non-patent results
• 20th-century patented inventions
• 21st-century patented inventions
• Patentable new inventions
GENETIC PROGRAMMING III: DARWINIAN
INVENTION AND PROBLEM SOLVING
(Koza, Bennett, Andre, Keane 1999)
SUBROUTINE DUPLICATION
SUBROUTINE CREATION
SUBROUTINE DELETION
ARGUMENT DUPLICATION
ARGUMENT DELETION
 16 ATTRIBUTES OF A SYSTEM FOR
AUTOMATICALLY CREATING COMPUTER
PROGRAMS

• Starts with "What needs to be • Self-organization of hierarchies

done"
• Tells us "How to do it"
• Produces a computer program
• Automatic determination of
program size
• Code reuse
• Parameterized reuse
• Internal storage
• Iterations, loops, and
recursions
• Automatic determination of
program architecture
• Wide range of programming
constructs
• Well-defined
• Problem-independent
• Wide applicability
• Scalable
• Competitive with human-
produced results
GENETIC PROGRAMMING PROBLEM
SOLVER (GPPS)
 AUTOMATIC SYNTHESIS OF
BOTH THE TOPOLOGY AND
SIZING OF ANALOG ELECTRICAL
CIRCUITS BY MEANS OF
DEVELOPMENTAL GENETIC
PROGRAMMING
AUTOMATED CIRCUIT SYNTHESIS

• The topology of a circuit includes specifying the

gross number of components in the circuit, the
type of each component (e.g., a capacitor), and
a netlist specifying where each lead of each
component is to be connected.
• Sizing involves specifying the values (typically
numerical) of each of the circuit's components.
COMPONENT-CREATING FUNCTIONS

• Resistor R function
• Capacitor C function
• Inductor L function
• Diode D function
• Transistor Q function (3-leaded)
COMPONENT-CREATING FUNCTIONS
TOPOLOGY-MODIFYING FUNCTIONS

• SERIES division
• PARALLEL division
• VIA
• FLIP
TOPOLOGY-MODIFYING FUNCTIONS
 DEVELOPMENT-CONTROLLING
FUNCTIONS

• END function
• NOP (No Operation) function
• SAFE_CUT function
THE INITIAL CIRCUIT
 DEVELOPMENTAL GP

(LIST (C (– 0.963 (– (– -0.875 -0.113)

0.880)) (series (flip end) (series
(flip end) (L -0.277 end) end) (L (–
-0.640 0.749) (L -0.123 end)))) (flip
(nop (L -0.657 end)))))
CAPACITOR-CREATING FUNCTION

(LIST (C (– 0.963 (– (– -0.875

-0.113) 0.880)) (series (flip
end) (series (flip end) (L –
0.277 end) end) (L (– -0.640
0.749) (L -0.123 end)))) (flip
(nop (L -0.657 end)))))
CAPACITOR-CREATING FUNCTION
 SERIES DIVISION FUNCTION

(LIST (C (– 0.963 (– (– -0.875

-0.113) 0.880)) (series (flip
end) (series (flip end) (L –
0.277 end) end) (L (– -0.640
0.749) (L -0.123 end)))) (flip
(nop (L -0.657 end)))))
SERIES DIVISION
DEVELOPMENTAL GP
 EVALUATION OF FITNESS

z0
+ IN OUT
Embryonic Circuit

Program Tree

Fully Designed Circuit (NetGraph)

Circuit Netlist (ascii)

Circuit Simulator (SPICE)

Circuit Behavior (Output)

Fitness
DESIRED BEHAVIOR OF A LOWPASS
FILTER
EVOLVED CAMPBELL FILTER

U. S. patent 1,227,113
George Campbell
American Telephone and Telegraph
1917
 EVOLVED ZOBEL FILTER

U. S. patent 1,538,964
Otto Zobel
American Telephone and Telegraph Company
1925
EVOLVED SALLEN-KEY FILTER
EVOLVED DARLINGTON EMITTER-
FOLLOWER SECTION

U. S. patent 2,663,806
Sidney Darlington
Bell Telephone Laboratories
1953
NEGATIVE FEEDBACK
HAROLD BLACK’S RIDE ON THE
LACKAWANNA FERRY

