def neat_GP_LS(population,
toolbox,
cxpb,
mutpb,
ngen,
neat_alg,
neat_cx,
neat_h,
neat_pelit,
LS_flag,
LS_select,
cont_evalf,
num_salto,
SaveMatrix,
GenMatrix,
pset,
n_corr,
num_p,
params,
direccion,
problem,
testing,
version,
benchmark_flag,
beta,
random_speciation,
config,
stats=None,
halloffame=None,
verbose=__debug__):
"""This algorithm reproduce the simplest evolutionary algorithm as
presented in chapter 7 of [Back2000]_.
:param population: A list of individuals.
:param toolbox: A :class:`~deap.base.Toolbox` that contains the evolution
operators.
:param cxpb: The probability of mating two individuals.
:param mutpb: The probability of mutating an individual.
:param ngen: The number of generation.
:param neat_alg: wheter or not to use species stuff.
:param neat_cx: wheter or not to use neatGP cx
:param neat_h: indicate the distance allowed between each specie
:param neat_pelit: probability of being elitist, it's used in the neat cx and mutation
:param LS_flag: wheter or not to use LocalSearchGP
:param LS_select: indicate the kind of selection to use the LSGP on the population.
:param cont_evalf: contador maximo del numero de evaluaciones
:param n_corr: run number just to wirte the txt file
:param p: problem number just to wirte the txt file
:param params:indicate the params for the fitness sharing, the diffetent
options are:
-DontPenalize(str): 'best_specie' or 'best_of_each_specie'
-Penalization_method(int):
1.without penalization
2.penalization fitness sharing
3.new penalization
-ShareFitness(str): 'yes' or 'no'
:param stats: A :class:`~deap.tools.Statistics` object that is updated
inplace, optional.
:param halloffame: A :class:`~deap.tools.HallOfFame` object that will
contain the best individuals, optional.
:param verbose: Whether or not to log the statistics.
:returns: The final population.
It uses :math:`\lambda = \kappa = \mu` and goes as follow.
It first initializes the population (:math:`P(0)`) by evaluating
every individual presenting an invalid fitness. Then, it enters the
evolution loop that begins by the selection of the :math:`P(g+1)`
population. Then the crossover operator is applied on a proportion of
:math:`P(g+1)` according to the *cxpb* probability, the resulting and the
untouched individuals are placed in :math:`P'(g+1)`. Thereafter, a
proportion of :math:`P'(g+1)`, determined by *mutpb*, is
mutated and placed in :math:`P''(g+1)`, the untouched individuals are
transferred :math:`P''(g+1)`. Finally, those new individuals are evaluated
and the evolution loop continues until *ngen* generations are completed.
Briefly, the operators are applied in the following order ::
evaluate(population)
for i in range(ngen):
offspring = select(population)
offspring = mate(offspring)
offspring = mutate(offspring)
evaluate(offspring)
population = offspring
This function expects :meth:`toolbox.mate`, :meth:`toolbox.mutate`,
:meth:`toolbox.select` and :meth:`toolbox.evaluate` aliases to be
registered in the toolbox.
.. [Back2000] Back, Fogel and Michalewicz, "Evolutionary Computation 1 :
Basic Algorithms and Operators", 2000.
"""
logbook = tools.Logbook()
logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])
#creating files to save data.
d = './Results/%s/pop_file_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
pop_file = open(d, 'a')
d = './Results/%s/bestind_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
best = open(d, 'w') # save data
d = './Results/%s/bestind_str_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
out = open(d, 'w')
d = './Timing/%s/pop_file_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
time_file = open(d, 'w')
d = './Timing/%s/specie_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
time_specie = open(d, 'w')
d = './Timing/%s/cruce_s_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
time_cx = open(d, 'w')
d = './Specie/%s/specieind_%d_%d.csv' % (problem, num_p, n_corr)
ensure_dir(d)
specie_file = open(d, 'w')
d = './Specie/%s/speciepop_%d_%d.csv' % (problem, num_p, n_corr)
ensure_dir(d)
specie_file_2 = open(d, 'w')
d = './Specie/%s/specist_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
specie_statis = open(d, 'w')
d = './Results/%s/bestind_LStr_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
bestind = open(d, 'w')
d = './Matrix/%s/' % (problem)
ensure_dir(d)
begin = time.time()
if SaveMatrix: # Saving data in matrix
num_r = 11
num_r_sp = 2
if GenMatrix:
num_salto = 1
num_c = ngen + 1
Matrix = np.empty((
num_c,
num_r,
))
Matrix_specie = np.empty((
num_c,
num_r_sp,
), dtype=object)
vector = np.arange(0, num_c, num_salto)
else:
num_c = (cont_evalf / num_salto) + 1
num_c_sp = (cont_evalf / num_salto) + 1
Matrix = np.empty((
num_c,
num_r,
))
Matrix_specie = np.empty((
num_c_sp,
num_r_sp,
), dtype=object)
vector = np.arange(1, cont_evalf + num_salto, num_salto)
for i in range(len(vector)):
Matrix[i, 0] = vector[i]
Matrix_specie[i, 0] = vector[i]
Matrix[:, 6] = 0.
if neat_alg:
begin_sp = time.time()
if version == 1:
for ind in population:
bit = p_bin(ind)
ind.binary_rep_set(bit)
elif version != 1:
for ind in population:
level_info = level_node(ind)
ind.nodefeat_set(level_info)
if random_speciation:
species_random(population, neat_h, version, beta)
else:
species(population, neat_h, version, beta)
end_sp = time.time()
time_specie.write(
'\n%s;%s;%s;%s' %
(0, begin_sp, end_sp, str(round(end_sp - begin_sp, 2))))
for ind in population:
specie_file_2.write('\n%s,%s,%s' %
(0, ind.get_specie(), ind.get_intracluster()))
list_s = list_species(population)
for specie in list_s:
list_ind = get_ind_specie(specie, population)
specie_file.write('\n%s,%s,%s' %
(0, specie, list_ind[0].get_intracluster()))
if funcEval.LS_flag:
for ind in population:
sizep = len(ind) + 2
param_ones = np.ones(sizep)
param_ones[0] = 0
ind.params_set(param_ones)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
funcEval.cont_evalp += 1
ind.fitness.values = fit
best_ind = best_pop(population) # best individual of the population
if testing:
fitnesst_best = toolbox.map(toolbox.evaluate_test, [best_ind])
best_ind.fitness_test.values = fitnesst_best[0]
if testing:
best.write(
'\n%s;%s;%s;%s;%s;%s' %
(0, funcEval.cont_evalp, best_ind.fitness_test.values[0],
best_ind.fitness.values[0], len(best_ind), avg_nodes(population)))
else:
best.write('\n%s;%s;%s;%s;%s;%s' %
(0, funcEval.cont_evalp, None, best_ind.fitness.values[0],
len(best_ind), avg_nodes(population)))
data_pop = avg_nodes(population)
if SaveMatrix:
idx = 0
Matrix[idx, 1] = best_ind.fitness.values[0]
if testing:
Matrix[idx, 2] = best_ind.fitness_test.values[0]
else:
Matrix[idx, 2] = None
Matrix[idx, 3] = len(best_ind)
Matrix[idx, 4] = data_pop[0]
Matrix[idx, 5] = 0.
Matrix[idx, 6] = 1 # just an id to know if the current row is full
Matrix[idx, 7] = data_pop[1] # max size
Matrix[idx, 8] = data_pop[2] # min size
Matrix[idx, 9] = ind.get_specie(
) # max number of species in the current population
Matrix[idx, 10] = max(ind_specie(population), key=lambda x: x[0])[
0] # max number of species in the current population
np.savetxt('./Matrix/%s/idx_%d_%d.txt' % (problem, num_p, n_corr),
Matrix,
delimiter=",",
fmt="%s")
if neat_alg:
SpeciesPunishment(population, params, neat_h)
if funcEval.LS_flag == 1:
strg = best_ind.__str__()
l_strg = add_subt_cf(strg, args=[])
c = tree2f()
cd = c.convert(l_strg)
out.write('\n%s;%s;%s;%s;%s;%s' %
(0, len(best_ind), best_ind.LS_applied_get(),
best_ind.get_params(), cd, best_ind))
else:
out.write('\n%s;%s;%s' % (0, len(best_ind), best_ind))
for ind in population:
pop_file.write('\n%s;%s;%s' % (0, ind.fitness.values[0], ind))
print '---- Generation %d -----' % (0)
print 'Problem: ', problem
print 'Problem No.: ', num_p
print 'Run No.: ', n_corr
print 'neat-GP:', neat_alg
print 'neat-cx:', neat_cx
print 'Local Search:', funcEval.LS_flag
if funcEval.LS_flag:
ls_type = ''
if LS_select == 1:
ls_type = 'LSHS'
elif LS_select == 2:
ls_type = 'Best-Sp'
elif LS_select == 3:
ls_type = 'LSHS-Sp'
elif LS_select == 4:
ls_type = 'Best-Pop'
elif LS_select == 5:
ls_type = 'All-Pop'
elif LS_select == 6:
ls_type = 'LSHS-test'
elif LS_select == 7:
ls_type = 'Best set'
elif LS_select == 8:
ls_type = 'Random set'
elif LS_select == 9:
ls_type = "Best-Random set"
print 'Local Search Heuristic: %s (%s)' % (LS_select, ls_type)
print 'Best Ind.:', best_ind
print 'Best Fitness:', best_ind.fitness.values[0]
if testing:
print 'Test fitness:', best_ind.fitness_test.values[0]
print 'Avg Nodes:', avg_nodes(population)
print 'Evaluations: ', funcEval.cont_evalp
end_t = time.time()
if SaveMatrix:
idx = 0
Matrix_specie[idx, 1] = ind_specie(population)
np.savetxt('./Specie/%s/specist_%d_%d.txt' % (problem, num_p, n_corr),
Matrix_specie,
delimiter=";",
fmt="%s")
if testing:
time_file.write(
'\n%s;%s;%s;%s;%s;%s' %
(0, begin, end_t, str(round(end_t - begin, 2)),
best_ind.fitness.values[0], best_ind.fitness_test.values[0]))
else:
time_file.write('\n%s;%s;%s;%s;%s' %
(0, begin, end_t, str(round(
end_t - begin, 2)), best_ind.fitness.values[0]))
# Begin the generational process
for gen in range(1, ngen + 1):
print "hola"
if not GenMatrix:
if funcEval.cont_evalp > cont_evalf:
break
begin = time.time()
print '---- Generation %d -----' % (gen)
print 'Problem: ', problem
print 'Problem No.: ', num_p
print 'Run No.: ', n_corr
print 'neat-GP:', neat_alg
print 'neat-cx:', neat_cx
print 'Local Search:', funcEval.LS_flag
if funcEval.LS_flag:
print 'Local Search Heuristic: %s (%s)' % (LS_select, ls_type)
best_ind = copy.deepcopy(best_pop(population))
if neat_alg:
# survival_p = p_worst
parents = p_selection(population, survival_p=0.5)
else:
parents = toolbox.select(population, len(population))
begin_cx = time.time()
