def main():
"""Run the demo."""
# grab a test function
f = SubprocessQuery("bc <<< 'scale=8; x={}; -((x-3)^2)'")
bounds = [0, 8]
x = np.linspace(bounds[0], bounds[1], 500)
# solve the model
xbest, model, info = solve_bayesopt(f, bounds, niter=30, verbose=True)
mu, s2 = model.predict(x[:, None])
# plot the final model
ax = figure().gca()
ax.plot_banded(x, mu, 2 * np.sqrt(s2))
ax.axvline(xbest)
ax.scatter(info.x.ravel(), info.y)
ax.figure.canvas.draw()
show()
def main(debug=False):
warnings.filterwarnings('ignore')
unbuffered = os.fdopen(sys.stdout.fileno(), 'w', 0)
sys.stdout = unbuffered
print 'Initiating hyperopt at {}'.format(datetime.now())
global train_data, test_data, id1_train, id1_test, DEBUG, NUM_CORES, NUM_EPOCHS
DEBUG = debug
NUM_CORES = 48
NUM_EPOCHS = 50
train_data, test_data, id1_train, id1_test = load_data(debug=DEBUG)
num_features = train_data.num_features
bounds = [
[2, 4], # num_layers
[10, num_features], # hidden_size
[0.001, 0.01], # learning_rate
[0.5, 1.0], # keep_prob
[1, 1], # num_steps
[0.0, 0.05], # init_scale
[15, 15] # max_grad_norm
]
xbest, model, info = solve_bayesopt(objective,
bounds,
niter=100,
verbose=True)
run_best_model(xbest)
save_path = train_data.config[
'OutputInSample'][:train_data.config['OutputInSample'].rfind('/')]
pickle.dump(info, open(save_path + '/trials', 'wb'))
def main():
"""Run the demo."""
# grab a test function
f = SubprocessQuery("bc <<< 'scale=8; x={}; -((x-3)^2)'")
bounds = [0, 8]
x = np.linspace(bounds[0], bounds[1], 500)
# solve the model
xbest, model, info = solve_bayesopt(f, bounds, niter=30, verbose=True)
mu, s2 = model.predict(x[:, None])
# plot the final model
ax = figure().gca()
ax.plot_banded(x, mu, 2*np.sqrt(s2))
ax.axvline(xbest)
ax.scatter(info.x.ravel(), info.y)
ax.figure.canvas.draw()
show()
def main():
"""Run the demo."""
# grab a test function
bounds = [0, 2*np.pi]
x = np.linspace(bounds[0], bounds[1], 500)
# solve the model
xbest, model, info = solve_bayesopt(f, bounds, niter=30, verbose=True)
# make some predictions
mu, s2 = model.predict(x[:, None])
# plot the final model
ax = figure().gca()
ax.plot_banded(x, mu, 2*np.sqrt(s2))
ax.axvline(xbest)
ax.scatter(info.x.ravel(), info.y)
ax.figure.canvas.draw()
show()
def main():
"""Run the demo."""
# initialize interactive function and 1d bounds
f = InteractiveQuery()
bounds = [0, 1]
x = np.linspace(bounds[0], bounds[1], 100)
# optimize the model and get final predictions
xbest, model, info = solve_bayesopt(f, bounds, niter=10)
mu, s2 = model.predict(x[:, None])
# plot the final model
fig = figure()
axs = fig.gca()
axs.plot_banded(x, mu, 2*np.sqrt(s2))
axs.axvline(xbest)
axs.scatter(info.x.ravel(), info.y)
fig.canvas.draw()
show()
xmax = 10 # FIXME - should this not be optional?
@staticmethod
def _f(x):
# iris = load_iris()
X, y = X, y = make_hastie_10_2(random_state=0)
x = np.ravel(x)
f = np.zeros(x.shape)
for i in range(f.size):
clf = RandomForestClassifier(n_estimators=1, min_samples_leaf=int(np.round(x[i])), random_state=0)
# scores = cross_val_score(clf, iris.data, iris.target)
scores = cross_val_score(clf, X, y, cv=5)
f[i] = -scores.mean()
return f.ravel()
if __name__ == '__main__':
objective = CV_RF()
info = pybo.solve_bayesopt(
objective,
objective.bounds,
niter=25,
noisefree=False,
rng=0,
init='uniform',
callback=callback_1d)
print('Finished')
raw_input('Press enter to finish')
Simplest demo performing Bayesian optimization on a one-dimensional test
function. This script also demonstrates user-defined visualization via a
callback function that is imported from the advanced demo.