Courtesy of Lucent Technologies

 20th-CENTURY PATENTS
Campbell ladder topology for filters
Zobel “M-derived half section” and “constant K” filter sections
Crossover filter
Negative feedback
Cauer (elliptic) topology for filters
PID and PID-D2 controllers
Darlington emitter-follower section and voltage gain stage
Sorting network for seven items using only 16 steps
60 and 96 decibel amplifiers
Analog computational circuits
Real-time analog circuit for time-optimal robot control
Electronic thermometer
Voltage reference circuit
Philbrick circuit
NAND circuit
Simultaneous synthesis of topology, sizing, placement, and routing
PROGRESSION OF QUALITATIVELY MORE
SUBSTANTIAL RESULTS PRODUCED BY GP

• Toy problems
• Human-competitive non-patent results
• 20th-century patented inventions
• 21st-century patented inventions
• Patentable new inventions
SIX POST-2000 PATENTED
INVENTIONS
EVOLVED HIGH CURRENT LOAD CIRCUIT
REGISTER-CONTROLLED CAPACITOR
CIRCUIT
LOW-VOLTAGE CUBIC CIRCUIT
VOLTAGE-CURRENT-CONVERSION
CIRCUIT
LOW-VOLTAGE BALUN CIRCUIT
TUNABLE INTEGRATED ACTIVE FILTER
21st-CENTURY PATENTED INVENTIONS

Low-voltage balun circuit

Mixed analog-digital variable capacitor circuit
High-current load circuit
Voltage-current conversion circuit
Cubic function generator
Tunable integrated active filter
PROGRESSION OF QUALITATIVELY MORE
SUBSTANTIAL RESULTS PRODUCED BY GP

• Toy problems
• Human-competitive non-patent results
• 20th-century patented inventions
• 21st-century patented inventions
• Patentable new inventions
 NOVELTY-DRIVEN EVOLUTION

• Two factors in fitness measure

– Circuit’s behavior in the frequency domain
– Largest number of nodes and edges (circuit
components) of a subgraph of the given circuit that
is isomorphic to a subgraph of a template
representing the prior art. Graph isomorphism
algorithm with the cost function being based on the
number of shared nodes and edges (instead of just
the number of nodes).
 NOVELTY-DRIVEN EVOLUTION

• For circuits not scoring the maximum

number of hits (101), the fitness of a
circuit is the product of the two factors.
• For circuits scoring 101 hits (100%-
compliant individuals), fitness is the
number of shared nodes and edges
divided by 10,000.
PRIOR ART TEMPLATE
NON-INFRINGING SOLUTION NO. 1
NON-INFRINGING SOLUTION NO. 5
GP AS AN INVENTION MACHINE
CIRCUIT-CONSTRUCTING PROGRAM TREE
WITH ADFs
LOWPASS FILTER WITH ADFs
ADF0
 AUTOMATIC SYNTHESIS OF
CIRCUIT LAYOUT

INCLUDING THE PLACEMENT OF

COMPONENTS AND ROUTING OF
WIRES

ALONG WITH THE TOPOLOGY

AND SIZING
 CIRCUIT LAYOUT

• Circuit placement involves the assignment of

each of the circuit's components to a particular
physical location on a printed circuit board or
silicon wafer.
• Routing involves the assignment of a particular
physical location to the wires between the leads
of the circuit's components.
LAYOUT
LAYOUT — GENERATION 0
 100%-COMPLIANT LOWPASS FILTER
 
GENERATION 25 WITH 5 CAPACITORS AND
11 INDUCTORS  AREA OF 1775.2
 100%-COMPLIANT LOWPASS FILTER

GENERATION 30 WITH 10 INDUCTORS AND

5 CAPACITORS  AREA OF 950.3
 100%-COMPLIANT LOWPASS FILTER

BEST-OF-RUN CIRCUIT OF GENERATION

138 WITH 4 INDUCTORS AND 4
CAPACITORS  AREA OF 359.4
LAYOUT  60 DB AMPLIFIER
AUTOMATIC SYNTHESIS
OF BOTH THE TOPOLOGY
AND TUNING OF
CONTROLLERS
PROGRAM TREE FOR A
CONTROLLER
 CONTROLLER BLOCKS

• gain • lead
• integrator • lag
• differentiator • two-parameter lag
• adder • absolute value
• subtractor • limiter
• multiplier • divider
• differential input • delay
integrators • conditional operators
• inverter (switches)
 FUNCTION SET FOR
CONTROLLER SYNTHESIS

