def GA(function, mutation_op, population_size=100, num_gen=50):
"""
function - the benchmark function to be run on
mutation_op - the type of mutation the children will be subjected to
population_size - number of possible solutions within a generation
num_gen - number of iterations
"""
num_func = bench_funcs[function]
bench = Function(num_func, 50)
info = bench.info()
fitness = bench.get_eval_function()
population = first_population(population_size, info)
best = population[0]
best_of_gen = []
for _ in range(num_gen):
for pop in population:
new_pop_fit = fitness(pop)
best_fit = fitness(best)
if (new_pop_fit < best_fit):
best = pop
best_fit = new_pop_fit
breeders = tournament(population, fitness)
children = create_children(breeders, mutation_op, info)
population = np.array(children)
best_of_gen.append(best_fit)
# each generations best, overall best
return best_of_gen, best_fit
def main(self, iterations):
self._initialize()
fbench = Function(self.func, self.dimen)
fitness_func = fbench.get_eval_function()
min_fitness = None # Best fitness of all individuals
for epoch in range(iterations):
#Begin search for global optimum
if epoch % 100 == 0 and epoch > 1:
print("Epoch = " + str(epoch) +
" best error = %s" % str(min_fitness))
pop_fitnesses = self._calculate_fitness(fitness_func)
min_fitness = pop_fitnesses.min()
# Determine the next generation
new_pop = np.empty(shape=(self.pop_size, self.dimen))
for i in np.arange(0, self.pop_size, 2):
idx1 = self._tournamentSelection(pop_fitnesses)
idx2 = self._tournamentSelection(pop_fitnesses)
# Perform crossover to produce children
child1, child2 = self._twoPointCrossover(
self.population[idx1], self.population[idx2])
# Save mutated children for next generation
new_pop[i] = self._mutate(child1)
new_pop[i + 1] = self._mutate(child2)
self.population = new_pop
print(str(min_fitness) + ",")
def get_best_nest(nest, newnest, fitness, n, dim, objf):
# Evaluating all new solutions
tempnest = numpy.zeros((n, dim))
tempnest = numpy.copy(nest)
fbench = Function(objf, dim)
info = fbench.info()
ub = info['upper']
lb = info['lower']
optimum = info['best']
fun_fitness = fbench.get_eval_function()
for j in range(0, n):
#for j=1:size(nest,1),
fnew = fun_fitness(newnest[j, :])
if fnew <= fitness[j]:
fitness[j] = fnew
tempnest[j, :] = newnest[j, :]
# Find the current best
fmin = min(fitness)
K = numpy.argmin(fitness)
bestlocal = tempnest[K, :]
return fmin, bestlocal, tempnest, fitness
def PSO(function, inf_count, swarm_size=100, num_movements=50):
"""
function - the benchmark function to be run on
inf_count - number of informants that each particle has
swarm_size - number of possible solutions within a generation
num_movements - the number of times the particles adjust their position
"""
num_func = bench_funcs[function]
bench = Function(num_func, 50)
info = bench.info()
fitness = bench.get_eval_function()
swarm = generate_swarm(swarm_size, info)
velocities = generate_velocities(swarm_size, info)
informants = get_informants(swarm_size, inf_count, info)
alpha, beta, gamma, delta = generate_weights()
# the index best known position of and individual particle i, init = self
p_best = np.arange(swarm_size, dtype=int)
best_inf_position = np.zeros(
swarm_size
) # the index of the best known position of an individual i's informants
g_best = 0 # index of global best location
# the best fitness calculated after position adjustment
best_of_movement = []
for _ in range(num_movements):
for i in range(len(swarm)):
particle = swarm[i]
curr_fit = fitness(particle)
p_fit = fitness(swarm[p_best[i]])
if (curr_fit < p_fit):
p_best[i] = i
if (fitness(swarm[p_best[i]]) < fitness(swarm[g_best])):
g_best = p_best[i]
for i in range(len(swarm)):
curr_best = swarm[p_best[i]]
inf_best_index = get_best_of_inf(swarm, informants[i], fitness)
inf_best = swarm[inf_best_index]
best_inf_position[i] = inf_best_index
overall_best = swarm[g_best]
particle = swarm[i]
for dim in range(len(particle)):
b = np.random.uniform(0, beta)
c = np.random.uniform(0, gamma)
d = np.random.uniform(0, delta)
velocities[i] = (alpha * velocities[i]) + (
b *
(curr_best - particle)) + (c * (inf_best - particle)) + (
d * (overall_best - particle))
for particle, vel in zip(swarm, velocities):
particle += vel
best_of_movement.append(fitness(swarm[g_best]))
# each adjustments best fitness, overall best fitness
return best_of_movement, fitness(swarm[g_best])
def main(args):
"Main program."
