def fit(self,X,y,**param):
self.neural_shape = param.get("neural_shape")
self.n_input = self.neural_shape[0]
self.n_output = self.neural_shape[-1]
self.n_hidden = self.neural_shape[1]
self.number_of_weights = self.n_hidden*(self.n_input+1)+self.n_output*(self.n_hidden+1)
self.score_fn = FeedFlow(self.neural_shape)
self.X = X
self.y = y
#setting params
self.weights = G1DList.G1DList(self.number_of_weights)
lim = np.sqrt(6)/np.sqrt((self.n_input+self.n_output))
#Khoi tao trong so
self.weights.setParams(rangemin=-lim,rangemax=lim)
# cai dat ham khoi tao
self.weights.initializator.set(Initializators.G1DListInitializatorReal)
#cai dat ham dot bien
self.weights.mutator.set(Mutators.G1DListMutatorRealGaussian)
#cai dat ham do thich nghi
self.weights.evaluator.set(self.eval_score)
# cai dat ham lai ghep
self.weights.crossover.set(Crossovers.G1DListCrossoverUniform)
#code genetic
# thiet lap he so lai ghep
self.ga = GSimpleGA.GSimpleGA(self.weights)
self.ga.selector.set(Selectors.GRouletteWheel)
self.ga.setMutationRate(self.mutation_rate)
self.ga.setCrossoverRate(self.cross_rate)
self.ga.setPopulationSize(self.pop_size)
self.ga.setGenerations(self.pop_size)
self.ga.terminationCriteria.set(GSimpleGA.ConvergenceCriteria)
self.ga.evolve(freq_stats=self.freq_stats)
self.best_archive = self.getParam()
return self
def fit(self, X, y, **param):
self.X = X
self.y = y
self.neural_shape = param.get('neural_shape')
self.archive = param.get("archive")
if param.has_key("top_k"):
self.top_k = param.get("top_k")
self.score_fn = FeedFlow(self.neural_shape)
self.score_fn.set_weights(self.optimize(X, y))
return self
def fit(self, X, y,**param):
self.X = X
self.y = y
self.neural_shape = param.get('neural_shape')
self.archive = param.get("archive")
if param.has_key("top_k"):
self.top_k = param.get("top_k")
self.score_fn = FeedFlow(self.neural_shape)
self.score_fn.set_weights(self.optimize(X,y))
return self
def fit(self, X, y,**param):
self.X = X
self.y = y
if (param.has_key('neural_shape')):
self.neural_shape = param.get("neural_shape")
self.n_output = self.neural_shape[-1]
self.n_hidden = self.neural_shape[1:-1]
self.number_of_layers = len(self.neural_shape)
else:
self.n_input = len(X[0])
self.n_output = len(y[0])
self.neural_shape = self.hidden_nodes.tolist()
self.neural_shape.insert(0, self.n_input)
self.neural_shape.append(self.n_output)
self.n_hidden = self.hidden_nodes
self.archive = param.get("archive")
if param.has_key("top_k"):
self.top_k = param.get("top_k")
self.score_fn = FeedFlow(self.neural_shape)
self.score_fn.set_weights(self.optimize(X,y))
return self
def fit(self, X, y,**param):
self.X = X
self.y = y
if (param.has_key('neural_shape')):
self.neural_shape = param.get("neural_shape")
self.n_output = self.neural_shape[-1]
self.n_hidden = self.neural_shape[1:-1]
self.number_of_layers = len(self.neural_shape)
else:
self.n_input = len(X[0])
self.n_output = len(y[0])
self.neural_shape = self.hidden_nodes.tolist()
self.neural_shape.insert(0, self.n_input)
self.neural_shape.append(self.n_output)
self.n_hidden = self.hidden_nodes
self.archive = param.get("archive")
if param.has_key("top_k"):
self.top_k = param.get("top_k")
self.score_fn = FeedFlow(self.neural_shape)
self.score_fn.set_weights(self.optimize(X,y))
return self
class GAEstimator(BaseEstimator):
def __init__(self,gen_size=400,pop_size = 225,cross_rate=0.9,mutation_rate = 0.01,freq_stats=10):
# self.n_input = n_input
# self.fan_in = n_input
# self.fan_out = 15
# self.theta_shape = (self.n_input,1)
self.gen_size = gen_size
self.pop_size = pop_size
self.cross_rate = cross_rate
self.mutation_rate = mutation_rate
self.freq_stats = freq_stats
def get_params(self, deep=True):
return {
"gen_size": self.gen_size,
"pop_size": self.pop_size,
"cross_rate": self.cross_rate,
"mutation_rate": self.mutation_rate,
"freq_stats": self.freq_stats