if neat_alg: # neat-Crossover neat_cx and
n = len(parents)
mut = 1
cx = 1
offspring = neatGP(toolbox, parents, cxpb, mutpb, n, mut, cx,
neat_pelit, neat_cx)
else:
offspring = varOr(parents, toolbox, cxpb, mutpb)
end_cx = time.time()
time_specie.write(
'\n%s;%s;%s;%s' %
(0, begin_cx, end_cx, str(round(end_cx - begin_cx, 2))))
if neat_alg: # Speciation of the descendants
begin_sp = time.time()
if version == 1:
for ind in offspring:
if ind.binary_rep_get() is None:
bit = p_bin(ind)
ind.binary_rep_set(bit)
elif version == 2:
for ind in offspring:
if ind.nodefeat_get() is None:
level_info = level_node(ind)
ind.nodefeat_set(level_info)
if random_speciation:
specie_offspring_random(parents, offspring, neat_h, version,
beta)
else:
specie_parents_child(parents, offspring, neat_h, version, beta)
#calc_intracluster(population)
offspring[:] = parents + offspring
calc_intracluster(offspring)
for ind in offspring:
specie_file_2.write(
'\n%s,%s,%s' %
(gen, ind.get_specie(), ind.get_intracluster()))
list_s = list_species(offspring)
for specie in list_s:
list_ind = get_ind_specie(specie, offspring)
specie_file.write(
'\n%s,%s,%s' %
(gen, specie, list_ind[0].get_intracluster()))
invalid_ind = [ind for ind in offspring]
if funcEval.LS_flag:
new_invalid_ind = []
for ind in invalid_ind:
strg = ind.__str__()
l_strg = add_subt(strg, ind)
c = tree2f()
cd = c.convert(l_strg)
new_invalid_ind.append(cd)
fitness_ls = toolbox.map(toolbox.evaluate, new_invalid_ind)
for ind, ls_fit in zip(invalid_ind, fitness_ls):
funcEval.cont_evalp += 1
ind.fitness.values = ls_fit
else:
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
funcEval.cont_evalp += 1
ind.fitness.values = fit
end_sp = time.time()
time_specie.write(
'\n%s;%s;%s;%s' %
(gen, begin_sp, end_sp, str(round(end_sp - begin_sp, 2))))
print "neat-alg"
else:
invalid_ind = [ind for ind in offspring]
if funcEval.LS_flag:
new_invalid_ind = []
for ind in invalid_ind:
strg = ind.__str__()
l_strg = add_subt(strg, ind)
c = tree2f()
cd = c.convert(l_strg)
new_invalid_ind.append(cd)
fitness_ls = toolbox.map(toolbox.evaluate, new_invalid_ind)
for ind, ls_fit in zip(invalid_ind, fitness_ls):
funcEval.cont_evalp += 1
ind.fitness.values = ls_fit
else:
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
funcEval.cont_evalp += 1
ind.fitness.values = fit
orderbyfit = sorted(offspring, key=lambda ind: ind.fitness.values)
if best_ind.fitness.values[0] <= orderbyfit[0].fitness.values[0]:
offspring[:] = [best_ind] + orderbyfit[:len(population) - 1]
if neat_alg:
SpeciesPunishment(offspring, params, neat_h)
if SaveMatrix:
if GenMatrix:
idx_aux = np.searchsorted(Matrix[:, 0], gen)
Matrix_specie[idx_aux, 1] = ind_specie(offspring)
else:
idx_aux = np.searchsorted(Matrix_specie[:, 0],
funcEval.cont_evalp)
try:
Matrix_specie[idx_aux, 1] = ind_specie(offspring)
except IndexError:
Matrix_specie[-1, 1] = ind_specie(offspring)
np.savetxt('./Specie/%s/specist_%d_%d.txt' %
(problem, num_p, n_corr),
Matrix_specie,
delimiter=";",
fmt="%s")
population[:] = offspring # population update
cond_ind = 0
cont_better = 0
if funcEval.LS_flag:
for ind in population:
ind.LS_applied_set(0)
if LS_select == 1:
trees_h(population, num_p, n_corr, pset, direccion, problem,
benchmark_flag)
elif LS_select == 2:
best_specie(population, num_p, n_corr, pset, direccion,
problem, benchmark_flag)
elif LS_select == 3:
specie_h(population, num_p, n_corr, pset, direccion, problem,
benchmark_flag)
elif LS_select == 4:
best_pop_ls(population, num_p, n_corr, pset, direccion,
problem, benchmark_flag)
elif LS_select == 5:
all_pop(population, num_p, n_corr, pset, direccion, problem,
benchmark_flag)
elif LS_select == 6:
trees_h_wo(population, num_p, n_corr, pset, direccion, problem,
benchmark_flag)
elif LS_select == 7:
ls_bestset(population, num_p, n_corr, pset, direccion, problem,
benchmark_flag)
elif LS_select == 8:
ls_random(population, num_p, n_corr, pset, direccion, problem,
benchmark_flag)
elif LS_select == 9:
ls_randbestset(population, num_p, n_corr, pset, direccion,
problem, benchmark_flag)
#
invalid_ind = [ind for ind in population]
new_invalid_ind = []
for ind in population:
strg = ind.__str__()
l_strg = add_subt(strg, ind)
c = tree2f()
cd = c.convert(l_strg)
new_invalid_ind.append(cd)
fitness_ls = toolbox.map(toolbox.evaluate, new_invalid_ind)
print 'Fitness comp.:',
for ind, ls_fit in zip(invalid_ind, fitness_ls):
if ind.LS_applied_get() == 1:
cond_ind += 1
if ind.fitness.values[0] < ls_fit:
print '-',
elif ind.fitness.values[0] > ls_fit:
cont_better += 1
print '+',
elif ind.fitness.values[0] == ls_fit:
print '=',
funcEval.cont_evalp += 1
pop_file.write(
'\n%s;%s;%s;%s;%s;%s;%s;%s' %
(gen, ind.fitness.values[0], ls_fit, ind.LS_applied_get(),
ind, [x for x in ind.get_parent()] if ind.get_parent()
is not None else [], [x for x in ind.get_params()
], ind.get_id()))
ind.fitness.values = ls_fit
print ''
#for ind in population:
else:
for ind in population:
pop_file.write('\n%s;%s;%s;%s;%s;%s;%s' %
(gen, ind.fitness.values[0],
ind.LS_applied_get(), ind.LS_story_get(),
ind.off_cx_get(), ind.off_mut_get(), ind))
best_ind = best_pop(population)
if funcEval.LS_flag:
strg = best_ind.__str__()
l_strg = add_subt(strg, best_ind)
c = tree2f()
cd = c.convert(l_strg)
new_invalid_ind.append(cd)
bestind.write('\n%s;%s;%s' % (gen, best_ind.fitness.values[0], cd))
toolbox.map(toolbox.evaluate_best_t, [cd])
if testing:
fit_best = toolbox.map(toolbox.evaluate_best, [cd])
best_ind.fitness_test.values = fit_best[0]
best.write(
'\n%s;%s;%s;%s;%s;%s;%s' %
(gen, funcEval.cont_evalp, best_ind.fitness.values[0],
best_ind.LS_fitness_get(),
best_ind.fitness_test.values[0], len(best_ind),
avg_nodes(population)))
else:
best.write(
'\n%s;%s;%s;%s;%s;%s;%s' %
(gen, funcEval.cont_evalp, best_ind.fitness.values[0],
best_ind.LS_fitness_get(), None, len(best_ind),
avg_nodes(population)))
out.write('\n%s;%s;%s;%s;%s;%s' %
(gen, len(best_ind), best_ind.LS_applied_get(),
best_ind.get_params(), cd, best_ind))
else:
toolbox.map(toolbox.evaluate_best_t, [best_ind])
if testing:
fitnesses_test = toolbox.map(toolbox.evaluate_best, [best_ind])
best_ind.fitness_test.values = fitnesses_test[0]
best.write(
'\n%s;%s;%s;%s;%s;%s' %
(gen, funcEval.cont_evalp, best_ind.fitness_test.values[0],
best_ind.fitness.values[0], len(best_ind),
avg_nodes(population)))
else:
best.write('\n%s;%s;%s;%s;%s;%s' %
(gen, funcEval.cont_evalp, None,
best_ind.fitness.values[0], len(best_ind),
avg_nodes(population)))
bestind.write('\n%s;%s;%s' %
(gen, best_ind.fitness.values[0], best_ind))
out.write('\n%s;%s;%s' % (gen, len(best_ind), best_ind))
if funcEval.LS_flag:
print 'Num. LS:', cond_ind
print 'Ind. Improvement:', cont_better
print 'Best Ind. LS:', best_ind.LS_applied_get()
print 'Best Ind.:', best_ind
print 'Best Fitness:', best_ind.fitness.values[0]
if testing:
print 'Test fitness:', best_ind.fitness_test.values[0]
print 'Avg Nodes:', avg_nodes(population)
print 'Evaluations: ', funcEval.cont_evalp
if SaveMatrix:
data_pop = avg_nodes(population)
if GenMatrix:
idx_aux = np.searchsorted(Matrix[:, 0], gen)
Matrix[idx_aux, 1] = best_ind.fitness.values[0]
if testing:
Matrix[idx_aux, 2] = best_ind.fitness_test.values[0]
else:
Matrix[idx_aux, 2] = None
Matrix[idx_aux, 3] = len(best_ind)
Matrix[idx_aux, 4] = data_pop[0]
Matrix[idx_aux, 5] = gen
Matrix[idx_aux, 6] = 1
Matrix[idx_aux, 7] = data_pop[1] # max nodes
Matrix[idx_aux, 8] = data_pop[2] # min nodes
if neat_alg:
Matrix[idx_aux, 9] = best_ind.get_specie()
Matrix[idx_aux, 10] = max(ind_specie(population),
key=lambda x: x[0])[0]
else:
if funcEval.cont_evalp >= cont_evalf:
num_c -= 1
idx_aux = num_c
Matrix[num_c, 1] = best_ind.fitness.values[0]
if testing:
Matrix[num_c, 2] = best_ind.fitness_test.values[0]
else:
Matrix[num_c, 2] = None
Matrix[num_c, 3] = len(best_ind)
Matrix[num_c, 4] = data_pop[0]
Matrix[num_c, 5] = gen
Matrix[num_c, 6] = 1
Matrix[num_c, 7] = data_pop[1] #max_nodes
Matrix[num_c, 8] = data_pop[2] #min nodes
if neat_alg:
Matrix[num_c, 9] = max(ind_specie(population),
key=lambda x: x[0])[0]
else:
idx_aux = np.searchsorted(Matrix[:, 0],
funcEval.cont_evalp)
Matrix[idx_aux, 1] = best_ind.fitness.values[0]
if testing:
Matrix[idx_aux, 2] = best_ind.fitness_test.values[0]
else:
Matrix[idx_aux, 2] = None
Matrix[idx_aux, 3] = len(best_ind)
Matrix[idx_aux, 4] = data_pop[0]
Matrix[idx_aux, 5] = gen
Matrix[idx_aux, 6] = 1
Matrix[idx_aux, 7] = data_pop[1] #max nodes
Matrix[idx_aux, 8] = data_pop[2] #min nodes
if neat_alg:
Matrix[idx_aux, 9] = max(ind_specie(population),
key=lambda x: x[0])[0]
id_it = idx_aux - 1
id_beg = 0
flag = True
flag2 = False
while flag:
if Matrix[id_it, 6] == 0:
id_it -= 1
flag2 = True
else:
id_beg = id_it
flag = False
if flag2:
x = Matrix[id_beg, 1:8]
Matrix[id_beg:idx_aux, 1:] = Matrix[id_beg, 1:]
np.savetxt('./Matrix/%s/idx_%d_%d.txt' % (problem, num_p, n_corr),
Matrix,
delimiter=",",
fmt="%s")
end_t = time.time()
if testing:
time_file.write(
'\n%s;%s;%s;%s;%s;%s' %
(gen, begin, end_t, str(round(end_t - begin, 2)),
best_ind.fitness.values[0], best_ind.fitness_test.values[0]))
else:
time_file.write('\n%s;%s;%s;%s;%s' %
(gen, begin, end_t, str(round(end_t - begin, 2)),
best_ind.fitness.values[0]))
# import convert_order
# convert_order.convert_(population)
return population, logbook, best_ind.fitness.values[
0], best_ind.fitness_test.values[0]
def GP_LS(population,
toolbox,
cxpb,
mutpb,
ngen,
LS_flag,
LS_select,
cont_evalf,
numsalto,
SaveMatrix,
GenMatrix,
pset,
n_corr,
num_p,
params,
direccion,
problem,
testing,
version,
benchmark_flag,
config,
stats=None,
halloffame=None,
verbose=__debug__):
"""This algorithm reproduce the simplest evolutionary algorithm in GP with a local search.