parser = argparse.ArgumentParser(description="Running SHADE with 2005 Benchmark")
parser.add_argument('-f', dest='fun', type=int, choices=range(1, 26),
required=True,
help="the function value [1-25]")
parser.add_argument('-d', dest='dim', type=int, choices=[2, 10, 30, 50],
required=True,
help="the dimensionality [2, 10, 30, 50]")
parser.add_argument('-r', dest='run', default=25, type=int,
help="run times")
parser.add_argument('-s', dest='seedid', required=True, type=int,
help="seed", choices=range(1, 6))
params = parser.parse_args(args)
seeds = [12345679, 32379553, 235325, 5746435, 253563]
if (params.run <= 0):
parser.print_help()
return
# Set the seeds
numpy.random.seed(seeds[params.seedid-1])
dim = params.dim
fid = params.fun
fun = Function(fid, dim)
info = fun.info()
fitness_fun = fun.get_eval_function()
output = "results/shade_cec2005_f{0}d{1}_s{2}r{3}".format(fid, dim, params.seedid, params.run)
info['best'] = 0
ignoreLimits = (fid != 7 and fid != 25)
noisy = (fid == 4 or fid == 25)
if os.path.exists(output):
return
for r in range(params.run):
result,bestIndex = shade.improve(fitness_fun, info, dim, 10000*dim,
name_output=output, replace=False, times=params.run, popsize=min(dim, 10), H=2*dim, ignoreLimits=ignoreLimits)
best_sol = result.solution
best_fitness = result.fitness
if not noisy:
assert(fitness_fun(best_sol)==best_fitness)
# Import all the DE algorithm variants from python Advanced DE libarary
import numpy as np
from helper import functions, algos, updateRuns, plotMedians, storeMeanResult, RUNS
import os
import commons
from cec2005real.cec2005 import Function
############################################
# Main Function #
############################################
dims = [2, 10, 30]
for dim in dims:
for funcNum in functions.keys():
fbench = Function(funcNum, dim)
info = fbench.info()
function = fbench.get_eval_function()
bounds = [(info['lower'], info['upper'])]
startingPopulations = [
commons.init_population(10 * dim, dim, np.array(bounds))
for x in range(RUNS)
]
for j, algo in enumerate(algos.keys()):
for x in range(0, RUNS):
params = algo.get_default_params(dim=dim)
bounds = np.array(bounds * dim)
params['func'] = function
params['bounds'] = bounds
#params['max_evals'] = 10000
params['opts'] = None
params['answer'] = None
params['population'] = startingPopulations[x].copy()
def testF4(sol_zeros):
b = Function(4, 10)
f = b.get_eval_function()
result1 = f(sol_zeros)
result2 = f(sol_zeros)
assert result1 != result2
def test_all_nozeros(sol_zeros):
for fid in range(1,26):
fn = Function(fid, 10).get_eval_function()
assert fn(sol_zeros) != 0
def CS(objf, dim, n, N_IterTotal):
# objf,n,dim,MaxGeneration
fbench = Function(objf, dim)
info = fbench.info()
ub = info['upper']
lb = info['lower']
optimum = info['best']
#lb=-1
#ub=1
#n=50
#N_IterTotal=1000
#dim=30
# Discovery rate of alien eggs/solutions
pa = 0.25
nd = dim
# Lb=[lb]*nd
# Ub=[ub]*nd
convergence = []
# RInitialize nests randomely
nest = numpy.random.rand(n, dim) * (ub - lb) + lb
new_nest = numpy.zeros((n, dim))
new_nest = numpy.copy(nest)
bestnest = [0] * dim
fitness = numpy.zeros(n)
fitness.fill(float("inf"))
s = solution()
print("CS is optimizing " + str(objf))
timerStart = time.time()
s.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
fmin, bestnest, nest, fitness = get_best_nest(nest, new_nest, fitness, n,
dim, objf)
convergence = []
