 # Evolutionary algorithms in Python

## What is context-free grammar?

A grammar is a set of production rules for a language. Context-free grammar is any grammar that is of the form $G = (V, \Sigma, R, S)$, where $V$ is a finite set of nonterminal characters, $\Sigma$ is a finite set of terminal characters, $R$ is the relation from $V$ to $\Sigma$, and $S$ is the start symbol. $S\ \to\ I+I,I-I,I*I,I/I$ $I\ \to\ I+I,I-I,I*I,I/I,(I),T$ $T\ \to\ x$ $x\ \to\ 1,2,3,4,5,6,7,8,9$

This is what it looks like in code form:

symbols = ['S','I','T','x']
grammar = {
'S':['I+I','I-I','I*I','I/I'],
'I':['I+I','I-I','I*I','I/I','(I)'] + ['T']*5,
'T':['x'],
'x':[str(float(x)) for x in range(1,10)]
}


I used multiple instances of the symbol $T$, which is a generic pointer to a terminal symbol. Using just one makes the nonterminal characters so much more likely to be chosen, that the expressions tend to never end.

We can think of an individual instance of resulting language to be the translation of the right-most character at any point. Then, an individual can be defined by a fixed-length list of numbers.

attribute_size = max([len(x) for x in grammar.values()])
individual = [random.randint(0,attribute_size-1) for _ in range(30)]
print(individual)


Running it results in the following output:

[6, 5, 3, 5, 1, 8, 3, 7, 9, 3, 9, 2, 6, 9, 1, 8, 3, 0, 6, 3, 4, 8, 8, 6, 8, 5, 4, 9, 7, 3]


Now we must define a method of converting this list to a string. I had to check for the case that it was done, by storing the string from the loop before and seeing if it has changed. Also note that we can disregard how large the rule numbers can be because we can use the modulo operation to index over the rules.

def express(individual, symbols, grammar):
expression = symbols
for branch in individual:
expression_old = expression
for symbol in symbols:
if symbol in expression:
i = expression.rindex(symbol)
rules = grammar[symbol]
replacement = rules[branch % len(rules)]
expression = expression[:i] + replacement + expression[i+1:]
break
if expression == expression_old:
break
return expression


Then, our individual from earlier becomes:

7.0/1.0-4.0/9.0*2.0


## Evolutionary algorithms using DEAP

Evolutionary algorithms describe the class of algorithms that use simulated evolution for the purpose of optimization. Given a fixed length of attributes, individuals can “breed” with each other using crossover points. After many generations, with an optional mutation factor, we arrive at increasingly optimal populations.

DEAP is a library for Distributed Evolutionary Algorithms in Python. I used their onemax example to write the code below to maximize arithmetic operations. In this case, I only made the individual long enough to result in two numbers, so the answer should be $9\times9=81$.

### optimizers.py

import random, math
random.seed(64)

from deap import base
from deap import creator
from deap import tools

class EvolutionaryCFG:
'''
Evolutionary Context-Free Grammar
'''

def __init__(self, symbols, grammar, evaluation_function, population_size=20, num_attributes=30):

self.symbols = symbols
self.grammar = grammar
attribute_size = max([len(x) for x in grammar.values()])
self.evaluation_function = evaluation_function

creator.create('FitnessMax', base.Fitness, weights=(1.0,))
creator.create('Individual', list, fitness=creator.FitnessMax)

self.toolbox = base.Toolbox()
self.toolbox.register('attr_int', random.randint, 0, attribute_size-1)
self.toolbox.register('individual', tools.initRepeat, creator.Individual, self.toolbox.attr_int, num_attributes)
self.toolbox.register('population', tools.initRepeat, list, self.toolbox.individual)
self.toolbox.register('evaluate', self.evaluate)
self.toolbox.register('mate', tools.cxOnePoint)
self.toolbox.register('mutate', tools.mutUniformInt, low=0, up=255, indpb=0.05)
self.toolbox.register('select', tools.selTournament, tournsize=3)

self.population = self.toolbox.population(n=population_size)
self.mate_prob = 0.5
self.mutant_prob = 0.2