:param population: A list of individuals.
:param toolbox: A :class:`~deap.base.Toolbox` that contains the evolution
operators.
:param cxpb: The probability of mating two individuals.
:param mutpb: The probability of mutating an individual.
:param ngen: The number of generation.
:param LS_flag: wheter or not to use LocalSearchGP
:param LS_select: indicate the kind of selection to use the LSGP on the population.
:param cont_evalf: maximum number of evaluations
:param n_corr: run number just to write the txt file
:param p: problem number just to write the txt file
:param stats: A :class:`~deap.tools.Statistics` object that is updated
inplace, optional.
:param halloffame: A :class:`~deap.tools.HallOfFame` object that will
contain the best individuals, optional.
:param verbose: Whether or not to log the statistics.
:returns: The final population.
It uses :math:`\lambda = \kappa = \mu` and goes as follow.
It first initializes the population (:math:`P(0)`) by evaluating
every individual presenting an invalid fitness. Then, it enters the
evolution loop that begins by the selection of the :math:`P(g+1)`
population. Then the crossover operator is applied on a proportion of
:math:`P(g+1)` according to the *cxpb* probability, the resulting and the
untouched individuals are placed in :math:`P'(g+1)`. Thereafter, a
proportion of :math:`P'(g+1)`, determined by *mutpb*, is
mutated and placed in :math:`P''(g+1)`, the untouched individuals are
transferred :math:`P''(g+1)`. Finally, those new individuals are evaluated
and the evolution loop continues until *ngen* generations are completed.
Briefly, the operators are applied in the following order ::
evaluate(population)
for i in range(ngen):
offspring = select(population)
offspring = mate(offspring)
offspring = mutate(offspring)
evaluate(offspring)
population = offspring
This function expects :meth:`toolbox.mate`, :meth:`toolbox.mutate`,
:meth:`toolbox.select` and :meth:`toolbox.evaluate` aliases to be
registered in the toolbox.
.. Adapted from NGP-LS
https://github.com/saarahy/NGP-LS
"""
logbook = tools.Logbook()
logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])
#creating files to save data.
d = './Results/%s/pop_file_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
pop_file = open(d, 'a')
d = './Results/%s/bestind_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
best = open(d, 'w') # save data
d = './Results/%s/bestind_str_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
out = open(d, 'w')
d = './Timing/%s/pop_file_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
time_file = open(d, 'w')
d = './Results/%s/bestind_LStr_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
bestind = open(d, 'w')
d = './Matrix/%s/' % (problem)
ensure_dir(d)
begin = time.time()
if funcEval.LS_flag:
for ind in population:
sizep = len(ind) + 2
param_ones = np.ones(sizep)
param_ones[0] = 0
ind.params_set(param_ones)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = list(toolbox.map(toolbox.evaluate, invalid_ind))
for ind, fit in zip(invalid_ind, fitnesses):
funcEval.cont_evalp += 1
ind.fitness.values = fit
best_ind = best_pop(population) # best individual of the population
if testing:
fitnesst_best = list(toolbox.map(toolbox.evaluate_test, [best_ind]))
best_ind.fitness_test.values = fitnesst_best[0]
if testing:
best.write(
'\n%s;%s;%s;%s;%s;%s' %
(0, funcEval.cont_evalp, best_ind.fitness_test.values[0],
best_ind.fitness.values[0], len(best_ind), avg_nodes(population)))
else:
best.write('\n%s;%s;%s;%s;%s;%s' %
(0, funcEval.cont_evalp, None, best_ind.fitness.values[0],
len(best_ind), avg_nodes(population)))
data_pop = avg_nodes(population)
if funcEval.LS_flag == 1:
strg = best_ind.__str__()
l_strg = add_subt_cf(strg, args=[])
c = tree2f()
cd = c.convert(l_strg)
out.write('\n%s;%s;%s;%s;%s;%s' %
(0, len(best_ind), best_ind.LS_applied_get(),
best_ind.get_params(), cd, best_ind))
else:
out.write('\n%s;%s;%s' % (0, len(best_ind), best_ind))
for ind in population:
pop_file.write('\n%s;%s;%s' % (0, ind.fitness.values[0], ind))
print('---- Generation %d -----' % (0))
print('Problem: ', problem)
print('Problem No.: ', num_p)
print('Run No.: ', n_corr)
print('Local Search:', funcEval.LS_flag)
if funcEval.LS_flag:
ls_type = ''
if LS_select == 1:
ls_type = 'LSHS'
elif LS_select == 2:
ls_type = 'Best-Pop'
elif LS_select == 3:
ls_type = 'All-Pop'
elif LS_select == 4:
ls_type = 'LSHS-test'
elif LS_select == 5:
ls_type = 'Best set'
elif LS_select == 6:
ls_type = 'Random set'
elif LS_select == 7:
ls_type = "Best-Random set"
print('Local Search Heuristic: %s (%s)' % (LS_select, ls_type))
print('Best Ind.:', best_ind)
print('Best Fitness:', best_ind.fitness.values[0])
if testing:
print('Test fitness:', best_ind.fitness_test.values[0])
print('Avg Nodes:', avg_nodes(population))
print('Evaluations: ', funcEval.cont_evalp)
end_t = time.time()
# Begin the generational process
for gen in range(1, ngen + 1):
if not GenMatrix:
if funcEval.cont_evalp > cont_evalf:
break
begin = time.time()
print('---- Generation %d -----' % (gen))
print('Problem: ', problem)
print('Problem No.: ', num_p)
print('Run No.: ', n_corr)
print('Local Search:', funcEval.LS_flag)
if funcEval.LS_flag:
print('Local Search Heuristic: %s (%s)' % (LS_select, ls_type))
best_ind = copy.deepcopy(best_pop(population))
parents = toolbox.select(population, len(population))
begin_cx = time.time()
offspring = varOr(parents, toolbox, cxpb, mutpb)
end_cx = time.time()
#time_specie.write('\n%s;%s;%s;%s' % (0, begin_cx, end_cx, str(round(end_cx - begin_cx, 2))))
invalid_ind = [ind for ind in offspring]
if funcEval.LS_flag:
new_invalid_ind = []
for ind in invalid_ind:
strg = ind.__str__()
l_strg = add_subt(strg, ind)
c = tree2f()
cd = c.convert(l_strg)
new_invalid_ind.append(cd)
fitness_ls = toolbox.map(toolbox.evaluate, new_invalid_ind)
for ind, ls_fit in zip(invalid_ind, fitness_ls):
funcEval.cont_evalp += 1
ind.fitness.values = ls_fit
else:
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
funcEval.cont_evalp += 1
ind.fitness.values = fit
orderbyfit = sorted(offspring, key=lambda ind: ind.fitness.values)
if best_ind.fitness.values[0] <= orderbyfit[0].fitness.values[0]:
offspring[:] = [best_ind] + orderbyfit[:len(population) - 1]
population[:] = offspring # population update
cond_ind = 0
cont_better = 0
if funcEval.LS_flag:
for ind in population:
ind.LS_applied_set(0)
if LS_select == 1:
trees_h(population, num_p, n_corr, pset, direccion, problem,
benchmark_flag)
elif LS_select == 2:
best_pop_ls(population, num_p, n_corr, pset, direccion,
problem, benchmark_flag)
elif LS_select == 3:
all_pop(population, num_p, n_corr, pset, direccion, problem,
benchmark_flag)
elif LS_select == 4:
trees_h_wo(population, num_p, n_corr, pset, direccion, problem,
benchmark_flag)
elif LS_select == 5:
ls_bestset(population, num_p, n_corr, pset, direccion, problem,
benchmark_flag)
elif LS_select == 6:
ls_random(population, num_p, n_corr, pset, direccion, problem,
benchmark_flag)
elif LS_select == 7:
ls_randbestset(population, num_p, n_corr, pset, direccion,
problem, benchmark_flag)
#
invalid_ind = [ind for ind in population]
new_invalid_ind = []
for ind in population:
strg = ind.__str__()
l_strg = add_subt(strg, ind)
c = tree2f()
cd = c.convert(l_strg)
new_invalid_ind.append(cd)
fitness_ls = toolbox.map(toolbox.evaluate, new_invalid_ind)
print('Fitness comp.:'),
for ind, ls_fit in zip(invalid_ind, fitness_ls):
if ind.LS_applied_get() == 1:
cond_ind += 1
if ind.fitness.values[0] < ls_fit:
print('-'),
elif ind.fitness.values[0] > ls_fit:
cont_better += 1
print('+'),
elif ind.fitness.values[0] == ls_fit:
print('='),
funcEval.cont_evalp += 1
pop_file.write(
'\n%s;%s;%s;%s;%s;%s;%s;%s' %
(gen, ind.fitness.values[0], ls_fit, ind.LS_applied_get(),
ind, [], [x for x in ind.get_params()], []))
ind.fitness.values = ls_fit
print('')
#for ind in population:
else:
for ind in population:
pop_file.write('\n%s;%s;%s;%s;%s;%s;%s' %
(gen, ind.fitness.values[0],
ind.LS_applied_get(), ind.LS_story_get(),
ind.off_cx_get(), ind.off_mut_get(), ind))
best_ind = best_pop(population)
if funcEval.LS_flag:
strg = best_ind.__str__()