# Main loop counter
for iter in range(0, N_IterTotal):
# Generate new solutions (but keep the current best)
new_nest = get_cuckoos(nest, bestnest, lb, ub, n, dim)
# Evaluate new solutions and find best
fnew, best, nest, fitness = get_best_nest(nest, new_nest, fitness, n,
dim, objf)
new_nest = empty_nests(new_nest, pa, n, dim)
# Evaluate new solutions and find best
fnew, best, nest, fitness = get_best_nest(nest, new_nest, fitness, n,
dim, objf)
if fnew < fmin:
fmin = fnew
bestnest = best
if (iter % 100 == 0):
print([
'At iteration ' + str(iter) + ' the best fitness is ' +
str(fmin) + ": CS" + " :" + str(objf)
])
convergence.append(fmin)
convergence.append(fitness[0])
convergence.append(fitness[6])
convergence.append(fitness[12])
convergence.append(fitness[18])
convergence.append(fitness[24])
convergence.append(numpy.sum(fitness) / n)
convergence.append(numpy.std(fitness))
timerEnd = time.time()
s.endTime = time.strftime("%Y-%m-%d-%H-%M-%S")
s.executionTime = timerEnd - timerStart
s.convergence = convergence
s.optimizer = "CS"
s.objfname = "F" + str(objf)
return s
for k in range(dim):
swarm[i].position[k] += swarm[i].velocity[k]
# Compute fitness of new position
swarm[i]._setFitness()
# Is new position a new best for the particle?
if swarm[i].fitness < swarm[i].best_part_fitness:
swarm[i].best_part_fitness = swarm[i].fitness
swarm[i].best_part_pos = np.copy(swarm[i].position)
# Is new position a new best overall?
if swarm[i].fitness < best_swarm_fitness:
best_swarm_fitness = swarm[i].fitness
best_swarm_pos = np.copy(swarm[i].position)
print ("Best fitness:" + str(best_swarm_fitness))
if __name__ == "__main__":
#np.random.seed(8)
pso = ParticleSwarmOptimisation()
# Desired number of runs
for i in range(1):
start_time = time.time()
dim=10 # Dimensionality (10, 30, or 50)
fbench = Function(4,dim) # Function number 1-> 25
fitnessFunc = fbench.get_eval_function()
pso.main(iterations=10000, n=50, func=fitnessFunc, dim=dim,
bound_min=-100., bound_max=100.)
print("Runtime: %s seconds" % (time.time() - start_time))
def PFA(objf, n, dim, MaxGeneration):
fbench = Function(objf, dim)
info = fbench.info()
ub = info['upper']
lb = info['lower']
optimum = info['best']
print(optimum)
#General parameters
#n=50 #number of fireflies
# dim=10000 #dim
#lb=-50
#ub=50
#MaxGeneration=500
#FFA parameters
alpha = 0.50 # Randomness 0--1 (highly random)
betamin = 0.50 # minimum value of beta
gamma = 1 # Absorption coefficient
zn = numpy.ones(n)
zn.fill(float("inf"))
#ns(i,:)=Lb+(Ub-Lb).*rand(1,d);
ns = numpy.random.uniform(0, 1, (n, dim)) * (ub - lb) + lb
Lightn = numpy.ones(n)
Lightn.fill(float("inf"))
Lightnprev = numpy.ones(n)
Lightnprev.fill(float("inf"))
#[ns,Lightn]=init_ffa(n,d,Lb,Ub,u0)
convergence = []
s = solution()
print("PFA is optimizing F" + str(objf))
timerStart = time.time()
s.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
# Main loop
for k in range(0, MaxGeneration): # start iterations
#% This line of reducing alpha is optional
#alpha=alpha_new(alpha,MaxGeneration);
Lightnprev = Lightn
#% Evaluate new solutions (for all n fireflies)
fun_fitness = fbench.get_eval_function()
for i in range(0, n):
zn[i] = fun_fitness(ns[i, :])
Lightn[i] = zn[i]
# Ranking fireflies by their light intensity/objectives
Lightn = numpy.sort(zn)
Index = numpy.argsort(zn)
ns = ns[Index, :]
#Find the current best
nso = ns
Lighto = Lightn
nbest = ns[0, :]
Lightbest = Lightn[0]