F = {GAIN,INVERTER,LEAD,LAG,LAG2,
DIFFERENTIAL_INPUT_INTEGRATOR,
DIFFERENTIATOR, ADD_SIGNAL,
SUB_SIGNAL,ADD_3_SIGNAL,ADF0,
ADF1,ADF2,ADF3,ADF4}
 TERMINAL SET FOR
CONTROLLER SYNTHESIS

T = { REFERENCE_SIGNAL,
CONTROLLER_OUTPUT,
PLANT_OUTPUT}
 CONSTRAINED SYNTACTIC
STRUCTURE

• A grammar that specifies what functions

and terminals are allowed as arguments
to particular functions
• For example, the first argument of the
GAIN function must be a value-setting
subtree whereas the second can be from
the general pool of functions
• Also known as strong typing
TWO-LAG PLANT
 8 FITNESS CASES

• 8 elements of the fitness measure

represent 2  2  2 choices:
– 2 different values of the plant's internal gain,
K (1.0 and 2.0),
– 2 different values of the plant's time constant
 (0.5 and 1.0),
– 2 different values for the height of the
reference signal (rising from 0 to 1 volts or
from 0 to 1 microvolts at t = 100 milliseconds
 FITNESS MEASURE

• For each of these 8 fitness cases, a transient

analysis (time domain) is performed using the
SPICE simulator.
• The contribution to fitness for the 8 elements is

– Integral of time-weighted absolute error (ITAE)

– e(t) is difference between plant output and reference signal.
– Multiplication by B (106 or 1) makes both reference signals equally
influential.
– Additional weighting function, A, heavily penalizes non-compliant
amounts of overshoot. A weights all variations up to 2% above the
reference signal by 1.0, but bigger variations by 10.0.
EVOLVED CONTROLLER FOR TWO-LAG
PLANT
LESS ITAE AND OVERSHOOT
BETTER DISTURBANCE REJECTION
REVERSE ENGINEERING OF METABOLIC
PATHWAYS
EVOLVED PATHWAY
ANTENNA SYNTHESIS USING GP

(PROGN3
(TURN-RIGHT 0.125)
(LANDMARK
(REPEAT 2
(PROGN2
(DRAW 1.0 HALF-MM-WIRE)
(DRAW 0.5 NO-WIRE)))
(TRANSLATE-RIGHT 0.125 0.75))
USING A TURTLE TO DRAW TWO-
DIMENSIONAL ANTENNA
BEST-OF-RUN ANTENNA FROM
GENERATION 90
3-DIMENSIONAL ANTENNA
 NASA EVOLVED ANTENNA

To be on satellite to be launched in 2004

OTHER STRUCTURES
GENETIC NETWORK FOR lac
operon
 EVOLVED NETWORK
(IF (< LACTOSE_LEVEL 9.139 ) (IF (<
REPRESSOR_LEVEL 6.270 ) (IF (> GLUCOSE_LEVEL
5.491 ) 2.02 (IF (< CAP_LEVEL 0.639 ) 2.033 (IF
(< CAP_LEVEL 4.858 ) (IF (> LACTOSE_LEVEL 2.511 )
(IF (> CAP_LEVEL 7.807 ) 5.586 (IF (>
LACTOSE_LEVEL 2.114 ) 1.978 2.137 ) ) 0.0 ) (IF
(> REPRESSOR_LEVEL 4.015 ) 0.036 (IF (<
GLUCOSE_LEVEL 5.128 ) 10.0 (IF (< REPRESSOR_LEVEL
4.268 ) 2.022 9.122 ) ) ) ) ) ) (IF (> CAP_LEVEL
0.842 ) 0.0 5.97 ) ) (IF (< CAP_LEVEL 1.769 )
2.022 (IF (< GLUCOSE_LEVEL 2.382 ) (IF (>
LACTOSE_LEVEL 1.256 ) (IF (> LACTOSE_LEVEL 1.933
) (IF (> GLUCOSE_LEVEL 2.022 ) (IF (<
GLUCOSE_LEVEL 5.183 ) 6.323 (IF (> CAP_LEVEL
1.208 ) 9.713 0.842 ) ) 10.0 ) (IF (>
GLUCOSE_LEVEL 6.270 ) 2.109 ) 1.965 ) ) 0.665 )
1.982 ) ) )
 IN C-STYLE PSEUDO CODE

if(LACTOSE_LEVEL < 9.139) else

{
{ if(CAP_LEVEL < 1.769)
if(REPRESSOR_LEVEL < {
6.270) LAC_mRNA_LEVEL =
{ 2.022;
LAC_mRNA_LEVEL = }
2.022; else
} {
else if(GLUCOSE_LEVEL <
{ 2.382)
{
LAC_mRNA_LEVEL = LAC_mRNA_LEVEL
0.0; = 10.0;
} }
} else
{
LAC_mRNA_LEVEL
= 1.982;
} } }
 PARAMETERIZED TOPOLOGIES

