N_test = test_set_x.get_value(borrow = True).shape[ 0 ]
layer_sizes = [ d, 100, len(mean_y_train) ]
n_samples = 50
alpha = 10e-6
learning_rate = 0.001
v_prior = 1.0
# NEED TO REDUCE BATCH SIZE IF AL EXPERIMENT IS STARTING WITH 20 DATA POINTS
# batch_size = 32
batch_size = 16
print '... building model'
sys.stdout.flush()
bb_alpha = BB_alpha(layer_sizes, n_samples, alpha, learning_rate, v_prior, batch_size, train_set_x, train_set_y, N_train, test_set_x, test_set_y, N_test, mean_y_train, std_y_train)
print '... training'
sys.stdout.flush()
#test_error, test_ll = bb_alpha.train_ADAM(adam_epochs)
test_error, test_ll = bb_alpha.train_ADAM(adam_epochs)
print('Test Error', test_error)
print('Test Log Likelihood', test_ll)
all_rmse = test_error
for i in range(acquisition_iterations):
# We load the data
datasets, n, d, n_labels = load_data('/tmp/mnist.pkl.gz')
train_set_x, train_set_y = datasets[ 0 ]
test_set_x, test_set_y = datasets[ 1 ]
N_train = train_set_x.get_value(borrow = True).shape[ 0 ]
N_test = test_set_x.get_value(borrow = True).shape[ 0 ]
layer_sizes = [ d, 400, 400, n_labels ]
n_samples = 50
alpha = 0.5
learning_rate = 0.0001
v_prior = 1.0
batch_size = 250
print '... building model'
sys.stdout.flush()
bb_alpha = BB_alpha(layer_sizes, n_samples, alpha, learning_rate, v_prior, batch_size, \
train_set_x, train_set_y, N_train, test_set_x, test_set_y, N_test)
print '... training'
sys.stdout.flush()
test_error, test_ll = bb_alpha.train(250)
with open("results/test_ll.txt", "a") as myfile:
myfile.write(repr(test_ll) + '\n')
with open("results/test_error.txt", "a") as myfile:
myfile.write(repr(test_error) + '\n')
layer_sizes = [ d, 100, len(mean_y_train) ]
n_samples = 50
alpha = 0.5
learning_rate = 0.001
v_prior = 1.0
# NEED TO REDUCE BATCH SIZE IF AL EXPERIMENT IS STARTING WITH 20 DATA POINTS
batch_size = 32
print '... building model'
sys.stdout.flush()
bb_alpha = BB_alpha(layer_sizes, n_samples, alpha, learning_rate, v_prior, batch_size, \
train_set_x, train_set_y, N_train, test_set_x, test_set_y, N_test, mean_y_train, std_y_train)
print '... training'
sys.stdout.flush()
#test_error, test_ll = bb_alpha.train_ADAM(500)
test_error, test_ll = bb_alpha.train_ADAM(20)
print('Test Error', test_error)
print('Test Log Likelihood', test_ll)
# with open("results/test_ll.txt", "a") as myfile:
# myfile.write(repr(test_ll) + '\n')
# with open("results/test_error.txt", "a") as myfile:
datasets, n, d, mean_y_train, std_y_train = load_data()
train_set_x, train_set_y = datasets[ 0 ]
test_set_x, test_set_y = datasets[ 1 ]
N_train = train_set_x.get_value(borrow = True).shape[ 0 ]
N_test = test_set_x.get_value(borrow = True).shape[ 0 ]
layer_sizes = [ d, 100, len(mean_y_train) ]
n_samples = 50
alpha = 0.0001
learning_rate = 0.001
v_prior = 1.0
batch_size = 32
print '... building model'
sys.stdout.flush()
bb_alpha = BB_alpha(layer_sizes, n_samples, alpha, learning_rate, v_prior, batch_size, \
train_set_x, train_set_y, N_train, test_set_x, test_set_y, N_test, mean_y_train, std_y_train)
print '... training'
sys.stdout.flush()
test_error, test_ll = bb_alpha.train_ADAM(500)
print('Test Error', test_error)
print('Test Log Likelihood', test_ll)
# with open("results/test_ll.txt", "a") as myfile:
# myfile.write(repr(test_ll) + '\n')
# with open("results/test_error.txt", "a") as myfile:
# myfile.write(repr(test_error) + '\n')
N_train = train_set_x.get_value(borrow=True).shape[0]
N_test = test_set_x.get_value(borrow=True).shape[0]
layer_sizes = [d, 100, len(mean_y_train)]
n_samples = 50
alpha = 0.5
learning_rate = 0.001
v_prior = 1.0
# NEED TO REDUCE BATCH SIZE IF AL EXPERIMENT IS STARTING WITH 20 DATA POINTS
batch_size = 32
print '... building model'
sys.stdout.flush()
bb_alpha = BB_alpha(layer_sizes, n_samples, alpha, learning_rate, v_prior,
batch_size, train_set_x, train_set_y, N_train, test_set_x,
test_set_y, N_test, mean_y_train, std_y_train)
print '... training'
sys.stdout.flush()
#test_error, test_ll = bb_alpha.train_ADAM(adam_epochs)
test_error, test_ll = bb_alpha.train_ADAM(adam_epochs)
print('Test Error', test_error)
print('Test Log Likelihood', test_ll)
all_rmse = test_error
for i in range(acquisition_iterations):
def main(input_directory, output_directory):
"""
:param input_directory: directory to which the output of Branin_Sampler.py was saved.