}
def set_params(self, **params):
for param,value in params.items():
self.__setattr__(param,value)
return self
# def activation(self,x):
# return sigmoid(x)
def eval_score(self,chronosome):
# theta = np.zeros(self.theta_shape)
# for i in np.arange(self.theta_shape[0]):
# theta[i] = chronosome[i]
# return self.costFunction(self.X_data,self.y_data,theta)
self.score_fn.set_weights(np.array(chronosome.genomeList))
return self.score_fn.score(self.X,self.y)
def fit(self,X,y,**param):
self.neural_shape = param.get("neural_shape")
self.n_input = self.neural_shape[0]
self.n_output = self.neural_shape[-1]
self.n_hidden = self.neural_shape[1]
self.number_of_weights = self.n_hidden*(self.n_input+1)+self.n_output*(self.n_hidden+1)
self.score_fn = FeedFlow(self.neural_shape)
self.X = X
self.y = y
#setting params
self.weights = G1DList.G1DList(self.number_of_weights)
lim = np.sqrt(6)/np.sqrt((self.n_input+self.n_output))
#Khoi tao trong so
self.weights.setParams(rangemin=-lim,rangemax=lim)
# cai dat ham khoi tao
self.weights.initializator.set(Initializators.G1DListInitializatorReal)
#cai dat ham dot bien
self.weights.mutator.set(Mutators.G1DListMutatorRealGaussian)
#cai dat ham do thich nghi
self.weights.evaluator.set(self.eval_score)
# cai dat ham lai ghep
self.weights.crossover.set(Crossovers.G1DListCrossoverUniform)
#code genetic
# thiet lap he so lai ghep
self.ga = GSimpleGA.GSimpleGA(self.weights)
self.ga.selector.set(Selectors.GRouletteWheel)
self.ga.setMutationRate(self.mutation_rate)
self.ga.setCrossoverRate(self.cross_rate)
self.ga.setPopulationSize(self.pop_size)
self.ga.setGenerations(self.pop_size)
self.ga.terminationCriteria.set(GSimpleGA.ConvergenceCriteria)
self.ga.evolve(freq_stats=self.freq_stats)
self.best_archive = self.getParam()
return self
def getParam(self):
return np.array(self.ga.bestIndividual().genomeList)
def predict(self,X):
return self.score_fn.predict(X)
def score(self,X,y):
return np.sqrt(mean_squared_error(y, self.predict(X)))
class ACOEstimator(BaseEstimator):
def __init__(self,neural_shape=None,number_of_weights=None,number_of_solutions=100,max_epochs = 100,error_criteria = 0.9,
epsilon = 0.75,const_sd = 0.1,Q=0.08,hidden_nodes=None,**kwargs):
self.epsilon = epsilon
self.max_epochs = max_epochs
self.error_criteria = error_criteria
self.number_of_solutions = self.k = number_of_solutions
self.number_of_weights = number_of_weights
self.const_sd = const_sd
self.neural_shape = neural_shape
self.Q = Q #Attractive param, q is small, the best-ranked solution is strongly preferred
self.best_loss = np.Inf
self.best_archive = []
self._estimator_type="regressor"
self.top_k = 1
self.hidden_nodes = hidden_nodes
#self.monitor = Monitor(type_train="ACO Optimization")
def get_params(self, deep=True):
return {
"epsilon":self.epsilon,
"max_epochs":self.max_epochs,
"number_of_solutions":self.number_of_solutions,
"Q":self.Q,
"error_criteria":self.error_criteria,
"number_of_weights":self.number_of_weights,
"neural_shape":self.neural_shape,
"const_sd":self.const_sd
}
def set_params(self, **params):
for param,value in params.items():
self.__setattr__(param,value)
return self
def optimize(self,X=None,y=None):
self.X = X
self.y = y
if self.archive == None:
self.archive = construct_solution(self.number_of_solutions,self.neural_shape)
self.sorted_archive = self.calculate_fitness(self.score_fn,self.archive)
weights = self.calculate_weights(self.archive.shape)
self.archive = self.sampling_more(self.sorted_archive,weights,self.epsilon)
self.sorted_archive = self.calculate_fitness(self.score_fn,self.archive)
for i in np.arange(self.max_epochs):
# try:
# print summary_writter[-1]
if(self.sorted_archive==None):
return self.archive[0]
self.archive = self.sampling_more(self.sorted_archive,weights,self.epsilon)
self.sorted_archive = self.calculate_fitness(self.score_fn,self.archive)