# Prevents re-evaluation of the same individuals (assumes determinism)
self.score_cache = {}

def express(self, individual):
expression = 'S'
for branch in individual:
expression_old = expression
for symbol in self.symbols:
if symbol in expression:
i = expression.rindex(symbol)
rules = self.grammar[symbol]
replacement = rules[branch % len(rules)]
expression = expression[:i] + replacement + expression[i+1:]
break
if expression == expression_old:
break
return expression

def evaluate(self, individual):
expression = self.express(individual)
if expression not in self.score_cache.keys():
if any([symbol in expression for symbol in self.symbols]):
score = float('-inf')
else:
try:
score = self.evaluation_function(expression)
except:
score = float('-inf')
self.score_cache[expression] = score
else:
score = self.score_cache[expression]
return score,

def evolve(self, generations):
print('Start of evolution')

# Evaluate the entire population
print('\tGeneration 0')
fitnesses = list(map(self.toolbox.evaluate, self.population))
for ind, fit in zip(self.population, fitnesses):
ind.fitness.values = fit

print('\t\tEvaluated %i individuals' % len(self.population))

# Gather all the fitnesses in one list and print the stats
fits = [ind.fitness.values for ind in self.population if ind.fitness.values != float('-inf')]
length = len(self.population)
mean = sum(fits) / length
sum2 = sum(x*x for x in fits)
std = abs(sum2 / length - mean**2)**0.5
print('\t\t\tMin %s' % min(fits))
print('\t\t\tMax %s' % max(fits))
print('\t\t\tAvg %s' % mean)
print('\t\t\tStd %s' % std)

for generation in xrange(1,generations+1):
print('\tGeneration %i' % generation)

# Select the next generation individuals
offspring = self.toolbox.select(self.population, len(self.population))
# Clone the selected individuals
offspring = list(map(self.toolbox.clone, offspring))

# Apply crossover and mutation on the offspring
for child1, child2 in zip(offspring[::2], offspring[1::2]):

# cross two individuals with probability self.mate_prob
if random.random() < self.mate_prob:
self.toolbox.mate(child1, child2)

# fitness values of the children must be recalculated later
del child1.fitness.values
del child2.fitness.values

# mutate an individual with probability self.mutant_prob
for mutant in offspring:
if random.random() < self.mutant_prob:
self.toolbox.mutate(mutant)
del mutant.fitness.values

# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = map(self.toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit

print('\t\tEvaluated %i individuals' % len(invalid_ind))

# The population is entirely replaced by the offspring
self.population[:] = offspring

# Gather all the fitnesses in one list and print the stats
fits = [ind.fitness.values for ind in self.population if ind.fitness.values != float('-inf')]
length = len(self.population)
mean = sum(fits) / length
sum2 = sum(x*x for x in fits)
std = abs(sum2 / length - mean**2)**0.5
print('\t\t\tMin %s' % min(fits))
print('\t\t\tMax %s' % max(fits))
print('\t\t\tAvg %s' % mean)
print('\t\t\tStd %s' % std)

print('Done!')

best_ind = tools.selBest(self.population, 1)
print('Best individual is\n\t%s\n\t%s\n\nResult:%s' % (best_ind, self.express(best_ind), best_ind.fitness.values))



### main.py

import math

from optimizers import EvolutionaryCFG

def evaluate(expression):
return math.fabs(eval(expression))

def main():
symbols = ['x','y','z','T','I','S']
grammar = {
'x':[str(float(x)) for x in xrange(1,10)],
'y':[str(float(x)) for x in xrange(1,10)],
'z':[str(float(x)) for x in xrange(1,10)],
'T':['x','y','z'],
'I':['I+I','I-I','I*I','I/I','(I)'] + ['T']*5,
'S':['I+I','I-I','I*I','I/I']
}

optimizer = EvolutionaryCFG(symbols, grammar, evaluate, population_size=300, num_attributes=7)
optimizer.evolve(generations=4)

if __name__ == '__main__':
main()


## Results

Running main.py has the following result:

Start of evolution
Generation 0
Evaluated 300 individuals
Min 0.0
Max 54.0
Avg 2.02304232804
Std 6.04227568275
Generation 1
Evaluated 167 individuals
Min 0.0
Max 63.0
Avg 5.24390740741
Std 9.29000294167
Generation 2
Evaluated 172 individuals
Min 0.0
Max 72.0
Avg 12.2283809524
Std 14.7002320802
Generation 3
Evaluated 188 individuals
Min 0.571428571429
Max 81.0
Avg 22.6207936508
Std 19.0033049194
Generation 4
Evaluated 180 individuals
Min 0.0
Max 81.0
Avg 37.4266666667
Std 19.6186464591
Done!
Best individual is
[6, 5, 4, 8, 6, 1, 8]
9.0*9.0

Result:(81.0,) 