def main():
goals = [101, 150]
routes = [(1, goals[0]), (1, goals[1])]
raw_graph = Graph(mapfile__name='./graph/waterloo.map')
# path = [1, 23, 45, 66, 88, 89, 67, 87, 66, 45, 24, 23, 45, 67, 68, 67, 89, 111, 131, 111, 133, 154, 155, 156, 135, 136, 156, 177, 156, 135, 157, 178, 179, 178, 179, 180, 159, 160, 182, 181, 161, 183, 184, 206, 228, 207, 228, 207, 206, 228, 208, 230]
# raw_graph.plotMovementsMultiPaths([path], [(1, 230)], './result/before_ga.png')
# path = remove_cycle(path)
# print path
# raw_graph.plotMovementsMultiPaths([path], [(1, 230)], './result/after_ga.png')
# return
graph = raw_graph.toGraphNode()
# generate ecegraph
# IOManager.export_graph(graph, '../aco/waterloo.ecegraph')
# graph = IOManager.import_graph('../aco/waterloo.ecegraph')
solver = ACOSolver.from_graph(graph, goals)
score, solutions, order = solver.solve()
solutions = [soln[0] for soln in solutions]
paths = []
ga_scores = []
removed = {}
for goal in goals:
end = goal
population = Population(graph[START_NODE], end, removed)
path = population.evolve()
path = remove_cycle(path)
new_cost = Chromosome.calc_costs(path, graph, goal, removed)
print 'new path: ' + str(path)
print 'new cost: ' + str(new_cost)
ga_scores.append(new_cost)
paths.append(path)
# remove path from graph
for p in path:
removed[p] = p
if raw_graph != None:
raw_graph.plotMovementsMultiPaths(solutions, routes,
'./result/aco.png')
raw_graph.plotMovementsMultiPaths(paths, routes, './result/ga.png')
print 'GA:'
print 'scores: ' + str(ga_scores)
print 'paths: ' + str(paths)
print 'ACO:'
print('Best overall score: {}'.format(score))
print('Best order of goal nodes: {}'.format(order))
print('Best path solutions: {}'.format(solutions))
def __generate_cities(map, hyperparameters, simulation):
max_pop_size = Population.max_pop_size(hyperparameters['pop_size'],
hyperparameters['elitism_n'],
hyperparameters['truncation_percentage'])
print('Maximum population size:', max_pop_size)
return [City.generate(map['size'], map['size'], map['intersections'], simulation['max_cars'], simulation['max_cars_spawn'], map['seed']) for _ in range(max_pop_size)]
def __init__(self):
if Handler.__instance is not None:
raise Exception("This is a Singleton!")
else:
Handler.__instance = self
self.is_running = True
self.window_size = (510, 600)
self.play_area_size = [(10, 10), (10, 500), (500, 500), (500, 10)]
self.play_area_boundaries = {
'top border': 10,
'bottom border': 490,
'left border': 10,
'right border': 490
}
self.directions = {
'up': [0, -10],
'down': [0, 10],
'left': [-10, 0],
'right': [10, 0]
}
self.current_direction = self.directions['right']
self.run_speed = 100
self.fuel = 130
self.points = 0
self.time_lasted = 0
self.edible = Edible()
self.snake = Snake()
self.ga = GeneticAlgorithm()
self.population = Population(50, True)
self.current_snake = 0
self.current_generation = 0
def plot_net():
node_ordering = node_ordering = {
0: 'asia',
1: 'tub',
2: 'smoke',
3: 'bronc',
4: 'lung',
5: 'either',
6: 'dysp',
7: 'xray'
}
Population.init_state(POPULATION_SIZE, DATA.columns, node_ordering)
new = as_net(
np.array([
1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 0, 1, 0, 0, 0,
1, 1, 1, 0, 0, 0
]))
new.plot()
def main():
env = gym.make('SlimeVolley-v0')
env.seed(123)
POPULATION_SIZE = 20
MAX_GENERATION = 100
MUTATION_RATE = 0.4
CROSSOVER_RATE = 0.7
INPUT_SIZE = 12
OUTPUT_SIZE = 3
assert POPULATION_SIZE % 2 == 0
p = Population(DeepMLPTorchIndividual(INPUT_SIZE, 0,
OUTPUT_SIZE), POPULATION_SIZE,
MAX_GENERATION, MUTATION_RATE, CROSSOVER_RATE, 0.0)
p.set_population([
DeepMLPTorchIndividual(INPUT_SIZE, 0, OUTPUT_SIZE)
for _ in range(POPULATION_SIZE)
])
p.run(
env,
generation,
verbose=True,
log=True,