The `pybo.solve_bayesopt()` function returns a numpy structured array, called
`info` below, which includes the observed input and output data, `info['x']` and
`info['y']`, respectively; and the recommendations made along the way in
`info['xbest']`.
The `callback` function plots the posterior with uncertainty bands, overlaid
onto the true function; below it we plot the acquisition function, and to the
right, the evolution of the recommendation over time.
"""
import pybo
# import callback from advanced demo
import os
import sys
sys.path.append(os.path.dirname(__file__))
from advanced import callback
if __name__ == '__main__':
objective = pybo.functions.Sinusoidal()
info = pybo.solve_bayesopt(objective,
objective.bounds,
noisefree=True,
rng=0,
callback=callback)
bounds = objective.bounds # bounds of search space
dim = bounds.shape[0] # dimension of space
# prescribe initial hyperparameters
sn = noise # likelihood std dev
sf = 1.0 # kernel amplitude
ell = 0.25 * (bounds[:, 1] - bounds[:, 0]) # kernel length scale
mu = 0.0 # prior mean
# define model
kernel = 'matern3' # kernel family
gp = pygp.BasicGP(sn, sf, ell, mu, kernel=kernel) # initialize base GP
prior = { # hyperparameter priors
'sn': pygp.priors.Horseshoe(0.1, min=1e-5),
'sf': pygp.priors.LogNormal(np.log(sf), sigma=1., min=1e-6),
'ell': pygp.priors.Uniform(ell / 100, ell * 2),
'mu': pygp.priors.Gaussian(mu, sf)}
model = pygp.meta.MCMC(gp, prior, n=10, rng=rng) # meta-model for MCMC
# marginalization
info = pybo.solve_bayesopt(
objective,
bounds,
niter=30*dim,
init='sobol', # initialization policy
policy='ei', # exploration policy
recommender='incumbent', # recommendation policy
model=model, # surrogate model
rng=rng,
callback=callback)
if __name__ == '__main__':
N = 200
D = 2
Z = np.random.randn(N, D)
m = N
num_folds = 5
num_repetitions = 10
lmbda = 0.0001
sigma = 0.92
objective = generator_sigma_lmbda_objective()
info = pybo.solve_bayesopt(objective,
bounds=np.array([[-5, 5], [-20, 1]]),
noisefree=False,
callback=callback_sigma_lmbda,
niter=15)
print("x")
print(info['x'])
print("y")
print(info['y'])
print("xbest")
print(info['xbest'])
pl.figure()
pl.plot(info['x'], info['y'], 'o')
pl.show()
@staticmethod
def _f(x):
# iris = load_iris()
X, y = X, y = make_hastie_10_2(random_state=0)
x = np.ravel(x)
f = np.zeros(x.shape)
for i in range(f.size):
clf = RandomForestClassifier(n_estimators=1,
min_samples_leaf=int(np.round(x[i])),
random_state=0)
# scores = cross_val_score(clf, iris.data, iris.target)
scores = cross_val_score(clf, X, y, cv=5)
f[i] = -scores.mean()
return f.ravel()
if __name__ == '__main__':
objective = CV_RF()
info = pybo.solve_bayesopt(objective,
objective.bounds,
niter=25,
noisefree=False,
rng=0,
init='uniform',
callback=callback_1d)
print('Finished')
raw_input('Press enter to finish')
import pybo
# import callback from advanced demo
import os
import sys
sys.path.append(os.path.dirname(__file__))
from advanced import callback
if __name__ == '__main__':
rng = 0 # random seed
bounds = np.array([3, 5]) # bounds of search space
dim = bounds.shape[0] # dimension of space
# define a GP which we will sample an objective from.
likelihood = pygp.likelihoods.Gaussian(sigma=1e-6)
kernel = pygp.kernels.Periodic(1, 1, 0.5) + pygp.kernels.SE(1, 1)
gp = pygp.inference.ExactGP(likelihood, kernel, mean=0.0)
objective = pybo.functions.GPModel(bounds, gp, rng=rng)
info = pybo.solve_bayesopt(
objective,
bounds,
niter=30*dim,
init='latin', # initialization policy
policy='thompson', # exploration policy
recommender='observed', # recommendation policy
noisefree=True,
rng=rng,
callback=callback)