# print "ACO - Epoch %s. Training loss: %s"%(i,self.best_loss)
#self.monitor.update(step=i,loss=self.best_loss)
# except Exception as e:
# print e
# break
sys.stdout.write("Found best loss %f"%self.monitor.min_loss)
return self.best_archive
def fit(self, X, y,**param):
self.X = X
self.y = y
if (param.has_key('neural_shape')):
self.neural_shape = param.get("neural_shape")
self.n_output = self.neural_shape[-1]
self.n_hidden = self.neural_shape[1:-1]
self.number_of_layers = len(self.neural_shape)
else:
self.n_input = len(X[0])
self.n_output = len(y[0])
self.neural_shape = self.hidden_nodes.tolist()
self.neural_shape.insert(0, self.n_input)
self.neural_shape.append(self.n_output)
self.n_hidden = self.hidden_nodes
self.archive = param.get("archive")
if param.has_key("top_k"):
self.top_k = param.get("top_k")
self.score_fn = FeedFlow(self.neural_shape)
self.score_fn.set_weights(self.optimize(X,y))
return self
def predict(self,X):
return self.score_fn.flow(X)
def score(self,X,y):
return self.score_fn.score(X,y)
def calculate_fitness(self,score_fn,archive):
fitness_solution = np.zeros(archive.shape[0])
for (index,candidate) in enumerate(archive):
score_fn.set_weights(candidate)
result = score_fn.score(self.X,self.y)
# print result
fitness_solution[index] = result
min_score = fitness_solution.min()
# print min_score
if(min_score >= self.error_criteria):
return None
sorted_idx = np.argsort(fitness_solution)
sorted_archive = np.zeros(archive.shape)
for (index,item) in enumerate(sorted_idx):
sorted_archive[item] = archive[index]
if min_score < self.best_loss :
self.best_loss = min_score
self.best_archive = sorted_archive[0]
return sorted_archive
# In[102]:
def calculate_weights(self,shape):
weights = np.zeros([shape[0],1])
# qk = 0.1
co_efficient = 1.0 / (0.1 * np.sqrt(2*np.pi))
for index in np.arange(shape[0]):
exponent = np.square(index-1) / (2*np.square(self.Q*shape[0]))
weights[index] = np.multiply(co_efficient,np.exp(-exponent))
return weights
def compute_standard_deviation(self,i,l,archive,epsilon):
__doc__ = " compute standard deviation with i, l, archive and epsilon"
#Constant sd
sd = 0.01
sum_dev = np.abs(np.sum(archive[l]-archive[l][i])/(archive.shape[0]-1))
# if(sum_dev <= 0.00001):
# return sd
return np.multiply(sum_dev,epsilon)
# In[104]:
def choose_pdf(self, archive_shape, weights):
sum_weights = np.sum(weights)
temp = 0
l = 0
pro_r = np.random.uniform(0.0, 1.0)
for (index,weight) in enumerate(weights):
temp = temp + weight/sum_weights
if(temp > pro_r):
l = index
return l
def sampling_more(self, archive, weights, epsilon):
# pdf = 0
len_of_weights = range(archive.shape[1])
next_archive = np.zeros(archive.shape)
for index in np.arange(archive.shape[0]):
i_pdf = self.choose_pdf(archive.shape,weights)
# for item in np.arange(archive.shape[1]):
# sigma = self.compute_standard_deviation(item,i_pdf,archive,epsilon)
# mu = archive[pdf][item]
# # print sigma,mu
# next_archive[index][item] = np.random.normal(mu,sigma)
next_archive[index] = [np.random.normal(archive[index,item],self.compute_standard_deviation(item,i_pdf,archive,epsilon)) for item in len_of_weights]
return next_archive
class ACOEstimator(BaseEstimator):
def __init__(self,
neural_shape=None,
number_of_weights=None,
number_of_solutions=100,
max_epochs=100,
error_criteria=0.9,
epsilon=0.75,
const_sd=0.1,
Q=0.08,
**kwargs):
self.epsilon = epsilon
self.max_epochs = max_epochs
self.error_criteria = error_criteria
self.number_of_solutions = self.k = number_of_solutions
self.number_of_weights = number_of_weights
self.const_sd = const_sd
self.neural_shape = neural_shape
self.Q = Q #Attractive param, q is small, the best-ranked solution is strongly preferred
self.best_loss = np.Inf
self.best_archive = []
self._estimator_type = "regressor"
self.top_k = 1
def get_params(self, deep=True):
return {
"epsilon": self.epsilon,