#% For output only
fbest = Lightbest
#% Move all fireflies to the better locations
# [ns]=ffa_move(n,d,ns,Lightn,nso,Lighto,nbest,...
# Lightbest,alpha,betamin,gamma,Lb,Ub);
scale = numpy.ones(dim) * abs(ub - lb)
for i in range(0, n):
# The attractiveness parameter beta=exp(-gamma*r)
for j in range(0, n):
# r=numpy.sqrt(numpy.sum((ns[i,:]-ns[j,:])**2));
# r2=numpy.sqrt(numpy.sum((ns[i,:]-ns[0,:])**2));
r = numpy.sum((ns[i, :] - ns[j, :]))
r2 = numpy.sum((ns[0, :] - ns[j, :]))
#r=1
# Update moves
if Lightn[i] > Lighto[j]: # Brighter and more attractive
# PropFA parameters
per = ((k / MaxGeneration) * 100) / 85
per2 = numpy.heaviside(per - 1, 0.5)
ratA = (numpy.absolute(Lightn[i]) - numpy.absolute(
Lightnprev[i])) / max(numpy.absolute(Lightn[i]),
numpy.absolute(Lightnprev[i]))
ratB = (numpy.absolute(Lightn[j]) - numpy.absolute(
Lightn[i])) / max(numpy.absolute(Lightn[j]),
numpy.absolute(Lightn[i]))
ratC = (numpy.absolute(fbest) - numpy.absolute(
Lightn[i])) / max(numpy.absolute(fbest),
numpy.absolute(Lightn[i]))
ratAvg = (ratA + ratB + ratC) / 3
scale2 = numpy.absolute(ub - lb)
# bet=3/2;
# sigma=(math.gamma(1+bet)*math.sin(math.pi*bet/2)/(math.gamma((1+bet)/2)*bet*2**((bet-1)/2)))**(1/bet);
# u=numpy.random.randn(dim)*sigma
# v=numpy.random.randn(dim)
# step=u/abs(v)**(1/bet)
# stepsize=0.001*(step*(ns[i,:]-ns[0,:]))
if (Lightnprev[i] == Lightn[i]):
alpha = 10
else:
r3 = numpy.sum((ns[0, :] - ns[n - 1, :]))
alpha = (r2 / 1000) * ratAvg * numpy.exp(-k * per2)
if (Lightnprev[i] == Lightn[i]):
gamma = 1
else:
gamma = (ratB / ratC)
beta0 = 1
beta = (beta0 - betamin) * numpy.exp(
-gamma * r**2) + betamin
beta2 = (beta0 - betamin) * numpy.exp(
-gamma * r2**2) + betamin
tmpf = alpha * (numpy.random.rand(dim) - 0.5) * 1
# tmpf=stepsize*numpy.random.randn(dim)
#
#ns[i,:]=ns[i,:]*(1-beta)+nso[j,:]*beta+tmpf
ns[i, :] = ns[i, :] + (beta * (nso[j, :] - ns[i, :])) + (
beta2 * (nso[0, :] - ns[i, :])) + tmpf
ns = numpy.clip(ns, lb, ub)
IterationNumber = k
BestQuality = fbest
if (k % 1 == 0):
print([
'At iteration ' + str(k) + ' the best fitness is ' +
str(BestQuality) + ": PFA" + " :" + str(objf)
])
if (k % 100 == 0):
convergence.append(fbest)
#
####################### End main loop
convergence.append(Lightn[0])
convergence.append(Lightn[6])
convergence.append(Lightn[12])
convergence.append(Lightn[18])
convergence.append(Lightn[24])
convergence.append(numpy.sum(Lightn) / n)
convergence.append(numpy.std(Lightn))
timerEnd = time.time()
s.endTime = time.strftime("%Y-%m-%d-%H-%M-%S")
s.executionTime = timerEnd - timerStart
s.convergence = convergence
s.optimizer = "PFA"
s.objfname = "F" + str(objf)
return s