def build_with_ga(self, X, y):
# accuracy fitness function
def accuracy_fitness_function(chromosome):
# decode the class model from gene
aggregation, mus = _decode(self.m, X, y, self.aggregation_rules__,
self.mu_factories, self.classes_,
chromosome)
y_pred = _predict(mus, aggregation, self.classes_, X)
return 1.0 - accuracy_score(y, y_pred)
# number of genes (2 for the aggregation, 4 for each attribute)
n_genes = 2 + (self.m * 5 * len(self.classes_))
logger.info("initializing GA %d iterations" % (self.iterations, ))
# initialize
ga = GeneticAlgorithm(
fitness_function=helper_fitness(accuracy_fitness_function),
scaling=1.0,
crossover_function=UniformCrossover(0.5),
# crossover_points=range(2, n_genes, 5),
elitism=5, # no elitism
n_chromosomes=100,
n_genes=n_genes,
p_mutation=0.3,
random_state=self.random_state)
last_fitness = None
#
iternum = 0
for generation in range(self.iterations):
ga.next()
logger.info("GA iteration %d Fitness (top-4) %s" %
(generation, str(np.sort(ga.fitness_)[:4])))
chromosomes, fitnesses = ga.best(10)
aggregation, protos = _decode(self.m, X, y,
self.aggregation_rules__,
self.mu_factories, self.classes_,
chromosomes[0])
self.aggregation = aggregation
self.protos_ = protos
# check stopping condition
new_fitness = np.mean(fitnesses)
if last_fitness is not None:
d_fitness = last_fitness - new_fitness
if self.epsilon is not None and d_fitness < self.epsilon:
logger.info("Early stop d_fitness %f" % (d_fitness, ))
break
last_fitness = new_fitness
iternum = iternum + 1
print("Iteration = ", iternum, "fitness = ", last_fitness)
# print learned.
logger.info("+- Final: Aggregation %s" % (str(self.aggregation), ))
for key, value in self.protos_.items():
logger.info("`- Class-%d" % (key, ))
logger.info("`- Membership-fs %s" %
(str([x.__str__() for x in value]), ))
def build_with_ga(self, X, y):
# accuracy fitness function
def accuracy_fitness_function(chromosome):
# decode the class model from gene
aggregation, mus = _decode(self.m, X, y, self.aggregation_rules__,
self.mu_factories, self.classes_, chromosome)
y_pred = _predict(mus, aggregation, self.classes_, X)
return 1.0 - accuracy_score(y, y_pred)
# number of genes (2 for the aggregation, 4 for each attribute)
n_genes = 2 + (self.m * 5 * len(self.classes_))
logger.info("initializing GA %d iterations" % (self.iterations,))
# initialize
ga = GeneticAlgorithm(fitness_function=helper_fitness(accuracy_fitness_function),
scaling=1.0,
crossover_function=UniformCrossover(0.5),
# crossover_points=range(2, n_genes, 5),
elitism=5, # no elitism
n_chromosomes=100,
n_genes=n_genes,
p_mutation=0.3)
last_fitness = None
#
for generation in range(self.iterations):
ga.next()
logger.info("GA iteration %d Fitness (top-4) %s" % (generation, str(np.sort(ga.fitness_)[:4])))
chromosomes, fitnesses = ga.best(10)
aggregation, protos = _decode(self.m, X, y, self.aggregation_rules__,
self.mu_factories, self.classes_, chromosomes[0])
self.aggregation = aggregation
self.protos_ = protos
# check stopping condition
new_fitness = np.mean(fitnesses)
if last_fitness is not None:
d_fitness = last_fitness - new_fitness
if self.epsilon is not None and d_fitness < self.epsilon:
logger.info("Early stop d_fitness %f" % (d_fitness,))
break
last_fitness = new_fitness
# print learned.
logger.info("+- Final: Aggregation %s" % (str(self.aggregation),))
for key, value in self.protos_.items():
logger.info("`- Class-%d" % (key,))
logger.info("`- Membership-fs %s" % (str([ x.__str__() for x in value ]),))
def build_for_class(self, X, y, class_idx):
y_target = np.zeros(y.shape) # create the target of 1 and 0.