l_strg = add_subt(strg, best_ind)
c = tree2f()
cd = c.convert(l_strg)
new_invalid_ind.append(cd)
bestind.write('\n%s;%s;%s' % (gen, best_ind.fitness.values[0], cd))
toolbox.map(toolbox.evaluate_best_t, [cd])
if testing:
fit_best = list(toolbox.map(toolbox.evaluate_best, [cd]))
best_ind.fitness_test.values = fit_best[0]
best.write(
'\n%s;%s;%s;%s;%s;%s;%s' %
(gen, funcEval.cont_evalp, best_ind.fitness.values[0],
best_ind.LS_fitness_get(),
best_ind.fitness_test.values[0], len(best_ind),
avg_nodes(population)))
else:
best.write(
'\n%s;%s;%s;%s;%s;%s;%s' %
(gen, funcEval.cont_evalp, best_ind.fitness.values[0],
best_ind.LS_fitness_get(), None, len(best_ind),
avg_nodes(population)))
out.write('\n%s;%s;%s;%s;%s;%s' %
(gen, len(best_ind), best_ind.LS_applied_get(),
best_ind.get_params(), cd, best_ind))
else:
toolbox.map(toolbox.evaluate_best_t, [best_ind])
if testing:
fitnesses_test = toolbox.map(toolbox.evaluate_best, [best_ind])
best_ind.fitness_test.values = fitnesses_test[0]
best.write(
'\n%s;%s;%s;%s;%s;%s' %
(gen, funcEval.cont_evalp, best_ind.fitness_test.values[0],
best_ind.fitness.values[0], len(best_ind),
avg_nodes(population)))
else:
best.write('\n%s;%s;%s;%s;%s;%s' %
(gen, funcEval.cont_evalp, None,
best_ind.fitness.values[0], len(best_ind),
avg_nodes(population)))
bestind.write('\n%s;%s;%s' %
(gen, best_ind.fitness.values[0], best_ind))
out.write('\n%s;%s;%s' % (gen, len(best_ind), best_ind))
if funcEval.LS_flag:
print('Num. LS:', cond_ind)
print('Ind. Improvement:', cont_better)
print('Best Ind. LS:', best_ind.LS_applied_get())
print('Best Ind.:', best_ind)
print('Best Fitness:', best_ind.fitness.values[0])
if testing:
print('Test fitness:', best_ind.fitness_test.values[0])
print('Avg Nodes:', avg_nodes(population))
print('Evaluations: ', funcEval.cont_evalp)
end_t = time.time()
if testing:
time_file.write(
'\n%s;%s;%s;%s;%s;%s' %
(gen, begin, end_t, str(round(end_t - begin, 2)),
best_ind.fitness.values[0], best_ind.fitness_test.values[0]))
else:
time_file.write('\n%s;%s;%s;%s;%s' %
(gen, begin, end_t, str(round(end_t - begin, 2)),
best_ind.fitness.values[0]))
return population, logbook
def neat_GP( population, toolbox, cxpb, mutpb, ngen, neat_alg, neat_cx, neat_h, neat_pelit, n_corr, num_p, params, problem, stats=None,
halloffame=None, verbose=__debug__):
"""This algorithm reproduce the simplest evolutionary algorithm as
presented in chapter 7 of [Back2000]_.
:param population: A list of individuals.
:param toolbox: A :class:`~deap.base.Toolbox` that contains the evolution
operators.
:param cxpb: The probability of mating two individuals.
:param mutpb: The probability of mutating an individual.
:param ngen: The number of generation.
:param neat_alg: wheter or not to use species stuff.
:param neat_cx: wheter or not to use neatGP cx
:param neat_h: indicate the distance allowed between each specie
:param neat_pelit: probability of being elitist, it's used in the neat cx and mutation
:param n_corr: run number just to wirte the txt file
:param num_p: problem number just to wirte the txt file
:param params:indicate the params for the fitness sharing, the diffetent
options are:
-DontPenalize(str): 'best_specie' or 'best_of_each_specie'
-Penalization_method(int):
1.without penalization
2.penalization fitness sharing
3.new penalization
-ShareFitness(str): 'yes' or 'no'
:param problem: (str) name of the problem.
:param stats: A :class:`~deap.tools.Statistics` object that is updated
inplace, optional.
:param halloffame: A :class:`~deap.tools.HallOfFame` object that will
contain the best individuals, optional.
:param verbose: Whether or not to log the statistics.
:returns: The final population.
It uses :math:`\lambda = \kappa = \mu` and goes as follow.
It first initializes the population (:math:`P(0)`) by evaluating
every individual presenting an invalid fitness. Then, it enters the
evolution loop that begins by the selection of the :math:`P(g+1)`
population. Then the crossover operator is applied on a proportion of
:math:`P(g+1)` according to the *cxpb* probability, the resulting and the
untouched individuals are placed in :math:`P'(g+1)`. Thereafter, a
proportion of :math:`P'(g+1)`, determined by *mutpb*, is
mutated and placed in :math:`P''(g+1)`, the untouched individuals are
transferred :math:`P''(g+1)`. Finally, those new individuals are evaluated
and the evolution loop continues until *ngen* generations are completed.
Briefly, the operators are applied in the following order ::
evaluate(population)
for i in range(ngen):
offspring = select(population)
offspring = mate(offspring)
offspring = mutate(offspring)
evaluate(offspring)
population = offspring
This function expects :meth:`toolbox.mate`, :meth:`toolbox.mutate`,
:meth:`toolbox.select` and :meth:`toolbox.evaluate` aliases to be
registered in the toolbox.
.. [Back2000] Back, Fogel and Michalewicz, "Evolutionary Computation 1 :
Basic Algorithms and Operators", 2000.
"""
logbook = tools.Logbook()
logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])
if neat_alg: # assign specie to each individual on the population
species(population,neat_h)
ind_specie(population)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# save data for the best individual
best = open('./Results/%s/bestind_%d_%d.txt'%(problem, num_p, n_corr), 'a')
best_st = open('./Results/%s/bestind_string_%d_%d.txt' % (problem, num_p, n_corr), 'a')
# take the best on the population
best_ind = best_pop(population)
fitnesst_best = toolbox.map(toolbox.evaluate_test, [best_ind])
best_ind.fitness_test.values=fitnesst_best[0]
best.write('\n%s;%s;%s;%s;%s' % (0, best_ind.fitness_test.values[0], best_ind.fitness.values[0], len(best_ind), avg_nodes(population)))
best_st.write('\n%s;%s' % (0, best_ind))
if neat_alg: # applying fitness sharing
SpeciesPunishment(population,params,neat_h)
if halloffame is not None:
halloffame.update(population)
record = stats.compile(population) if stats else {}
logbook.record(gen=0, nevals=len(invalid_ind), **record)
if verbose:
print logbook.stream
# Begin the generational process
for gen in range(1, ngen+1):
best_ind = copy.deepcopy(best_pop(population))
if neat_alg: # select set of parents
parents = p_selection(population, gen)
else:
parents = toolbox.select(population, len(population))
if neat_cx: # applying neat-crossover
n = len(parents)
mut = 1
cx = 1
offspring = neatGP(toolbox, parents, cxpb, mutpb, n, mut, cx, neat_pelit)
else:
offspring = varOr(parents, toolbox, cxpb, mutpb)
if neat_alg: # Assign species
specie_parents_child(parents, offspring, neat_h)
offspring[:] = parents+offspring
ind_specie(offspring)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
else:
invalid_ind = [ind for ind in offspring]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
orderbyfit = sorted(offspring, key=lambda ind: ind.fitness.values)
if best_ind.fitness.values[0] <= orderbyfit[0].fitness.values[0]:
offspring[:] = [best_ind] + orderbyfit[:len(population) - 1]
if neat_alg:
SpeciesPunishment(offspring, params, neat_h)
# Update the hall of fame with the generated individuals
if halloffame is not None:
halloffame.update(offspring)
# Replace the current population by the offspring
population[:] = offspring
# Append the current generation statistics to the logbook
record = stats.compile(population) if stats else {}
logbook.record(gen=gen, nevals=len(population), **record)
if verbose:
print logbook.stream
best_ind = best_pop(population)
fitnesses_test = toolbox.map(toolbox.evaluate_test, [best_ind])
best_ind.fitness_test.values = fitnesses_test[0]
best.write('\n%s;%s;%s;%s;%s'%(gen, best_ind.fitness_test.values[0], best_ind.fitness.values[0], len(best_ind), avg_nodes(population)))
best_st.write('\n%s;%s' % (gen, best_ind))
return population, logbook
def neat_GP_LS(population, toolbox, cxpb, mutpb, ngen, neat_alg, neat_cx, neat_h,neat_pelit, LS_flag, LS_select, cont_evalf,
num_salto, SaveMatrix, GenMatrix, pset,n_corr, num_p, params, direccion, problem, testing, version,
stats=None, halloffame=None, verbose=__debug__):
"""This algorithm reproduce the simplest evolutionary algorithm as
presented in chapter 7 of [Back2000]_.