:param output_directory: directory in which to save the plots.
"""
np.random.seed(2)
# Load the dataset
X_bran = genfromtxt(input_directory + '/inputs.csv',
delimiter=',',
dtype='float32')
y_con = genfromtxt(input_directory + '/constraint_targets.csv',
delimiter=',',
dtype='int')
y_reg = genfromtxt(input_directory + '/branin_targets.csv',
delimiter=',',
dtype='float32')
y_reg = y_reg.reshape((-1, 1))
# We convert constraint targets from one-hot to categorical.
y_con_cat = np.zeros(len(y_con), dtype=int)
i = 0
for element in y_con:
if element[0] == 1:
y_con_cat[i] = 1
else:
y_con_cat[i] = 0
i += 1
y_con = y_con_cat
n_bran = X_bran.shape[0] # number of examples
permutation = np.random.choice(n_bran, n_bran,
replace=False) # We shuffle the data
X_tr_bran = X_bran[permutation, :][40:np.int(np.round(
0.9 * n_bran)), :] # 50/10 train/test split.
X_te_bran = X_bran[permutation, :][
np.int(np.round(0.8 * n_bran)):np.int(np.round(0.9 * n_bran)), :]
y_tr_reg = y_reg[permutation][40:np.int(
np.round(0.9 * n_bran)
)] # 10:20 have balanced class split after the permutation is applied with random seed = 1
y_te_reg = y_reg[permutation][np.int(np.round(0.8 * n_bran)):np.
int(np.round(0.9 * n_bran))]
y_tr_con = y_con[permutation][40:np.int(
np.round(0.9 * n_bran)
)] # no test set for constraint as traning subroutine for BNN doesn't require it
y_te_con = y_con[permutation][np.int(np.round(0.8 * n_bran)):np.
int(np.round(0.9 * n_bran))]
# We plot the data used to initialise the surrogate model
X1 = X_tr_bran[:, 0]
X2 = X_tr_bran[:, 1]
save_object(X1, output_directory + "/X1.dat")
save_object(X2, output_directory + "/X2.dat")
# We store the best feasible value found in the training set for reference
feasible_vals = []
for i in range(X_tr_bran.shape[0]):
if y_tr_con[i] == 0:
continue
feasible_vals.append([branin(tuple(X_tr_bran[i]))])
best_tr = min(feasible_vals)
best_tr = best_tr[0]
save_object(best_tr,
output_directory + "/best_feasible_training_point.dat")
# We set the number of data colletion iterations
num_iters = 4
for iteration in range(num_iters):
# We train the regression model
# We fit the GP
# M = np.int(np.maximum(10,np.round(0.1 * n_bran)))
M = 20
sgp = SparseGP(X_tr_bran, 0 * X_tr_bran, y_tr_reg, M)
sgp.train_via_ADAM(X_tr_bran,
0 * X_tr_bran,
y_tr_reg,
X_te_bran,
X_te_bran * 0,
y_te_reg,
minibatch_size=M,
max_iterations=400,
learning_rate=0.005)
save_object(sgp, output_directory + "/sgp{}.dat".format(iteration))
# We load the saved gp
sgp = load_object(output_directory + "/sgp{}.dat".format(iteration))
# We load some previous trained gp
pred, uncert = sgp.predict(X_te_bran, 0 * X_te_bran)
error = np.sqrt(np.mean((pred - y_te_reg)**2))
testll = np.mean(
sps.norm.logpdf(pred - y_te_reg, scale=np.sqrt(uncert)))
print('Test RMSE: ', error)
print('Test ll: ', testll)
pred, uncert = sgp.predict(X_tr_bran, 0 * X_tr_bran)
error = np.sqrt(np.mean((pred - y_tr_reg)**2))
trainll = np.mean(
sps.norm.logpdf(pred - y_tr_reg, scale=np.sqrt(uncert)))
print('Train RMSE: ', error)
print('Train ll: ', trainll)
# we train the constraint network
# We load the random seed
seed = 1
np.random.seed(seed)
# We load the data
datasets, n, d, n_labels = load_data(X_tr_bran, y_tr_con, X_te_bran,
y_te_con)
train_set_x, train_set_y = datasets[0]
test_set_x, test_set_y = datasets[1]
N_train = train_set_x.get_value(borrow=True).shape[0]
N_test = test_set_x.get_value(borrow=True).shape[0]