output_folder=f'model-layers={INPUT_SIZE}-{HIDDEN_SIZE}-{OUTPUT_SIZE}',
save_as_pytorch=False)
def generate(self) -> Population:
"""
种群生成算法
"""
individuals = []
for _ in range(self.individual_num):
# setup phenotype
phenotype = Phenotype()
values = []
for val_range in self.individual_meta.range_list:
val = random() * (val_range[1] - val_range[0]) + val_range[0]
values.append(val)
phenotype.phenotype = values
individual = Individual()
individual.meta = self.individual_meta
individual.phenotype = phenotype
individuals.append(individual)
population = Population()
population.individuals = individuals
return population
def evolve(self, population):
new_population = Population(len(population.individuals), False)
new_population.individuals.append(population.get_fittest())
for i in range(len(population.individuals) - self.elitism_offset):
if i <= self.elitism_offset:
continue
mother = self.tournament(population)
father = self.tournament(population)
baby = self.reproduce(mother, father)
new_population.individuals.append(baby)
for i in range(len(new_population.individuals)):
if i <= self.elitism_offset:
continue
self.mutate(new_population.individuals[i])
return new_population
class PopulationTestCase(TestCase):
def setUp(self):
self.population = Population()
def testMutateCross(self):
fake_cm_plugin = FakeCmPlugin()
self.population.individuals = [1, 2, 3]
self.population(fake_cm_plugin)
self.population.mutate()
self.population.cross()
self.assertEqual(self.population.cm_plugin, fake_cm_plugin)
self.assertEqual(
fake_cm_plugin.c_count, fake_cm_plugin.m_count)
def testSelect(self):
fake_selector = FakeSelector()
self.population.use_selector(fake_selector)
self.population.individuals = [1, 2, 3]
self.population.select()
self.assertEqual(
fake_selector.i_count, len(self.population.individuals))
# If children fitness is greater thant parents update population
if child1.fitness + child2.fitness > parent1.fitness + parent2.fitness:
new_population[i] = child1
new_population[i + 1] = child2
else:
new_population[i] = parent1
new_population[i + 1] = parent2
if __name__ == '__main__':
env = gym.make('CarRacing-v0')
POPULATION_SIZE = 100
MAX_GENERATION = 2
MUTATION_RATE = 0.1
CROSSOVER_RATE = 0.8
p = Population(ConvNetTorchIndividal(None, None, None), POPULATION_SIZE, MAX_GENERATION, MUTATION_RATE, CROSSOVER_RATE, 0)
p.run(env, generation, verbose=False, output_folder='')
env.close()
'''
초기화
for in max_generation (총 세대수){
for old_population : 적합성 계산 ( 100 episode * population_size )
run_generation(env, old, new, mutation, crossover){
for old population / 2
parent1,parent2 = 적합성 기준 2개 select
def ga(maxPop, mutation_rate, chromosome_length, maxGen):
pop = Population(maxPop,
mutation_rate,
chromosome_length=chromosome_length)
# populating with maxPop elements
pop.populate()
i = 0
for i in range(maxGen):
# calculating fitness
pop.calc_fitness()
# natural selection
parents = pop.selection()
# crossover + mutation
pop.crossover(parents)
pop.mutate()
# printing
print('Gen ' + str(i) + ": ", pop.getFittest()[0], pop.getAvgFitness())
pop.population[pop.getFittest()[1]].plot()
pop.population[pop.getFittest()[1]].plot()
def main(dataset):
# node_ordering = order_based_on_conditional_entropy_sum_on_line(dataset) #un dictionar de forma{i:nume variabila}. variabila[i] poate fi parinte pentru orice j>i
# print(node_ordering)
# node_ordering = {0: 'asia', 1: 'tub', 2: 'bronc', 3: 'xray', 4: 'lung', 5: 'smoke', 6: 'dysp', 7: 'either'}
# node_ordering ={0: 'asia', 1: 'tub', 2: 'smoke', 3: 'bronc', 4: 'lung', 5: 'either', 6: 'dysp', 7: 'xray'} #perfect node ordering
# node_ordering = {0: 'diabetes', 1: 'flatulence', 2: 'upper_pain', 3: 'hepatotoxic', 4: 'anorexia', 5: 'nausea', 6: 'hepatomegaly', 7: 