"max_epochs": self.max_epochs,
"number_of_solutions": self.number_of_solutions,
"Q": self.Q,
"error_criteria": self.error_criteria,
"number_of_weights": self.number_of_weights,
"neural_shape": self.neural_shape,
"const_sd": self.const_sd
}
def set_params(self, **params):
for param, value in params.items():
self.__setattr__(param, value)
return self
def optimize(self, X=None, y=None):
self.X = X
self.y = y
if self.archive == None:
self.archive = construct_solution(self.number_of_solutions,
self.neural_shape)
self.sorted_archive = self.calculate_fitness(self.score_fn,
self.archive)
weights = self.calculate_weights(self.archive.shape)
self.archive = self.sampling_more(self.sorted_archive, weights,
self.epsilon)
self.sorted_archive = self.calculate_fitness(self.score_fn,
self.archive)
for i in np.arange(self.max_epochs):
# try:
# print summary_writter[-1]
if (self.sorted_archive == None):
return self.archive[0]
# best_error = summary_writter[-1]
# weights = self.calculate_weights(self.archive.shape)
self.archive = self.sampling_more(self.sorted_archive, weights,
self.epsilon)
self.sorted_archive = self.calculate_fitness(
self.score_fn, self.archive)
# except Exception as e:
# print e
# break
print "Found best loss %f" % self.best_loss
return self.best_archive
def fit(self, X, y, **param):
self.X = X
self.y = y
self.neural_shape = param.get('neural_shape')
self.archive = param.get("archive")
if param.has_key("top_k"):
self.top_k = param.get("top_k")
self.score_fn = FeedFlow(self.neural_shape)
self.score_fn.set_weights(self.optimize(X, y))
return self
def predict(self, X):
return self.score_fn.flow(X)
def score(self, X, y):
return self.score_fn.score(X, y)
def calculate_fitness(self, score_fn, archive):
fitness_solution = np.zeros(archive.shape[0])
for (index, candidate) in enumerate(archive):
score_fn.set_weights(candidate)
result = score_fn.score(self.X, self.y)
# print result
fitness_solution[index] = result
min_score = fitness_solution.min()
# print min_score
if (min_score >= self.error_criteria):
return None
sorted_idx = np.argsort(fitness_solution)
sorted_archive = np.zeros(archive.shape)
for (index, item) in enumerate(sorted_idx):
sorted_archive[item] = archive[index]
if min_score < self.best_loss:
self.best_loss = min_score
self.best_archive = sorted_archive[0]
return sorted_archive
# In[102]:
def calculate_weights(self, shape):
weights = np.zeros([shape[0], 1])
# qk = 0.1
co_efficient = 1.0 / (0.1 * np.sqrt(2 * np.pi))
for index in np.arange(shape[0]):
exponent = np.square(index - 1) / (2 *
np.square(self.Q * shape[0]))
weights[index] = np.multiply(co_efficient, np.exp(-exponent))
return weights
def compute_standard_deviation(self, i, l, archive, epsilon):
__doc__ = " compute standard deviation with i, l, archive and epsilon"
#Constant sd
sd = 0.01
sum_dev = np.abs(
np.sum(archive[l] - archive[l][i]) / (archive.shape[0] - 1))
# if(sum_dev <= 0.00001):
# return sd
return np.multiply(sum_dev, epsilon)
# In[104]:
def choose_pdf(self, archive_shape, weights):
sum_weights = np.sum(weights)
temp = 0
l = 0
pro_r = np.random.uniform(0.0, 1.0)
for (index, weight) in enumerate(weights):
temp = temp + weight / sum_weights
if (temp > pro_r):
l = index
return l
def sampling_more(self, archive, weights, epsilon):
# pdf = 0
len_of_weights = range(archive.shape[1])
next_archive = np.zeros(archive.shape)
for index in np.arange(archive.shape[0]):
i_pdf = self.choose_pdf(archive.shape, weights)
# for item in np.arange(archive.shape[1]):
# sigma = self.compute_standard_deviation(item,i_pdf,archive,epsilon)
# mu = archive[pdf][item]
# # print sigma,mu
# next_archive[index][item] = np.random.normal(mu,sigma)
next_archive[index] = [
np.random.normal(
archive[index, item],
self.compute_standard_deviation(item, i_pdf, archive,
epsilon))
for item in len_of_weights
]
return next_archive