• One of the most important

characteristics of computer programs is
that they ordinarily contain inputs (free
variables) and conditional operations
PARAMETERIZED TOPOLOGY FOR
LOWPASS FILTER
PARAMETERIZED TOPOLOGY FOR
HIGHPASS FILTER
PARAMETERIZED TOPOLOGY FOR
GENERAL-PURPOSE CONTROLLER
EVOLVED EQUATIONS FOR GENERAL-
PURPOSE CONTROLLER
EVOLVED EQUATIONS FOR GENERAL-
PURPOSE CONTROLLER
 PATENTABLE NEW INVENTIONS

PID tuning rules that outperform the Ziegler-Nichols and Åström-Hägglund tuning rules
General-purpose controllers outperforming Ziegler-Nichols and Åström-Hägglund rules
PROGRESSION OF QUALITATIVELY MORE
SUBSTANTIAL RESULTS PRODUCED BY GP

• Toy problems
• Human-competitive non-patent results
• 20th-century patented inventions
• 21st-century patented inventions
• Patentable new inventions
PARALLELIZATION WITH SEMI-ISOLATED
SUBPOPULATIONS
 GP PARALLELIZATION

• Like Hormel, Get Everything Out of the

Pig, Including the Oink
• Keep on Trucking
• It Takes a Licking and Keeps on Ticking
• The Whole is Greater than the Sum of
the Parts
 PETA-OPS

• Human brain operates at 1012 neurons

operating at 103 per second = 1015 ops per
second
• 1015 ops = 1 peta-op = 1 bs (brain second)
 EVOLVABLE HARDWARE
CORNER OF XILINX XC6216
FUNCTION UNIT FOR CELL OF
XILINIX XC6216
 SORTING NETWORK
A B C

D
H G F E
EVOLVED SORTING NETWORK
 GP 1987–2002

System Dates Speed-up Human- Problem Category

over first competitive
system results
Serial LISP 1987–1994 1 (base) 0 toy problems
64 transputers 1994–1997 9 2 human-competitive
results not related to
patented inventions
64 PowerPC’s 1995–2000 204 12 20th-century
patented inventions
70 Alpha’s 1999–2001 1,481 2 20th-century
patented inventions
1,000 Pentium II’s 2000–2002 13,900 12 21st-century
patented inventions
4-week runs on 2002-2003 130,000 2 patentable new
1,000 Pentium II’s inventions
 PROMISING GP APPLICATION AREAS

• Problem areas involving many variables

that are interrelated in highly non-linear
ways
• Inter-relationship of variables is not well
understood
• Discovery of the size and shape of the
solution is a major part of the problem
• "Black art" problems
 PROMISING GP APPLICATION AREAS
(CONTINUED)

• Areas where you simply have no idea

how to program a solution, but where
you know what you want
 PROMISING GP APPLICATION AREAS
(CONTINUED)

• Problem areas where a good approximate

solution is satisfactory
 design
 control
 bioinformatics
 classification
 data mining
 system identification
 forecasting
 PROMISING GP APPLICATION AREAS
(CONTINUED)

 Areas where large computerized databases are

accumulating and computerized techniques are
needed to analyze the data
 genome, protein, microarray data
 satellite image data
 astronomical data
 petroleum databases
 financial databases
 medical records
 marketing databases
 PROMISING GP APPLICATION AREAS
(CONTINUED)

 Areas for which humans find it very

difficult to write good programs
 parallel computers
 cellular automata
 multi-agent strategies
 field-programmable game arrays
 digital signal processors
 swarm intelligence
CHARACTERISTICS SUGGESTING
USE OF GP

(1) discovering the size and shape of the solution,

(2) reusing substructures,
(3) discovering the number of substructures,
(4) discovering the nature of the hierarchical references among
substructures,
(5) passing parameters to a substructure,
(6) discovering the type of substructures (e.g., subroutines, iterations,
loops, recursions, or storage),
(7) discovering the number of arguments possessed by a substructure,
(8) maintaining syntactic validity and locality by means of a
developmental process, or
(9) discovering a general solution in the form of a parameterized
topology containing free variables
 DESIGNING A GIRAFFE