'hepatalgia', 8: 'bleeding', 9: 'vh_amn', 10: 'hospital', 11: 'fat', 12: 'transfusion', 13: 'joints', 14: 'proteins', 15: 'hbsag', 16: 'density', 17: 'le_cells', 18: 'ascites', 19: 'skin', 20: 'alcoholism', 21: 'surgery', 22: 'spiders', 23: 'hcv_anti', 24: 'RHepatitis', 25: 'hbsag_anti', 26: 'choledocholithotomy', 27: 'fatigue', 28: 'hbc_anti', 29: 'THepatitis', 30: 'palms', 31: 'edema', 32: 'pain', 33: 'consciousness', 34: 'pain_ruq', 35: 'obesity', 36: 'alcohol', 37: 'edge', 38: 'jaundice', 39: 'itching', 40: 'gallstones', 41: 'injections', 42: 'spleen', 43: 'sex', 44: 'pressure_ruq', 45: 'Hyperbilirubinemia', 46: 'irregular_liver', 47: 'hbeag', 48: 'encephalopathy', 49: 'ama', 50: 'fibrosis', 51: 'amylase', 52: 'PBC', 53: 'Steatosis', 54: 'urea', 55: 'alt', 56: 'ESR', 57: 'triglycerides', 58: 'inr', 59: 'albumin', 60: 'ChHepatitis', 61: 'phosphatase', 62: 'cholesterol', 63: 'ast', 64: 'carcinoma', 65: 'platelet', 66: 'bilirubin', 67: 'Cirrhosis', 68: 'age', 69: 'ggtp'}
node_ordering = perfect_order_alarm()
Population.init_state(POPULATION_SIZE, dataset.columns, node_ordering)
generation = Population()
generation.random()
generation.load()
print('Population shape:', generation.shape)
no_generation = 0
log = open(LOG_FILE, 'a')
init_writer()
no_same_score = 0
old_fitness = 0
ttt = time.time()
while no_generation < MAX_NO_GENERATION and no_same_score < MAX_NO_GENERATION_SAME_SCORE:
print('Generation: ', no_generation, generation.shape)
t=time.time()
fitness = np.array(get_fitness(generation.population_as_nets))
print(" after fitness computation", time.time() - t)
# t = time.time()
indexes_of_best_fitnesses = np.argsort(fitness)[-ELITIST:]
new_generation = Population(
generation.population_as_array[indexes_of_best_fitnesses],
generation.population_as_nets[indexes_of_best_fitnesses]
)
# print(" after elitism", time.time() - t)
# t = time.time()
log.write(str(np.max(fitness)) + '\n')
log.flush()
print(str(np.max(fitness)) + '\n')
if np.max(fitness) == old_fitness:
no_same_score+=1
else:
no_same_score = 0
old_fitness = np.max(fitness)
no_pairs = int((POPULATION_SIZE - ELITIST) / 2)
for _ in range(no_pairs):
index_p1, index_p2 = select(fitness)
offsprings = crossover(generation.get(index_p1), generation.get(index_p2))
new_generation.add_individs(offsprings)
# print(" after crossover", time.time() - t)
# t=time.time()
for i in range(POPULATION_SIZE):
new_generation.add_individs([mutate(generation.get(i), Population.index_to_feature,dataset)])
print(" after mutation")
generation = copy.deepcopy(new_generation)
no_generation += 1
if no_generation % INTERMEDIAR_SAVE == 0:
fitness = np.array(get_fitness(generation.population_as_nets))
write(fitness, generation)
if no_generation%25 ==0:
checkpoint(generation)
# print(" end generation", time.time() - t)
else:
fitness = np.array(get_fitness(generation.population_as_nets))
write(fitness, generation)
checkpoint(generation)
print('final time: ', time.time() - ttt)
def revolution(self, args):
# Config
if (args.crossmode == "one"):
cross_func = Crossover.onePoint
elif (args.crossmode == "two"):
cross_func = Crossover.twoPoints
else:
cross_func = Crossover.randomPoints
# Prepare dataset
dataset = readDataset(args.dpath)
# Create individuals & population
ppl = Population()
for i in range(args.individuals):
individual = Individual()
individual.createGene(dataset, args.gene)
ppl.addInd(individual)
# Evolution
for i in range(args.revolution):
# Evaluation population in individuals
ppl.calcFitness(self.evaluate, args)
if ((i % 10) == 0):
ppl.show()
# Select parents
if (args.elite):
parents = Select.Elite(ppl, args.esize, args.mode)
parents.extend(
Select.Tournament(ppl, args.individuals - args.esize,