:param population: A list of individuals.
:param toolbox: A :class:`~deap.base.Toolbox` that contains the evolution
operators.
:param cxpb: The probability of mating two individuals.
:param mutpb: The probability of mutating an individual.
:param ngen: The number of generation.
:param neat_alg: wheter or not to use species stuff.
:param neat_cx: wheter or not to use neat-crossover
:param neat_h: indicate the distance allowed between each specie
:param neat_pelit: probability of being elitist, it's used in the neat cx and mutation
:param LS_flag: wheter or not to use GP-LS
:param LS_select: indicate the heuristic to select individuals for the LS method.
LS_select == 1:'LSHS' -- Heurisitic proposed by Z-Flores (2015)
LS_select == 2:'Best-Sp' -- Best individual of the specie
LS_select == 3:'LSHS-Sp' -- Heuristic 1 in each specie
LS_select == 4:'Best-Pop' -- Best ind of the population
LS_select == 5:'All-Pop' -- All population
LS_select == 6:'LSHS-test' -- Heuristic 1 only in the test data
LS_select == 7:'Best set' -- Best individuals set
LS_select == 8:'Random set' -- Random individuals set
LS_select == 9:'Best-Random set' -- Best individual set and then random selection of this individuals
:param cont_evalf: Counter of the function evaluations
:param num_salto: This is a parameter to save data in the Matrix, indicates the range for each row
:param SaveMatrix: wheter or not to save data on a Matrix
:param GenMatrix: wheter or not to save data in the Matrix on a generations form or function evals form
:param pset: this is the primitive set
:param n_corr: run number just to write the txt file
:param num_p: problem number just to write the txt file
:param params:indicate the params for the fitness sharing, the different
options are:
-DontPenalize(str): 'best_specie' or 'best_of_each_specie'
-Penalization_method(int):
1.without penalization
2.penalization fitness sharing
3.new penalization
-ShareFitness(str): 'yes' or 'no'
:param stats: A :class:`~deap.tools.Statistics` object that is updated
inplace, optional.
:param direccion: Path to find the training data. This parameter works in the g_address.py file.
:param problem: Name of the problem. Save and Get data.
:param testing: Wheter or not to use testing data.
:param version: Number of the version to make the speciation.
:param halloffame: A :class:`~deap.tools.HallOfFame` object that will
contain the best individuals, optional.
:param verbose: Whether or not to log the statistics.
:returns: The final population.
It uses :math:`\lambda = \kappa = \mu` and goes as follow.
It first initializes the population (:math:`P(0)`) by evaluating
every individual presenting an invalid fitness. Then, it enters the
evolution loop that begins by the selection of the :math:`P(g+1)`
population. Then the crossover operator is applied on a proportion of
:math:`P(g+1)` according to the *cxpb* probability, the resulting and the
untouched individuals are placed in :math:`P'(g+1)`. Thereafter, a
proportion of :math:`P'(g+1)`, determined by *mutpb*, is
mutated and placed in :math:`P''(g+1)`, the untouched individuals are
transferred :math:`P''(g+1)`. Finally, those new individuals are evaluated
and the evolution loop continues until *ngen* generations are completed.
Briefly, the operators are applied in the following order ::
evaluate(population)
for i in range(ngen):
offspring = select(population)
offspring = mate(offspring)
offspring = mutate(offspring)
evaluate(offspring)
population = offspring
This function expects :meth:`toolbox.mate`, :meth:`toolbox.mutate`,
:meth:`toolbox.select` and :meth:`toolbox.evaluate` aliases to be
registered in the toolbox.
.. [Back2000] Back, Fogel and Michalewicz, "Evolutionary Computation 1 :
Basic Algorithms and Operators", 2000.
"""
logbook = tools.Logbook()
logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])
# creating files to save data.
d = './Results/%s/pop_file_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
pop_file = open(d, 'a')
d = './Results/%s/bestind_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
best = open(d, 'w')
d = './Results/%s/bestind_str_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
out = open(d, 'w')
d='./Timing/%s/pop_file_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
time_file = open(d, 'w')
d = './Timing/%s/specie_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
time_specie = open(d, 'w')
d = './Timing/%s/cruce_s_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
time_cx = open(d, 'w')
d = './Specie/%s/specieind_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
specie_file = open(d, 'w')
d = './Specie/%s/specist_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
specie_statis = open(d, 'w')
d = './Results/%s/bestind_LStr_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
bestind = open(d, 'w')
begin = time.time()
if SaveMatrix: # Saving data in matrix
num_r = 11
if GenMatrix: # To save the data in matrix by generations
num_salto = 1
num_c = ngen+1
Matrix = np.empty((num_c, num_r,))
vector = np.arange(0, num_c, num_salto)
else: # To save the data in matrix by function evaluations
num_c = (cont_evalf/num_salto) + 1
Matrix = np.empty((num_c, num_r,))
vector = np.arange(1, cont_evalf+num_salto, num_salto)
for i in range(len(vector)):
Matrix[i, 0] = vector[i]
Matrix[:, 6] = 0.
begin_sp = time.time() # Saving data: speciaton init timing
if neat_alg: # before version 3
for ind in population:
level_info = level_node(ind)
ind.nodefeat_set(level_info)
species(population, neat_h, version)
end_sp = time.time() # Saving data: speciaton end timing
time_specie.write('\n%s;%s;%s;%s' % (0, begin_sp, end_sp, str(round(end_sp - begin_sp, 2)))) # Saving data in file
specie_file.write('\n-------')
for ind in population:
specie_file.write('\n%s;%s;%s' % (ind.get_specie(),ind,version))
# Adding parameters for the LS algorithms
if funcEval.LS_flag:
for ind in population:
sizep = len(ind)+2
param_ones = np.ones(sizep)
param_ones[0] = 0
ind.params_set(param_ones)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
funcEval.cont_evalp += 1
ind.fitness.values = fit
best_ind = best_pop(population) # best individual of the population
if testing:
fitnesst_best = toolbox.map(toolbox.evaluate_test, [best_ind])
best_ind.fitness_test.values = fitnesst_best[0]
best.write('\n%s;%s;%s;%s;%s;%s' % (0, funcEval.cont_evalp, best_ind.fitness_test.values[0], best_ind.fitness.values[0], len(best_ind), avg_nodes(population)))
else:
best.write('\n%s;%s;%s;%s;%s;%s' % (
0, funcEval.cont_evalp, None, best_ind.fitness.values[0], len(best_ind),
avg_nodes(population)))
data_pop = avg_nodes(population)
if SaveMatrix:
idx = 0
Matrix[idx, 1] = best_ind.fitness.values[0] # best ind train data
if testing:
Matrix[idx, 2] = best_ind.fitness_test.values[0] # best ind test data
else:
Matrix[idx, 2] = None
Matrix[idx, 3] = len(best_ind) # best individual size (number of nodes)
Matrix[idx, 4] = data_pop[0] # avg size of the population
Matrix[idx, 5] = 0.
Matrix[idx, 6] = 1 # id to know if the current row is full
Matrix[idx, 7] = data_pop[1] # max size of the population
Matrix[idx, 8] = data_pop[2] # min size of the population
Matrix[idx, 9] = best_ind.get_specie() # specie of the best individual
Matrix[idx, 10] = max(ind_specie(population), key=lambda x: x[0])[0] # max number of species on current pop
np.savetxt('./Matrix/%s/idx_%d_%d.txt' % (problem,num_p, n_corr), Matrix, delimiter=",", fmt="%s")
if neat_alg:
SpeciesPunishment(population,params,neat_h)
if funcEval.LS_flag == 1:
strg = best_ind.__str__()
l_strg = add_subt_cf(strg, args=[])
c = tree2f()
cd = c.convert(l_strg)
out.write('\n%s;%s;%s;%s;%s;%s' % (0, len(best_ind), best_ind.LS_applied_get(), best_ind.get_params(), cd, best_ind))
else:
out.write('\n%s;%s;%s' % (0, len(best_ind), best_ind))
for ind in population:
pop_file.write('\n%s;%s'%(ind.fitness.values[0], ind))
ls_type = ''
if LS_select == 1:
ls_type = 'LSHS'
elif LS_select == 2:
ls_type = 'Best-Sp'
elif LS_select == 3:
ls_type = 'LSHS-Sp'
elif LS_select == 4:
ls_type = 'Best-Pop'
elif LS_select == 5:
ls_type = 'All-Pop'
elif LS_select == 6:
ls_type = 'LSHS-test'
elif LS_select == 7:
ls_type = 'Best set'
elif LS_select == 8:
ls_type = 'Random set'
elif LS_select == 9:
ls_type = 'Best-Random set'
################################
# Printing data
################################
print '---- Generation %d -----' % (0)
print 'Problem: ', problem
print 'Problem No.: ', num_p
print 'Run No.: ', n_corr
print 'neat-GP:', neat_alg
print 'neat-cx:', neat_cx
print 'Local Search:', funcEval.LS_flag
if funcEval.LS_flag:
print 'Local Search Heuristic: %s (%s)' % (LS_select,ls_type)
print 'Best Ind.:', best_ind
print 'Best Fitness:', best_ind.fitness.values[0]
if testing:
print 'Test fitness:', best_ind.fitness_test.values[0]
print 'Avg Nodes:', avg_nodes(population)
print 'Evaluations: ', funcEval.cont_evalp
##################################
end_t = time.time()
specie_statis.write('\n%s;%s' % (0, count_species(population)))
if testing:
time_file.write('\n%s;%s;%s;%s;%s;%s' % (0, begin,end_t, str(round(end_t - begin, 2)), best_ind.fitness.values[0], best_ind.fitness_test.values[0]))
else:
time_file.write('\n%s;%s;%s;%s;%s' % (
0, begin, end_t, str(round(end_t - begin, 2)), best_ind.fitness.values[0]))
# Begin the generational process
for gen in range(1, ngen+1):
if not GenMatrix:
if funcEval.cont_evalp > cont_evalf:
break
begin = time.time()
print '---- Generation %d -----' % (gen)
print 'Problem: ', problem
print 'Problem No.: ', num_p
print 'Run No.: ', n_corr
print 'neat-GP:', neat_alg
print 'neat-cx:', neat_cx
print 'Local Search:', funcEval.LS_flag
if funcEval.LS_flag:
print 'Local Search Heuristic: %s (%s)' % (LS_select, ls_type)
best_ind = copy.deepcopy(best_pop(population))
if neat_alg:
parents = p_selection(population, neat_pelit)
else:
parents = toolbox.select(population, len(population))
begin_cx = time.time()
if neat_cx and neat_alg: # neat-Crossover
n = len(parents)
mut = 1
cx = 1
offspring = neatGP(toolbox, parents, cxpb, mutpb, n, mut, cx, neat_pelit)
else:
offspring = varOr(parents, toolbox, cxpb, mutpb)
end_cx = time.time()
time_specie.write('\n%s;%s;%s;%s' % (0, begin_cx, end_cx, str(round(end_sp - begin_sp, 2))))
if neat_alg: # Speciation of the descendants and fitness evaluation
begin_sp = time.time()
specie_parents_child(parents,offspring, neat_h, version)
offspring[:] = parents+offspring
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
funcEval.cont_evalp += 1
ind.fitness.values = fit
end_sp = time.time()
time_specie.write('\n%s;%s;%s;%s' % (gen, begin_sp, end_sp, str(round(end_sp - begin_sp, 2))))
else: # evaluation of descendants
invalid_ind = [ind for ind in offspring]
if funcEval.LS_flag: # evaluating with the parameters set
new_invalid_ind = []
for ind in invalid_ind:
strg = ind.__str__()
l_strg = add_subt(strg, ind)
c = tree2f()
cd = c.convert(l_strg)
new_invalid_ind.append(cd)
fitness_ls = toolbox.map(toolbox.evaluate, new_invalid_ind)
for ind, ls_fit in zip(invalid_ind, fitness_ls):
funcEval.cont_evalp += 1
ind.fitness.values = ls_fit
else: # normal evaluation
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
funcEval.cont_evalp += 1
ind.fitness.values = fit
orderbyfit = sorted(offspring, key=lambda ind:ind.fitness.values)
#print len(orderbyfit),len(best_ind)
# Applying elitism: Best individual survives
if best_ind.fitness.values[0] <= orderbyfit[0].fitness.values[0]:
offspring[:] = [best_ind]+orderbyfit[:len(population)-1]
if neat_alg:
SpeciesPunishment(offspring, params, neat_h)
specie_statis.write('\n%s;%s' % (gen, ind_specie(offspring)))
population[:] = offspring # population update
specie_file.write('\n%s--------------------------------' % gen)
if neat_alg:
for ind in population:
specie_file.write('\n%s;%s;%s' % (ind.get_specie(), ind, version))
cond_ind = 0
cont_better = 0
if funcEval.LS_flag:
for ind in population:
ind.LS_applied_set(0)
if LS_select == 1:
trees_h(population, num_p, n_corr, pset, direccion, problem)
elif LS_select == 2:
best_specie(population, num_p, n_corr, pset, direccion, problem)
elif LS_select == 3:
specie_h(population, num_p, n_corr, pset, direccion, problem)
elif LS_select == 4:
best_pop_ls(population, num_p, n_corr, pset, direccion, problem)
elif LS_select == 5:
all_pop(population, num_p, n_corr, pset, direccion, problem)
elif LS_select == 6:
trees_h_wo(population, num_p, n_corr, pset, direccion, problem)
elif LS_select == 7:
ls_bestset(population, num_p, n_corr, pset, direccion, problem)
elif LS_select == 8:
ls_random(population, num_p, n_corr, pset, direccion, problem)
elif LS_select == 9:
ls_randbestset(population, num_p, n_corr, pset, direccion, problem)
invalid_ind = [ind for ind in population]
new_invalid_ind = []
for ind in population:
strg = ind.__str__()
l_strg = add_subt(strg, ind)
c = tree2f()
cd = c.convert(l_strg)
new_invalid_ind.append(cd)
fitness_ls = toolbox.map(toolbox.evaluate, new_invalid_ind)
print 'Fitness comp.:',
# Information about how goes the optimization
for ind, ls_fit in zip(invalid_ind, fitness_ls):
if ind.LS_applied_get() == 1:
cond_ind += 1
if ind.fitness.values[0] < ls_fit:
print '-',
elif ind.fitness.values[0] > ls_fit:
cont_better += 1
print '+',
elif ind.fitness.values[0] == ls_fit:
print '=',
funcEval.cont_evalp += 1
ind.fitness.values = ls_fit
print ''
pop_file.write('\n----------------------------------------%s'%(gen))
for ind in population:
pop_file.write('\n%s;%s;%s;%s'%(ind.LS_applied_get(),ind.fitness.values[0], ind, [x for x in ind.get_params()]))
else:
pop_file.write('\n----------------------------------------')
for ind in population:
pop_file.write('\n%s;%s;%s;%s;%s;%s'%(ind.LS_applied_get(),ind.LS_story_get(),ind.off_cx_get(),ind.off_mut_get(),ind.fitness.values[0], ind))
best_ind = best_pop(population)
if funcEval.LS_flag:
strg = best_ind.__str__()
l_strg = add_subt(strg, best_ind)
c = tree2f()
cd = c.convert(l_strg)
new_invalid_ind.append(cd)
bestind.write('\n%s;%s;%s' % (gen, best_ind.fitness.values[0],cd))
if testing:
fit_best = toolbox.map(toolbox.evaluate_test, [cd])
best_ind.fitness_test.values = fit_best[0]
best.write('\n%s;%s;%s;%s;%s;%s;%s' % (gen, funcEval.cont_evalp, best_ind.fitness.values[0], best_ind.LS_fitness_get(), best_ind.fitness_test.values[0], len(best_ind), avg_nodes(population)))
else:
best.write('\n%s;%s;%s;%s;%s;%s;%s' % (
gen, funcEval.cont_evalp, best_ind.fitness.values[0], best_ind.LS_fitness_get(),
None, len(best_ind), avg_nodes(population)))
out.write('\n%s;%s;%s;%s;%s;%s' % (gen, len(best_ind), best_ind.LS_applied_get(), best_ind.get_params(), cd, best_ind))
else:
if testing:
fitnesses_test = toolbox.map(toolbox.evaluate_test, [best_ind])
best_ind.fitness_test.values = fitnesses_test[0]
best.write('\n%s;%s;%s;%s;%s;%s' % (gen, funcEval.cont_evalp, best_ind.fitness_test.values[0], best_ind.fitness.values[0], len(best_ind), avg_nodes(population)))
else:
best.write('\n%s;%s;%s;%s;%s;%s' % (
gen, funcEval.cont_evalp, None, best_ind.fitness.values[0], len(best_ind),
avg_nodes(population)))
bestind.write('\n%s;%s;%s' % (gen, best_ind.fitness.values[0], best_ind))
out.write('\n%s;%s;%s' % (gen, len(best_ind), best_ind))
if funcEval.LS_flag:
print 'Num. LS:', cond_ind
print 'Ind. Improvement:', cont_better
print 'Best Ind. LS:', best_ind.LS_applied_get()
print 'Best Ind.:', best_ind
print 'Best Fitness:', best_ind.fitness.values[0]
if testing:
print 'Test fitness:',best_ind.fitness_test.values[0]
print 'Avg Nodes:', avg_nodes(population)
print 'Evaluations: ', funcEval.cont_evalp
if SaveMatrix:
data_pop=avg_nodes(population)
if GenMatrix:
idx_aux = np.searchsorted(Matrix[:, 0], gen)
Matrix[idx_aux, 1] = best_ind.fitness.values[0]
if testing:
Matrix[idx_aux, 2] = best_ind.fitness_test.values[0]
else:
Matrix[idx_aux, 2] = None
Matrix[idx_aux, 3] = len(best_ind)
Matrix[idx_aux, 4] = data_pop[0]
Matrix[idx_aux, 5] = gen
Matrix[idx_aux, 6] = 1
Matrix[idx_aux, 7] = data_pop[1] # max nodes
Matrix[idx_aux, 8] = data_pop[2] # min nodes
if neat_alg:
Matrix[idx_aux, 9] = best_ind.get_specie()
Matrix[idx_aux, 10] = max(ind_specie(population), key=lambda x: x[0])[0]
else:
if funcEval.cont_evalp >= cont_evalf:
num_c -= 1
idx_aux = num_c
Matrix[num_c, 1] = best_ind.fitness.values[0]
if testing:
Matrix[num_c, 2] = best_ind.fitness_test.values[0]
else:
Matrix[num_c, 2] = None
Matrix[num_c, 3] = len(best_ind)
Matrix[num_c, 4] = data_pop[0]
Matrix[num_c, 5] = gen
Matrix[num_c, 6] = 1
Matrix[num_c, 7] = data_pop[1] # max_nodes
Matrix[num_c, 8] = data_pop[2] # min nodes
if neat_alg:
Matrix[num_c, 9] = max(ind_specie(population), key=lambda x: x[0])[0]
else:
idx_aux = np.searchsorted(Matrix[:, 0], funcEval.cont_evalp)
Matrix[idx_aux, 1] = best_ind.fitness.values[0]
if testing:
Matrix[idx_aux, 2] = best_ind.fitness_test.values[0]
else:
Matrix[idx_aux, 2] = None
Matrix[idx_aux, 3] = len(best_ind)
Matrix[idx_aux, 4] = data_pop[0]
Matrix[idx_aux, 5] = gen
Matrix[idx_aux, 6] = 1
Matrix[idx_aux, 7] = data_pop[1] # max nodes
Matrix[idx_aux, 8] = data_pop[2] # min nodes
if neat_alg:
Matrix[idx_aux, 9] = max(ind_specie(population), key=lambda x: x[0])[0]
id_it = idx_aux-1
id_beg = 0
flag = True
flag2 = False
while flag:
if Matrix[id_it, 6] == 0:
id_it -= 1
flag2 = True
else:
id_beg = id_it
flag = False
if flag2:
x = Matrix[id_beg, 1:8]
Matrix[id_beg:idx_aux, 1:] = Matrix[id_beg, 1:]
np.savetxt('./Matrix/%s/idx_%d_%d.txt' % (problem, num_p, n_corr), Matrix, delimiter=",", fmt="%s")
end_t = time.time()
if testing:
time_file.write('\n%s;%s;%s;%s;%s;%s' % (gen, begin, end_t, str(round(end_t - begin, 2)), best_ind.fitness.values[0], best_ind.fitness_test.values[0]))
else:
time_file.write('\n%s;%s;%s;%s;%s' % (
gen, begin, end_t, str(round(end_t - begin, 2)), best_ind.fitness.values[0]))
return population, logbook
def evo_neat_GP_LS(population, toolbox, cxpb, mutpb, ngen, neat_alg, neat_cx, neat_h,neat_pelit, LS_flag, LS_select, cont_evalf, num_salto, SaveMatrix, GenMatrix, pset,n_corr, num_p, params, direccion, problem,stats=None,
halloffame=None, verbose=__debug__):
"""This algorithm reproduce the simplest evolutionary algorithm as
presented in chapter 7 of [Back2000]_.