layer_sizes = [d, 50, n_labels]
n_samples = 50
alpha = 0.5
learning_rate = 0.001
v_prior = 1.0
batch_size = 10
print('... building model')
sys.stdout.flush()
bb_alpha = BB_alpha(layer_sizes, n_samples, alpha, learning_rate,
v_prior, batch_size, train_set_x, train_set_y,
N_train, test_set_x, test_set_y, N_test)
print('... training')
sys.stdout.flush()
test_error, test_ll = bb_alpha.train(400)
# We save the trained BNN
sys.setrecursionlimit(4000) # Required to save the BNN
save_object(bb_alpha,
output_directory + "/bb_alpha{}.dat".format(iteration))
# We pick the next 5 inputs based on random sampling
np.random.seed()
num_inputs = 1
x1 = np.random.uniform(-5, 10, size=num_inputs)
x2 = np.random.uniform(0, 15, size=num_inputs)
random_inputs = np.zeros([num_inputs, 2])
random_inputs[:, 0] = x1
random_inputs[:, 1] = x2
reg_scores = [] # collect y-values for Branin-Hoo function
con_scores = [] # collect y-values for Constraint function
probs = [] # collect the probabilities of satisfying the constraint
log_probs = [
] # collect the log probabilities of satisfying the constraint
for i in range(random_inputs.shape[0]):
reg_scores.append([branin(tuple(random_inputs[i]))])
if (random_inputs[i][0] - 2.5)**2 + (random_inputs[i][1] -
7.5)**2 <= 50:
con_scores.append(np.int64(1))
else:
con_scores.append(np.int64(0))
probs.append(
bb_alpha.prediction_probs(random_inputs[i].reshape(
1, d))[0][0][1])
log_probs.append(
bb_alpha.pred_log_probs(random_inputs[i].reshape(1,
d))[0][0][1])
print(i)
# print the value of the Branin-Hoo function at the data points we have acquired
print(reg_scores)
# save y-values and (x1,x2)-coordinates of locations chosen for evaluation
save_object(reg_scores,
output_directory + "/scores{}.dat".format(iteration))
save_object(random_inputs,
output_directory + "/next_inputs{}.dat".format(iteration))
save_object(con_scores,
output_directory + "/con_scores{}.dat".format(iteration))
save_object(probs, output_directory + "/probs{}.dat".format(iteration))
save_object(log_probs,
output_directory + "/log_probs{}.dat".format(iteration))
# extend labelled training data for next cycle
X_tr_bran = np.concatenate([X_tr_bran, random_inputs], 0)
y_tr_reg = np.concatenate([y_tr_reg, np.array(reg_scores)], 0)
y_tr_con = np.concatenate([y_tr_con, np.array(con_scores)], 0)
best_so_far(
output_directory, num_iters
) # Plot the best point as a function of the data collection iteration number
GP_contours(output_directory,
num_iters) # Plot the contours of the GP regression model
BNN_contours(output_directory,
num_iters) # Plot the contours of the BNN constraint model
initial_data(
output_directory) # Plot the data used to initialise the model
layer_sizes = [ d, 100, len(mean_y_train) ]
n_samples = 50
alpha = 0.5
learning_rate = 0.001
v_prior = 1.0
# NEED TO REDUCE BATCH SIZE IF AL EXPERIMENT IS STARTING WITH 20 DATA POINTS
batch_size = 32
print '... building model'
sys.stdout.flush()
bb_alpha = BB_alpha(layer_sizes, n_samples, alpha, learning_rate, v_prior, batch_size, train_set_x, train_set_y, N_train, test_set_x, test_set_y, N_test, mean_y_train, std_y_train)
print '... training'
sys.stdout.flush()
#test_error, test_ll = bb_alpha.train_ADAM(adam_epochs)
test_error, test_ll = bb_alpha.train_ADAM(adam_epochs)
print('Test Error', test_error)
print('Test Log Likelihood', test_ll)
all_rmse = test_error
for i in range(acquisition_iterations):