args.tornsize, args.mode))
else:
parents = Select.Tournament(ppl, args.individuals,
args.tornsize, args.mode)
# Clossover
children = cross_func(parents, args.individuals, args.gene,
args.crossrate)
# Mutation
children = Mutation.mutation(children, args.mutaterate, dataset)
# Swap children
ppl.setPpl(children)
# show result
ppl.calcFitness(self.evaluate, args)
ppl.show()
from ga.population import Population
import numpy as np
dataHandler = DataHandler(['apple_test_data.csv', 'NASDAQ_test_data.csv'])
#dataHandler = DataHandler(['apple_data.csv', 'NASDAQ_data.csv'])
data = dataHandler.get_signal_list()
signal_ranges = dataHandler.signal_ranges()
#print signal_ranges
data_element = len(data[0])
#print "data[0]"
#print data[0]
population = Population(100 , signal_ranges, data)
#for i in population:
# print i.transform_individual(signal_ranges)
initial_fitess_values = map(population.fitness_function, population)
#print initial_fitess_values
number_generations = 100
population.sus_sampler(initial_fitess_values)
max_list = []
mean_list = []
for i in xrange(number_generations):
#print "initial population"
#for i in population:
if __name__ == '__main__':
env = gym.make('BipedalWalker-v2')
env.seed(123)
POPULATION_SIZE = 10
MAX_GENERATION = 10
MUTATION_RATE = 0.01
CROSSOVER_RATE = 0.8
INPUT_SIZE = 24
OUTPUT_SIZE = 4
assert POPULATION_SIZE % 2 == 0
p = Population(DeepBipedalWalkerIndividual(INPUT_SIZE, 0,
OUTPUT_SIZE), POPULATION_SIZE,
MAX_GENERATION, MUTATION_RATE, CROSSOVER_RATE, 0.0)
p.set_population([
DeepBipedalWalkerIndividual(INPUT_SIZE, 0, OUTPUT_SIZE)
for _ in range(POPULATION_SIZE)
])
p.run(
env,
generation,
verbose=True,
log=True,
output_folder=f'model-layers={INPUT_SIZE}-{HIDDEN_SIZE}-{OUTPUT_SIZE}',
save_as_pytorch=False)
env.close()
# 4.
if np.random.rand() < p_inversion:
child1.weights_biases = inversion(child1.weights_biases)
child2.weights_biases = inversion(child2.weights_biases)
new_population.append(child1)
new_population.append(child2)
if __name__ == '__main__':
env = gym.make('BipedalWalker-v2')
env.seed(123)
POPULATION_SIZE = 10
MAX_GENERATION = 20
MUTATION_RATE = 0.01
CROSSOVER_RATE = 0.8
INVERSION_RATE = 0.02
INPUT_SIZE = 10
HIDDEN_SIZE = 16
OUTPUT_SIZE = 4
p = Population(MLPTorchIndividual(INPUT_SIZE, HIDDEN_SIZE, OUTPUT_SIZE),
POPULATION_SIZE, MAX_GENERATION, MUTATION_RATE,
CROSSOVER_RATE, INVERSION_RATE)
p.run(env, generation_new, verbose=True, log=True, output_folder='')
env.close()
def setUp(self):
self.population = Population()
child2.calculate_fitness(env)
# If children fitness is greater thant parents update population
if child1.fitness + child2.fitness > parent1.fitness + parent2.fitness:
new_population[i] = child1
new_population[i + 1] = child2
else:
new_population[i] = parent1
new_population[i + 1] = parent2
if __name__ == '__main__':
env = gym.make('BipedalWalker-v2')
env.seed(123)
POPULATION_SIZE = 10
MAX_GENERATION = 10
MUTATION_RATE = 0.2
CROSSOVER_RATE = 0.9
INPUT_SIZE = 24
HIDDEN_SIZE = 16
OUTPUT_SIZE = 4
p = Population(RNNIndividual(INPUT_SIZE, HIDDEN_SIZE,
OUTPUT_SIZE), POPULATION_SIZE, MAX_GENERATION,
MUTATION_RATE, CROSSOVER_RATE)
p.run(env, generation, verbose=True, output_folder='')
env.close()
def run_genetics(map, hyperparameters, simulation):
init = time()
cities = __generate_cities(map, hyperparameters, simulation)
number_of_lights = len(cities[0].grid.roads_with_lights)
lights_steps = ceil(simulation['sim_steps'] / simulation['light_duration_steps']) + 1 # Todo +1 should not be needed
dna_size = lights_steps * number_of_lights
population = Population(pop_size=hyperparameters['pop_size'],
dna_size=dna_size,
elitism_n=hyperparameters['elitism_n'],
truncation_percentage=hyperparameters['truncation_percentage'],