• Long neck
• Long tongue
• Vegetable-digesting enzymes in stomach
• 4 legs
• Long legs
• Brown coloration
 THE DESIGN OF A GOOD GIRAFE

Neck Tongue Carnivorous? Number Leg Coloration

length length of legs length

15.11 14 inches No 4 9.96 feet Brown

feet
Floating Floating Boolean Integer Floating Categorical
point point point
 NON-LINEARITY — GIRAFE

• Taken one-by-one, some gene values found in a

giraffe, such as the long neck contribute (alone)
negatively to fitness
– requires considerable material to construct
– requires considerable energy to maintain
– prone to injury (thereby hurting rate of survival and
reproduction)
• Thus, maximizing any one variable will not
lead to the global optimum solution
 NON-LINEARITY (CONTINUED)

• When the variables are taken in pairs

(there are 15 possible pairs), many
combinations of pairs (e.g., Long neck
and long tongue) are doubly detrimental
 NON-LINEARITY (CONTINUED)

• But, certain combinations of traits, when taken

together, are "co-adapted sets of alleles" that
yield a very fit animal for eating high acacia
leaves in the jungle environment, having good
camouflage, having high escape velocity when
faced with predators, and exploiting a niche
(and avoiding competition) with other animals
feeding on low-hanging vegetation
SEARCH METHODS IN GENERAL

• Initial structure(s)
• Fitness measure
• Operations for creating new structures
• Parameters
• Termination criterion and method of
designating the result
SPACE WITH MANY LOCAL OPTIMA
 SEARCH METHODS

• Blind random search does not use acquired

information in deciding on the future direction
of the search
• Hill combing and gradient descent use acquired
information; however, they are prone to
becoming trapped on local optima
• The previous point is especially true for non-
trivial search spaces
 7 DIFFERENCES BETWEEN GP
AND ARTIFICIAL INTELLIGENCE
AND MACHINE LEARNING
APPROACHES
 REPRESENTATION

Genetic programming overtly conducts it

search for a solution to the given problem
in program space
 ROLE OF POINT-TO-POINT
TRANSFORMATIONS IN THE
SEARCH

Genetic programming does not conduct its

search by transforming a single point in the
search space into another single point, but
instead transforms a set of points into
another set of points
ROLE OF HILL CLIMBING IN THE
SEARCH

Genetic programming does not rely

exclusively on greedy hill climbing to
conduct its search, but instead allocates a
certain number of trials, in a principled
way, to choices that are known to be
inferior
 DETERMINISM IN THE SEARCH

Genetic programming conducts its search

probabilistically
 ROLE OF AN EXPLICIT
KNOWLEDGE BASE

Genetic programming does NOT make use

of a knowledge base
ROLE OF FORMAL LOGIC IN THE
SEARCH

Genetic programming does not utilize

formal logic in it’s search strategy.
Contradictory alternatives are created
and actively maintained.
 UNDERPINNINGS OF THE
TECHNIQUE

Biologically inspired
 TURING (1948)

Turing made the connection between

searches and the challenge of getting a
computer to solve a problem without
explicitly programming it in his 1948 essay
“Intelligent Machines”

"Further research into intelligence of

machinery will probably be very greatly
concerned with 'searches' ... “
 TURING’S 3 APPROACHES TO
MACHINE INTELLIGENCE (1948)

LOGIC-BASED SEARCH

One approach that Turing identified is a

search through the space of integers
representing candidate computer
programs.
 TURING’S 3 APPROACHES
(CONTINUED)

CULTURAL SEARCH

A second approach is the "cultural search“

which relies on knowledge and expertise
acquired over a period of years from
others (akin to present-day knowledge-
based systems).
 TURING’S 3 APPROACHES
(CONTINUED)

GENETICAL OR EVOLUTIONARY
SEARCH

"There is the genetical or evolutionary

search by which a combination of genes is
looked for, the criterion being the survival
value.“
 TURING (1950)

From Turing’s 1950 paper "Computing

Machinery and Intelligence" …

“We cannot expect to find a good child-

machine at the first attempt. One must
experiment with teaching one such machine
and see how well it learns. One can then try
another and see if it is better or worse.
There is an obvious connection between this
process and evolution, by the identifications”
 TURING (1950) (CONTINUED)

“Structure of the child machine =

Hereditary material

“Changes of the child machine =

Mutations

“Natural selection = Judgment

of the experimenter”