y_target[class_idx] = 1.0
n_genes = 5 * self.m
def rmse_fitness_function(chromosome):
proto = self.decode(chromosome)
y_pred = _predict_one(proto, self.aggregation, X)
return mean_squared_error(y_target, y_pred)
logger.info("initializing GA %d iterations" % (self.iterations, ))
# initialize
ga = GeneticAlgorithm(
fitness_function=helper_fitness(rmse_fitness_function),
scaling=1.0,
crossover_function=UniformCrossover(0.5),
# crossover_points=range(0, n_genes, 5),
elitism=5, # no elitism
n_chromosomes=100,
n_genes=n_genes,
p_mutation=0.3)
# print "population", ga.population_
# print "fitness", ga.fitness_
chromosomes, fitnesses = ga.best(10)
last_fitness = np.mean(fitnesses)
proto = None
#
for generation in range(self.iterations):
ga.next()
logger.info("GA iteration %d Fitness (top-4) %s" %
(generation, str(ga.fitness_[:4])))
chromosomes, fitnesses = ga.best(10)
proto = self.decode(chromosomes[0])
# check stopping condition
new_fitness = np.mean(fitnesses)
d_fitness = last_fitness - new_fitness
if self.epsilon is not None and d_fitness < self.epsilon:
logger.info("Early stop d_fitness %f" % (d_fitness, ))
break
last_fitness = new_fitness
return proto
def build_for_class(self, X, y, class_idx):
# take column-wise min/mean/max for class
mins = np.nanmin(X[class_idx], 0)
means = np.nanmean(X[class_idx], 0)
maxs = np.nanmax(X[class_idx], 0)
ds = (maxs - mins) / 2.0
n_genes = 2 * self.m # adjustment for r and shrinking/expanding value for p/q
B = np.ones(n_genes)
def decode_with_shrinking_expanding(C):
def dcenter(j):
return min(1.0, max(0.0,
C[j])) - 0.5 if self.adjust_center else 1.0
return [
fl.PiSet(r=means[j] * dcenter(j),
p=means[j] - (ds[j] * C[j + 1]),
q=means[j] + (ds[j] * C[j + 1]))
for j in range(self.m)
]
y_target = np.zeros(y.shape) # create the target of 1 and 0.
y_target[class_idx] = 1.0
def rmse_fitness_function(chromosome):
proto = decode_with_shrinking_expanding(chromosome)
y_pred = _predict_one(proto, self.aggregation, X)
return mean_squared_error(y_target, y_pred)
logger.info("initializing GA %d iterations" % (self.iterations, ))
# initialize
ga = UnitIntervalGeneticAlgorithm(
fitness_function=helper_fitness(rmse_fitness_function),
crossover_function=UniformCrossover(0.5),
elitism=3,
n_chromosomes=100,
n_genes=n_genes,
p_mutation=0.3)
ga = helper_n_generations(ga, self.iterations)
chromosomes, fitnesses = ga.best(1)
return decode_with_shrinking_expanding(
chromosomes[0]), decode_with_shrinking_expanding(B)
def build_for_class(self, X, y, class_idx):
y_target = np.zeros(y.shape) # create the target of 1 and 0.
y_target[class_idx] = 1.0
n_genes = 5 * self.m
def rmse_fitness_function(chromosome):
proto = self.decode(chromosome)
y_pred = _predict_one(proto, self.aggregation, X)
return mean_squared_error(y_target, y_pred)
logger.info("initializing GA %d iterations" % (self.iterations,))
# initialize
ga = GeneticAlgorithm(fitness_function=helper_fitness(rmse_fitness_function),
scaling=1.0,
crossover_function=UniformCrossover(0.5),
# crossover_points=range(0, n_genes, 5),
elitism=5, # no elitism
n_chromosomes=100,
n_genes=n_genes,
p_mutation=0.3)
# print "population", ga.population_
# print "fitness", ga.fitness_
chromosomes, fitnesses = ga.best(10)
last_fitness = np.mean(fitnesses)
proto = None
#
for generation in range(self.iterations):
ga.next()
logger.info("GA iteration %d Fitness (top-4) %s" % (generation, str(ga.fitness_[:4])))
chromosomes, fitnesses = ga.best(10)
proto = self.decode(chromosomes[0])
# check stopping condition
new_fitness = np.mean(fitnesses)
d_fitness = last_fitness - new_fitness
if self.epsilon is not None and d_fitness < self.epsilon:
logger.info("Early stop d_fitness %f" % (d_fitness,))
break
last_fitness = new_fitness
return proto
def build_for_class(self, rs, X):
def distance_fitness(c):
return np.sum(np.abs(X - c))
# setup GA
ga = GeneticAlgorithm(fitness_function=helper_fitness(distance_fitness),
elitism=3,
n_chromosomes=100,
n_genes=X.shape[1],
p_mutation=0.3,
random_state=rs)