crossover_type=hyperparameters['crossover_type'],
crossover_points=hyperparameters['crossover_points'],
crossover_probability=hyperparameters['crossover_probability'],
mutation_probability=hyperparameters['mutation_probability'],
spread_mutation=hyperparameters['spread_mutation'],
objects_codified=number_of_lights,
multiprocessing=False)
best_performance_steps = []
while population.generation_id < hyperparameters['max_generations'] \
and not population.convergence_criteria():
# Print information
print('Step: {:3d}'.format(population.generation_id), end=' ')
init = time()
# Generate arguments to run individuals
args = __generate_args(cities,
population,
simulation['light_duration_steps'],
hyperparameters['sim_per_individual'],
simulation['sim_steps'])
# Run all individuals
if hyperparameters['multiprocessing']:
pool = Pool(hyperparameters['processes'])
scores = pool.starmap(__run_gene, args)
pool.close()
for i, score in enumerate(scores):
population.genes[i].score = score
else:
for i, gene in enumerate(population.genes):
gene.score = __run_gene(cities[i], gene,
hyperparameters['sim_per_individual'],
simulation['sim_steps'],
simulation['light_duration_steps'])
# Update genes
best_performance, _, pop_size = population.update_genes()
best_performance_steps.append(best_performance)
# Print information
print('| New pop size: {:3d} | Fitness: [Best step: {:3.2f}, Best all: {:3.2f}] | Gene size {:d} | Took {:s}'
.format(pop_size,
best_performance,
population.best_historical_performance,
dna_size,
str(timedelta(seconds=(time() - init)))))
best_performance = population.best_historical_performance
best_gene = population.best_historical_individual
print('Done !, took', timedelta(seconds=(time() - init)), 'Saving best...')
name = generate_filename(simulation, map, hyperparameters)
np.save('../data/{:d}_best_{:s}.npy'.format(int(time()), name), best_gene)
np.savetxt('../data/{:d}_fitness_{:s}.txt'.format(int(time()), name), np.array(best_performance_steps), delimiter="\n", fmt="%s")
return best_performance, best_gene, best_performance_steps
from data.read_stock import DataHandler
from ga.individual import Individual
from ga.population import Population
import numpy as np
dataHandler = DataHandler(['apple_test_data.csv', 'NASDAQ_test_data.csv'])
#dataHandler = DataHandler(['apple_data.csv', 'NASDAQ_data.csv'])
data = dataHandler.get_signal_list()
signal_ranges = dataHandler.signal_ranges()
#print signal_ranges
data_element = len(data[0])
#print "data[0]"
#print data[0]
population = Population(100, signal_ranges, data)
#for i in population:
# print i.transform_individual(signal_ranges)
initial_fitess_values = map(population.fitness_function, population)
#print initial_fitess_values
number_generations = 100
population.sus_sampler(initial_fitess_values)
max_list = []
mean_list = []
for i in xrange(number_generations):
#print "initial population"
#for i in population:
# print i.rep
def tournament(self, population):
tournament_population = Population(self.tournament_size, False)
for i in range(self.tournament_size):
tournament_population.individuals.append(
random.choice(population.individuals))
return tournament_population.get_fittest()
new_population[i + 1] = child2
else:
new_population[i] = parent1
new_population[i + 1] = parent2
if __name__ == '__main__':
env = gym.make('CartPole-v1')
env.seed(123)
POPULATION_SIZE = 100
MAX_GENERATION = 20
MUTATION_RATE = 0.4
CROSSOVER_RATE = 0.9
INPUT_SIZE = 4
HIDDEN_SIZE = 2
OUTPUT_SIZE = 1
p = Population(MLPIndividual(INPUT_SIZE, HIDDEN_SIZE,
OUTPUT_SIZE), POPULATION_SIZE, MAX_GENERATION,
MUTATION_RATE, CROSSOVER_RATE, 0)
p.run(env,
generation,
verbose=True,
output_folder='../../models/cartpole',
log=True)
env.close()