人工免疫算法-python实现
AIAIndividual.py
import numpy as np
import ObjFunction class AIAIndividual: '''
individual of artificial immune algorithm
''' def __init__(self, vardim, bound):
'''
vardim: dimension of variables
bound: boundaries of variables
'''
self.vardim = vardim
self.bound = bound
self.fitness = 0.
self.trials = 0
self.concentration = 0 def generate(self):
'''
generate a random chromsome for artificial immune algorithm
'''
len = self.vardim
rnd = np.random.random(size=len)
self.chrom = np.zeros(len)
for i in xrange(0, len):
self.chrom[i] = self.bound[0, i] + \
(self.bound[1, i] - self.bound[0, i]) * rnd[i] def calculateFitness(self):
'''
calculate the fitness of the chromsome
'''
self.fitness = ObjFunction.GrieFunc(
self.vardim, self.chrom, self.bound)
AIA.py
import numpy as np
from AIAIndividual import AIAIndividual
import random
import copy
import matplotlib.pyplot as plt class ArtificialImmuneAlgorithm: '''
The class for artificial immune algorithm
''' def __init__(self, sizepop, sizemem, vardim, bound, MAXGEN, params):
'''
sizepop: population sizepop
vardim: dimension of variables
bound: boundaries of variables
MAXGEN: termination condition
params: algorithm required parameters, it is a list which is consisting of [mutation rate, cloneNum]
'''
self.sizepop = sizepop
self.sizemem = sizemem
self.MAXGEN = MAXGEN
self.vardim = vardim
self.bound = bound
self.population = []
self.clonePopulation = []
self.memories = []
self.cloneMemories = []
self.popFitness = np.zeros(self.sizepop)
self.popCloneFitness = np.zeros(
int(self.sizepop * self.sizepop * params[1]))
self.memfitness = np.zero(self.sizemem)
self.memClonefitness = np.zero(
int(self.sizemem * self.sizemem * params[1]))
self.trace = np.zeros((self.MAXGEN, 2))
self.params = params def initialize(self):
'''
initialize the population
'''
for i in xrange(0, self.sizepop):
ind = AIAIndividual(self.vardim, self.bound)
ind.generate()
self.population.append(ind)
for i in xrange(0, self.sizemem):
ind = AIAIndividual(self.vardim, self.bound)
ind.generate()
self.memories.append(ind) def evaluatePopulation(self, flag):
'''
evaluation of the population fitnesses
'''
if flag == 1:
for i in xrange(0, self.sizepop):
self.population[i].calculateFitness()
self.popFitness[i] = self.population[i].fitness
else:
for i in xrange(0, self.sizemem):
self.memories[i].calculateFitness()
self.memfitness[i] = self.memories[i].fitness def evaluateClone(self, flag):
'''
evaluation of the clone fitnesses
'''
if flag == 1:
for i in xrange(0, self.sizepop):
self.clonePopulation[i].calculateFitness()
self.popCloneFitness[i] = self.clonePopulation[i].fitness
else:
for i in xrange(0, self.sizemem):
self.cloneMemories[i].calculateFitness()
self.memClonefitness[i] = self.cloneMemories[i].fitness def solve(self):
'''
evolution process of artificial immune algorithm
'''
self.t = 0
self.initialize()
self.best = AIAIndividual(self.vardim, self.bound)
while (self.t < self.MAXGEN):
# evolution of population
self.cloneOperation(1)
self.mutationOperation(1)
self.evaluatePopulation(1)
self.selectionOperation(1) # evolution of memories
self.cloneOperation(2)
self.mutationOperation(2)
self.evaluatePopulation()
self.selectionOperation(2) best = np.max(self.popFitness)
bestIndex = np.argmax(self.popFitness)
if best > self.best.fitness:
self.best = copy.deepcopy(self.population[bestIndex])
self.avefitness = np.mean(self.popFitness)
self.trace[self.t, 0] = (1 - self.best.fitness) / self.best.fitness
self.trace[self.t, 1] = (1 - self.avefitness) / self.avefitness
print("Generation %d: optimal function value is: %f; average function value is %f" % (
self.t, self.trace[self.t, 0], self.trace[self.t, 1]))
self.t += 1 print("Optimal function value is: %f; " %
self.trace[self.t - 1, 0])
print "Optimal solution is:"
print self.best.chrom
self.printResult() def cloneOperation(self, individuals):
'''
clone operation for alforithm immune algorithm
'''
newpop = []
sizeInds = len(individuals)
for i in xrange(0, sizeInds):
for j in xrange(0, int(self.params[1] * sizeInds)):
newpop.append(copy.deepcopy(individuals[i]))
return newpop def selectionOperation(self, flag):
'''
selection operation for artificial immune algorithm
'''
if flag == 1:
sortedIdx = np.argsort(-self.clonefit)
for i in xrange(0, int(self.sizepop*self.sizepop*self.params[1]):
tmpInd = individuals[sortedIdx[i]]
if tmpInd.fitness > self.population[i].fitness:
self.population[i] = tmpInd
self.popFitness[i] = tmpInd.fitness
else:
pass
newpop = []
sizeInds = len(individuals)
fitness = np.zeros(sizeInds)
for i in xrange(0, sizeInds):
fitness[i] = individuals[i].fitness
sortedIdx = np.argsort(-fitness)
for i in xrange(0, sizeInds):
tmpInd = individuals[sortedIdx[i]]
if tmpInd.fitness > self.population[i].fitness:
self.population[i] = tmpInd
self.popFitness[i] = tmpInd.fitness def mutationOperation(self, individuals):
'''
mutation operation for artificial immune algorithm
'''
newpop = []
sizeInds = len(individuals)
for i in xrange(0, sizeInds):
newpop.append(copy.deepcopy(individuals[i]))
r = random.random()
if r < self.params[0]:
mutatePos = random.randint(0, self.vardim - 1)
theta = random.random()
if theta > 0.5:
newpop[i].chrom[mutatePos] = newpop[i].chrom[
mutatePos] - (newpop[i].chrom[mutatePos] - self.bound[0, mutatePos]) * (1 - random.random() ** (1 - self.t / self.MAXGEN))
else:
newpop[i].chrom[mutatePos] = newpop[i].chrom[
mutatePos] + (self.bound[1, mutatePos] - newpop[i].chrom[mutatePos]) * (1 - random.random() ** (1 - self.t / self.MAXGEN))
for k in xrange(0, self.vardim):
if newpop.chrom[mutatePos] < self.bound[0, mutatePos]:
newpop.chrom[mutatePos] = self.bound[0, mutatePos]
if newpop.chrom[mutatePos] > self.bound[1, mutatePos]:
newpop.chrom[mutatePos] = self.bound[1, mutatePos]
newpop.calculateFitness()
return newpop def printResult(self):
'''
plot the result of the artificial immune algorithm
'''
x = np.arange(0, self.MAXGEN)
y1 = self.trace[:, 0]
y2 = self.trace[:, 1]
plt.plot(x, y1, 'r', label='optimal value')
plt.plot(x, y2, 'g', label='average value')
plt.xlabel("Iteration")
plt.ylabel("function value")
plt.title("Artificial immune algorithm for function optimization")
plt.legend()
plt.show()
运行程序:
if __name__ == "__main__": bound = np.tile([[-600], [600]], 25)
aia = AIA(100, 25, bound, 100, [0.9, 0.1])
aia.solve()
ObjFunction见简单遗传算法-python实现。
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