ga = helper_n_generations(ga, self.n_iterations) # advance the GA
# return the best found parameters for this class.
chromosomes, fitness = ga.best(1)
return chromosomes[0]
def build_for_class(self, rs, X):
def distance_fitness(c):
return np.sum(np.abs(X - c))
# setup GA
ga = GeneticAlgorithm(
fitness_function=helper_fitness(distance_fitness),
elitism=3,
n_chromosomes=100,
n_genes=X.shape[1],
p_mutation=0.3,
random_state=rs)
ga = helper_n_generations(ga, self.n_iterations) # advance the GA
# return the best found parameters for this class.
chromosomes, fitness = ga.best(1)
return chromosomes[0]
def build_for_class(self, X, y, class_idx):
# take column-wise min/mean/max for class
mins = np.nanmin(X[class_idx], 0)
means = np.nanmean(X[class_idx], 0)
maxs = np.nanmax(X[class_idx], 0)
ds = (maxs - mins) / 2.0
n_genes = 2 * self.m # adjustment for r and shrinking/expanding value for p/q
B = np.ones(n_genes)
def decode_with_shrinking_expanding(C):
def dcenter(j):
return min(1.0, max(0.0, C[j])) - 0.5 if self.adjust_center else 1.0
return [ fl.PiSet(r=means[j] * dcenter(j),
p=means[j] - (ds[j] * C[j + 1]),
q=means[j] + (ds[j] * C[j + 1]))
for j in range(self.m) ]
y_target = np.zeros(y.shape) # create the target of 1 and 0.
y_target[class_idx] = 1.0
def rmse_fitness_function(chromosome):
proto = decode_with_shrinking_expanding(chromosome)
y_pred = _predict_one(proto, self.aggregation, X)
return mean_squared_error(y_target, y_pred)
logger.info("initializing GA %d iterations" % (self.iterations,))
# initialize
ga = UnitIntervalGeneticAlgorithm(fitness_function=helper_fitness(rmse_fitness_function),
crossover_function=UniformCrossover(0.5),
elitism=3,
n_chromosomes=100,
n_genes=n_genes,
p_mutation=0.3)
ga = helper_n_generations(ga, self.iterations)
chromosomes, fitnesses = ga.best(1)
return decode_with_shrinking_expanding(chromosomes[0]), decode_with_shrinking_expanding(B)
def fit_weights(self, rs, models, X, y):
n_genes = self.n_models * len(self.classes_)
def fitness_function(c):
M = self.predict_(X, models, c)
y_pred = np.argmin(M, 1)
return 1.0 - accuracy_score(y, y_pred)
ga = GeneticAlgorithm(fitness_function=helper_fitness(fitness_function),
elitism=3,
n_chromosomes=100,
n_genes=n_genes,
p_mutation=0.3,
random_state=rs)
ga = helper_n_generations(ga, self.n_iterations_weights) # advance the GA
chromosomes, fitness = ga.best(1)
return chromosomes[0]
def fit_weights(self, rs, models, X, y):
n_genes = self.n_models * len(self.classes_)
def fitness_function(c):
M = self.predict_(X, models, c)
y_pred = np.argmin(M, 1)
return 1.0 - accuracy_score(y, y_pred)
ga = GeneticAlgorithm(
fitness_function=helper_fitness(fitness_function),
elitism=3,
n_chromosomes=100,
n_genes=n_genes,
p_mutation=0.3,
random_state=rs)
ga = helper_n_generations(ga,
self.n_iterations_weights) # advance the GA
chromosomes, fitness = ga.best(1)
return chromosomes[0]