:param population: A list of individuals.
:param toolbox: A :class:`~deap.base.Toolbox` that contains the evolution
operators.
:param cxpb: The probability of mating two individuals.
:param mutpb: The probability of mutating an individual.
:param ngen: The number of generation.
:param neat_alg: wheter or not to use species stuff.
:param neat_cx: wheter or not to use neatGP cx
:param neat_h: indicate the distance allowed between each specie
:param neat_pelit: probability of being elitist, it's used in the neat cx and mutation
:param LS_flag: wheter or not to use LocalSearchGP
:param LS_select: indicate the kind of selection to use the LSGP on the population.
:param cont_evalf: contador maximo del numero de evaluaciones
:param n_corr: run number just to wirte the txt file
:param p: problem number just to wirte the txt file
:param params:indicate the params for the fitness sharing, the diffetent
options are:
-DontPenalize(str): 'best_specie' or 'best_of_each_specie'
-Penalization_method(int):
1.without penalization
2.penalization fitness sharing
3.new penalization
-ShareFitness(str): 'yes' or 'no'
:param stats: A :class:`~deap.tools.Statistics` object that is updated
inplace, optional.
:param halloffame: A :class:`~deap.tools.HallOfFame` object that will
contain the best individuals, optional.
:param verbose: Whether or not to log the statistics.
:returns: The final population.
It uses :math:`\lambda = \kappa = \mu` and goes as follow.
It first initializes the population (:math:`P(0)`) by evaluating
every individual presenting an invalid fitness. Then, it enters the
evolution loop that begins by the selection of the :math:`P(g+1)`
population. Then the crossover operator is applied on a proportion of
:math:`P(g+1)` according to the *cxpb* probability, the resulting and the
untouched individuals are placed in :math:`P'(g+1)`. Thereafter, a
proportion of :math:`P'(g+1)`, determined by *mutpb*, is
mutated and placed in :math:`P''(g+1)`, the untouched individuals are
transferred :math:`P''(g+1)`. Finally, those new individuals are evaluated
and the evolution loop continues until *ngen* generations are completed.
Briefly, the operators are applied in the following order ::
evaluate(population)
for i in range(ngen):
offspring = select(population)
offspring = mate(offspring)
offspring = mutate(offspring)
evaluate(offspring)
population = offspring
This function expects :meth:`toolbox.mate`, :meth:`toolbox.mutate`,
:meth:`toolbox.select` and :meth:`toolbox.evaluate` aliases to be
registered in the toolbox.
.. [Back2000] Back, Fogel and Michalewicz, "Evolutionary Computation 1 :
Basic Algorithms and Operators", 2000.
"""
logbook = tools.Logbook()
logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])
pop_file = open('./Results/%s/pop_file_%d_%d.txt' % (problem, num_p, n_corr), 'a')
if SaveMatrix: # Saving data in matrix
num_r = 9
if GenMatrix:
num_salto=1
num_c=ngen+1
Matrix= np.empty((num_c, num_r,))
vector = np.arange(0, num_c, num_salto)
else:
num_c = (cont_evalf/num_salto) + 1
Matrix = np.empty((num_c, num_r,))
vector = np.arange(1, cont_evalf+num_salto, num_salto)
for i in range(len(vector)):
Matrix[i, 0] = vector[i]
#num_r-1
Matrix[:, 6] = 0.
#Creation of the species
# if neat_alg:
# species(population,neat_h)
# ind_specie(population)
if funcEval.LS_flag:
for ind in population:
sizep = len(ind)+2
param_ones = np.ones(sizep)
param_ones[0] = 0
ind.params_set(param_ones)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
funcEval.cont_evalp += 1
ind.fitness.values = fit
best = open('./Results/%s/bestind_%d_%d.txt' % (problem, num_p, n_corr), 'a') # save data
best_ind = best_pop(population) # best individual of the population
fitnesst_best = toolbox.map(toolbox.evaluate_test, [best_ind])
best_ind.fitness_test.values = fitnesst_best[0]
best.write('\n%s;%s;%s;%s;%s;%s' % (0, funcEval.cont_evalp, best_ind.fitness_test.values[0], best_ind.fitness.values[0], len(best_ind), avg_nodes(population)))
data_pop=avg_nodes(population)
if SaveMatrix:
idx = 0
Matrix[idx, 1] = best_ind.fitness.values[0]
Matrix[idx, 2] = best_ind.fitness_test.values[0]
Matrix[idx, 3] = len(best_ind)
Matrix[idx, 4] = data_pop[0]
Matrix[idx, 5] = 0.
Matrix[idx, 6] = 1 # just an id to know if the current row is full
Matrix[idx, 7] = data_pop[1] # max size
Matrix[idx, 8] = data_pop[2] # min size
np.savetxt('./Matrix/%s/idx_%d_%d.txt' % (problem,num_p, n_corr), Matrix, delimiter=",", fmt="%s")
if neat_alg:
SpeciesPunishment(population,params,neat_h)
out = open('./Results/%s/bestind_str_%d_%d.txt' % (problem, num_p, n_corr), 'a')
if funcEval.LS_flag == 1:
strg = best_ind.__str__()
l_strg = add_subt_cf(strg, args=[])
c = tree2f()
cd = c.convert(l_strg)
out.write('\n%s;%s;%s;%s;%s;%s' % (0, len(best_ind), best_ind.LS_applied_get(), best_ind.get_params(), cd, best_ind))
else:
out.write('\n%s;%s;%s' % (0, len(best_ind), best_ind))
for ind in population:
pop_file.write('\n%s;%s'%(ind.fitness.values[0], ind))
ls_type = ''
if LS_select == 1:
ls_type = 'LSHS'
elif LS_select == 2:
ls_type = 'Best-Sp'
elif LS_select == 3:
ls_type = 'LSHS-Sp'
elif LS_select == 4:
ls_type = 'Best-Pop'
elif LS_select == 5:
ls_type = 'All-Pop'
elif LS_select == 6:
ls_type = 'LSHS-test'
elif LS_select == 7:
ls_type = 'Best set'
elif LS_select == 8:
ls_type = 'Random set'
elif LS_select == 9:
ls_type = "Best-Random set"
print '---- Generation %d -----' % (0)
print 'Problem: ', problem
print 'Problem No.: ', num_p
print 'Run No.: ', n_corr
print 'neat-GP:', neat_alg
print 'neat-cx:', neat_cx
print 'Local Search:', funcEval.LS_flag
if funcEval.LS_flag:
print 'Local Search Heuristic: %s (%s)' % (LS_select,ls_type)
print 'Best Ind.:', best_ind
print 'Best Fitness:', best_ind.fitness.values[0]
print 'Test fitness:',best_ind.fitness_test.values[0]
print 'Avg Nodes:', avg_nodes(population)
print 'Evaluations: ', funcEval.cont_evalp
# Begin the generational process
for gen in range(1, ngen+1):
if funcEval.cont_evalp > cont_evalf:
break
print '---- Generation %d -----' % (gen)
print 'Problem: ', problem
print 'Problem No.: ', num_p
print 'Run No.: ', n_corr
print 'neat-GP:', neat_alg
print 'neat-cx:', neat_cx
print 'Local Search:', funcEval.LS_flag
if funcEval.LS_flag:
print 'Local Search Heuristic: %s (%s)' % (LS_select, ls_type)
best_ind = copy.deepcopy(best_pop(population))
if neat_alg:
parents = p_selection(population, gen)
else:
parents = toolbox.select(population, len(population))
if neat_cx:
n = len(parents)
mut = 1
cx = 1
offspring = neatGP(toolbox, parents, cxpb, mutpb, n, mut, cx, neat_pelit)
else:
offspring = varOr(parents, toolbox, cxpb, mutpb)
if neat_alg:
specie_parents_child(parents,offspring, neat_h)
offspring[:] = parents+offspring
ind_specie(offspring)
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
funcEval.cont_evalp += 1
ind.fitness.values = fit
else:
invalid_ind = [ind for ind in offspring]
if funcEval.LS_flag:
new_invalid_ind = []
for ind in invalid_ind:
strg = ind.__str__()
l_strg = add_subt(strg, ind)
c = tree2f()
cd = c.convert(l_strg)
new_invalid_ind.append(cd)
fitness_ls = toolbox.map(toolbox.evaluate, new_invalid_ind)
for ind, ls_fit in zip(invalid_ind, fitness_ls):
funcEval.cont_evalp += 1
ind.fitness.values = ls_fit
else:
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
funcEval.cont_evalp += 1
ind.fitness.values = fit
orderbyfit = sorted(offspring, key=lambda ind:ind.fitness.values)
print len(orderbyfit),len(best_ind)
if best_ind.fitness.values[0] <= orderbyfit[0].fitness.values[0]:
offspring[:] = [best_ind]+orderbyfit[:len(population)-1]
if neat_alg:
SpeciesPunishment(offspring, params, neat_h)
population[:] = offspring # population update
cond_ind = 0
cont_better=0
if funcEval.LS_flag:
for ind in population:
ind.LS_applied_set(0)
if LS_select == 1:
trees_h(population, num_p, n_corr, pset, direccion)
elif LS_select == 2:
best_specie(population, num_p, n_corr, pset, direccion)
elif LS_select == 3:
specie_h(population, num_p, n_corr, pset, direccion)
elif LS_select == 4:
best_pop_ls(population, num_p, n_corr, pset, direccion)
elif LS_select == 5:
all_pop(population, num_p, n_corr, pset, direccion)
elif LS_select == 6:
trees_h_wo(population, num_p, n_corr, pset, direccion)
elif LS_select == 7:
ls_bestset(population, num_p, n_corr, pset, direccion)
elif LS_select == 8:
ls_random(population, num_p, n_corr, pset, direccion)
elif LS_select == 9:
ls_randbestset(population, num_p, n_corr, pset, direccion)
#
invalid_ind = [ind for ind in population]
new_invalid_ind = []
for ind in population:
strg = ind.__str__()
l_strg = add_subt(strg, ind)
c = tree2f()
cd = c.convert(l_strg)
new_invalid_ind.append(cd)
fitness_ls = toolbox.map(toolbox.evaluate, new_invalid_ind)
print 'Fitness comp.:',
for ind, ls_fit in zip(invalid_ind, fitness_ls):
if ind.LS_applied_get() == 1:
cond_ind += 1
if ind.fitness.values[0] < ls_fit:
print '-',
elif ind.fitness.values[0] > ls_fit:
cont_better += 1
print '+',
elif ind.fitness.values[0] == ls_fit:
print '=',
funcEval.cont_evalp += 1
ind.fitness.values = ls_fit
print ''
pop_file.write('\n----------------------------------------%s'%(gen))
for ind in population:
pop_file.write('\n%s;%s;%s;%s'%(ind.LS_applied_get(),ind.fitness.values[0], ind, [x for x in ind.get_params()]))
else:
pop_file.write('\n----------------------------------------')
for ind in population:
pop_file.write('\n%s;%s;%s;%s;%s;%s'%(ind.LS_applied_get(),ind.LS_story_get(),ind.off_cx_get(),ind.off_mut_get(),ind.fitness.values[0], ind))
best_ind = best_pop(population)
if funcEval.LS_flag:
strg = best_ind.__str__()
l_strg = add_subt(strg, best_ind)
c = tree2f()
cd = c.convert(l_strg)
new_invalid_ind.append(cd)
fit_best = toolbox.map(toolbox.evaluate_test, [cd])
best_ind.fitness_test.values = fit_best[0]
best.write('\n%s;%s;%s;%s;%s;%s;%s' % (gen, funcEval.cont_evalp, best_ind.fitness.values[0], best_ind.LS_fitness_get(), best_ind.fitness_test.values[0], len(best_ind), avg_nodes(population)))
out.write('\n%s;%s;%s;%s;%s;%s' % (gen, len(best_ind), best_ind.LS_applied_get(), best_ind.get_params(), cd, best_ind))
else:
fitnesses_test = toolbox.map(toolbox.evaluate_test, [best_ind])
best_ind.fitness_test.values = fitnesses_test[0]
best.write('\n%s;%s;%s;%s;%s;%s' % (gen, funcEval.cont_evalp, best_ind.fitness_test.values[0], best_ind.fitness.values[0], len(best_ind), avg_nodes(population)))
out.write('\n%s;%s;%s' % (gen, len(best_ind), best_ind))
if funcEval.LS_flag:
print 'Num. LS:', cond_ind
print 'Ind. Improvement:', cont_better
print 'Best Ind. LS:', best_ind.LS_applied_get()
print 'Best Ind.:', best_ind
print 'Best Fitness:', best_ind.fitness.values[0]
print 'Test fitness:',best_ind.fitness_test.values[0]
print 'Avg Nodes:', avg_nodes(population)
print 'Evaluations: ', funcEval.cont_evalp
if SaveMatrix:
data_pop=avg_nodes(population)
if GenMatrix:
idx_aux = np.searchsorted(Matrix[:, 0], gen)
Matrix[idx_aux, 1] = best_ind.fitness.values[0]
Matrix[idx_aux, 2] = best_ind.fitness_test.values[0]
Matrix[idx_aux, 3] = len(best_ind)
Matrix[idx_aux, 4] = data_pop[0]
Matrix[idx_aux, 5] = gen
Matrix[idx_aux, 6] = 1
Matrix[idx_aux, 7] = data_pop[1] # max nodes
Matrix[idx_aux, 8] = data_pop[2] # min nodes
else:
if funcEval.cont_evalp >= cont_evalf:
num_c -= 1
idx_aux=num_c
Matrix[num_c, 1] = best_ind.fitness.values[0]
Matrix[num_c, 2] = best_ind.fitness_test.values[0]
Matrix[num_c, 3] = len(best_ind)
Matrix[num_c, 4] = data_pop[0]
Matrix[num_c, 5] = gen
Matrix[num_c, 6] = 1
Matrix[num_c, 7] = data_pop[1] #max_nodes
Matrix[num_c, 8] = data_pop[2] #min nodes
else:
idx_aux = np.searchsorted(Matrix[:, 0], funcEval.cont_evalp)
Matrix[idx_aux, 1] = best_ind.fitness.values[0]
Matrix[idx_aux, 2] = best_ind.fitness_test.values[0]
Matrix[idx_aux, 3] = len(best_ind)
Matrix[idx_aux, 4] = data_pop[0]
Matrix[idx_aux, 5] = gen
Matrix[idx_aux, 6] = 1
Matrix[idx_aux, 7] = data_pop[1] #max nodes
Matrix[idx_aux, 8] = data_pop[2] #min nodes
id_it = idx_aux-1
id_beg = 0
flag = True
flag2 = False
while flag:
if Matrix[id_it, 6] == 0:
id_it -= 1
flag2 = True
else:
id_beg = id_it
flag = False
if flag2:
x = Matrix[id_beg, 1:8]
Matrix[id_beg:idx_aux, 1:] = Matrix[id_beg, 1:]
np.savetxt('./Matrix/%s/idx_%d_%d.txt' % (problem, num_p, n_corr), Matrix, delimiter=",", fmt="%s")
return population, logbook
def neat_GP(population,
toolbox,
cxpb,
mutpb,
ngen,
neat_alg,
neat_cx,
neat_h,
neat_pelit,
n_corr,
num_p,
params,
problem,
beta,
stats=None,
halloffame=None,
verbose=__debug__):
"""This algorithm reproduce the simplest evolutionary algorithm as
presented in chapter 7 of [Back2000]_.
:param population: A list of individuals.
:param toolbox: A :class:`~deap.base.Toolbox` that contains the evolution
operators.
:param cxpb: The probability of mating two individuals.
:param mutpb: The probability of mutating an individual.
:param ngen: The number of generation.
:param neat_alg: wheter or not to use species stuff.
:param neat_cx: wheter or not to use neatGP cx
:param neat_h: indicate the distance allowed between each specie
:param neat_pelit: probability of being elitist, it's used in the neat cx and mutation
:param n_corr: run number just to wirte the txt file
:param num_p: problem number just to wirte the txt file
:param params:indicate the params for the fitness sharing, the diffetent
options are:
-DontPenalize(str): 'best_specie' or 'best_of_each_specie'
-Penalization_method(int):
1.without penalization
2.penalization fitness sharing
3.new penalization
-ShareFitness(str): 'yes' or 'no'
:param problem: (str) name of the problem.
:param stats: A :class:`~deap.tools.Statistics` object that is updated
inplace, optional.
:param halloffame: A :class:`~deap.tools.HallOfFame` object that will
contain the best individuals, optional.
:param verbose: Whether or not to log the statistics.
:returns: The final population.
It uses :math:`\lambda = \kappa = \mu` and goes as follow.
It first initializes the population (:math:`P(0)`) by evaluating
every individual presenting an invalid fitness. Then, it enters the
evolution loop that begins by the selection of the :math:`P(g+1)`
population. Then the crossover operator is applied on a proportion of
:math:`P(g+1)` according to the *cxpb* probability, the resulting and the
untouched individuals are placed in :math:`P'(g+1)`. Thereafter, a
proportion of :math:`P'(g+1)`, determined by *mutpb*, is
mutated and placed in :math:`P''(g+1)`, the untouched individuals are
transferred :math:`P''(g+1)`. Finally, those new individuals are evaluated
and the evolution loop continues until *ngen* generations are completed.
Briefly, the operators are applied in the following order ::
evaluate(population)
for i in range(ngen):
offspring = select(population)
offspring = mate(offspring)
offspring = mutate(offspring)
evaluate(offspring)
population = offspring
This function expects :meth:`toolbox.mate`, :meth:`toolbox.mutate`,
:meth:`toolbox.select` and :meth:`toolbox.evaluate` aliases to be
registered in the toolbox.
.. [Back2000] Back, Fogel and Michalewicz, "Evolutionary Computation 1 :
Basic Algorithms and Operators", 2000.
"""
d = './Results/%s/bestind_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
best = open(d, 'w') # save data
d = './Results/%s/bestind_string_%d_%d.txt' % (problem, num_p, n_corr)
ensure_dir(d)
best_st = open(d, 'w')
logbook = tools.Logbook()
logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])
if neat_alg: # assign specie to each individual on the population
species(population, neat_h, beta)
ind_specie(population)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# take the best on the population
best_ind = best_pop(population)
fitnesst_best = toolbox.map(toolbox.evaluate_test, [best_ind])
best_ind.fitness_test.values = fitnesst_best[0]
best.write('\n%s;%s;%s;%s;%s' %
(0, best_ind.fitness_test.values[0], best_ind.fitness.values[0],
len(best_ind), avg_nodes(population)))
best_st.write('\n%s;%s' % (0, best_ind))
if neat_alg: # applying fitness sharing
SpeciesPunishment(population, params, neat_h)
if halloffame is not None:
halloffame.update(population)
record = stats.compile(population) if stats else {}
logbook.record(gen=0, nevals=len(invalid_ind), **record)
if verbose:
print(logbook.stream)
# Begin the generational process
for gen in range(1, ngen + 1):
best_ind = copy.deepcopy(best_pop(population))
if neat_alg: # select set of parents
parents = p_selection(population, gen)
else:
parents = toolbox.select(population, len(population))
if neat_cx: # applying neat-crossover
n = len(parents)
mut = 1
cx = 1
offspring = neatGP(toolbox, parents, cxpb, mutpb, n, mut, cx,
neat_pelit)
else:
offspring = varOr(parents, toolbox, cxpb, mutpb)
if neat_alg: # Assign species
specie_parents_child(parents, offspring, neat_h, beta)
offspring[:] = parents + offspring
ind_specie(offspring)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
else:
invalid_ind = [ind for ind in offspring]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
orderbyfit = sorted(offspring, key=lambda ind: ind.fitness.values)
if best_ind.fitness.values[0] <= orderbyfit[0].fitness.values[0]:
offspring[:] = [best_ind] + orderbyfit[:len(population) - 1]
if neat_alg:
SpeciesPunishment(offspring, params, neat_h)
# Update the hall of fame with the generated individuals
if halloffame is not None:
halloffame.update(offspring)
# Replace the current population by the offspring
population[:] = offspring
# Append the current generation statistics to the logbook
record = stats.compile(population) if stats else {}
logbook.record(gen=gen, nevals=len(population), **record)
if verbose:
print(logbook.stream)
best_ind = best_pop(population)
fitnesses_test = toolbox.map(toolbox.evaluate_test, [best_ind])
best_ind.fitness_test.values = fitnesses_test[0]
best.write(
'\n%s;%s;%s;%s;%s' %
(gen, best_ind.fitness_test.values[0], best_ind.fitness.values[0],
len(best_ind), avg_nodes(population)))
best_st.write('\n%s;%s' % (gen, best_ind))
return population, logbook