def test_bounded_bq_raises(gpy_model):
gpy_model, _ = gpy_model
measure = LebesgueMeasure.from_bounds(gpy_model.X.shape[1] * [(0, 1)],
normalized=False)
qrbf = QuadratureRBFLebesgueMeasure(RBFGPy(gpy_model.kern),
measure=measure)
base_gp_wrong_kernel = BaseGaussianProcessGPy(kern=qrbf,
gpy_model=gpy_model)
# wrong kernel embedding
with pytest.raises(ValueError):
BoundedBayesianQuadrature(
base_gp=base_gp_wrong_kernel,
X=base_gp_wrong_kernel.X,
Y=base_gp_wrong_kernel.Y,
lower_bound=np.min(base_gp_wrong_kernel.Y) - 0.5,
)
# both upper and lower bound are given
with pytest.raises(ValueError):
BoundedBayesianQuadrature(
base_gp=base_gp_wrong_kernel,
X=base_gp_wrong_kernel.X,
Y=base_gp_wrong_kernel.Y,
lower_bound=np.min(base_gp_wrong_kernel.Y) - 0.5,
upper_bound=np.min(base_gp_wrong_kernel.Y) - 0.5,
)
# no bound is given
with pytest.raises(ValueError):
BoundedBayesianQuadrature(base_gp=base_gp_wrong_kernel,
X=base_gp_wrong_kernel.X,
Y=base_gp_wrong_kernel.Y)
def test_vanilla_bq_loop():
init_size = 5
x_init = np.random.rand(init_size, 2)
y_init = np.random.rand(init_size, 1)
bounds = [(-1, 1), (0, 1)]
gpy_model = GPy.models.GPRegression(X=x_init,
Y=y_init,
kernel=GPy.kern.RBF(
input_dim=x_init.shape[1],
lengthscale=1.,
variance=1.))
emukit_qrbf = QuadratureRBFLebesgueMeasure(RBFGPy(gpy_model.kern),
integral_bounds=bounds)
emukit_model = BaseGaussianProcessGPy(kern=emukit_qrbf,
gpy_model=gpy_model)
emukit_method = VanillaBayesianQuadrature(base_gp=emukit_model,
X=x_init,
Y=y_init)
emukit_loop = VanillaBayesianQuadratureLoop(model=emukit_method)
num_iter = 5
emukit_loop.run_loop(user_function=UserFunctionWrapper(func),
stopping_condition=num_iter)
assert emukit_loop.loop_state.X.shape[0] == num_iter + init_size
assert emukit_loop.loop_state.Y.shape[0] == num_iter + init_size
def create_vanilla_bq_loop_with_rbf_kernel(X: np.ndarray, Y: np.ndarray, integral_bounds: List,
rbf_lengthscale: float=1.0, rbf_variance: float=1.0) -> \
VanillaBayesianQuadratureLoop:
"""
:param X: initial training point locations, shape (n_points, input_dim)
:param Y: initial training point function values, shape (n_points, 1)
:param integral_bounds: List of input_dim tuples, where input_dim is the dimensionality of the integral
and the tuples contain the lower and upper bounds of the integral i.e.,
[(lb_1, ub_1), (lb_2, ub_2), ..., (lb_D, ub_D)].
:param rbf_lengthscale: the lengthscale of the rbf kernel, defaults to 1.
:param rbf_variance: the variance of the rbf kernel, defaults to 1.
:return: The vanilla BQ loop
"""
if not len(integral_bounds) == X.shape[1]:
D_bounds = len(integral_bounds)
input_dim = X.shape[1]
raise ValueError("number of integral bounds " + str(D_bounds) + " provided does not match the input dimension "
+ str(input_dim) + ".")
if rbf_lengthscale <= 0:
raise ValueError("rbf lengthscale must be positive. The current value is " + str(rbf_lengthscale) + ".")
if rbf_variance <= 0:
raise ValueError("rbf variance must be positive. The current value is " + str(rbf_variance) + ".")
gpy_model = GPy.models.GPRegression(X=X, Y=Y, kernel=GPy.kern.RBF(input_dim=X.shape[1],
lengthscale=rbf_lengthscale,
variance=rbf_variance))
emukit_rbf = RBFGPy(gpy_model.kern)
emukit_qrbf = QuadratureRBF(emukit_rbf, integral_bounds=integral_bounds)
emukit_model = BaseGaussianProcessGPy(kern=emukit_qrbf, gpy_model=gpy_model)
emukit_method = VanillaBayesianQuadrature(base_gp=emukit_model)
emukit_loop = VanillaBayesianQuadratureLoop(model=emukit_method)
return emukit_loop
class EmukitRBF:
variance = 0.5
lengthscales = np.array([0.8, 1.3])
kern = RBFGPy(
GPy.kern.RBF(input_dim=2,
lengthscale=lengthscales,
variance=variance,
ARD=True))
def model_lebesgue_normalized(gpy_model):
measure = LebesgueMeasure.from_bounds(bounds=gpy_model.X.shape[1] *
[(-1, 2)],
normalized=True)
qrbf = QuadratureRBFLebesgueMeasure(RBFGPy(gpy_model.kern), measure)
basegp = BaseGaussianProcessGPy(kern=qrbf, gpy_model=gpy_model)
return VanillaBayesianQuadrature(base_gp=basegp,
X=gpy_model.X,
Y=gpy_model.Y)
def base_gp_data():
X = np.array([[-1, 1], [0, 0], [-2, 0.1]])
Y = np.array([[1], [2], [3]])
gpy_model = GPy.models.GPRegression(
X=X, Y=Y, kernel=GPy.kern.RBF(input_dim=X.shape[1]))
measure = GaussianMeasure(mean=np.array([0.1, 1.8]), variance=0.8)
qrbf = QuadratureRBFGaussianMeasure(RBFGPy(gpy_model.kern),
measure=measure)
base_gp = BaseGaussianProcessGPy(kern=qrbf, gpy_model=gpy_model)
return base_gp, X, Y
def model_gaussian(gpy_model):
X, Y = gpy_model.X, gpy_model.Y
measure = GaussianMeasure(mean=np.arange(gpy_model.X.shape[1]),
variance=np.linspace(0.2, 1.5, X.shape[1]))
qrbf = QuadratureRBFGaussianMeasure(RBFGPy(gpy_model.kern),
measure=measure)
basegp = BaseGaussianProcessGPy(kern=qrbf, gpy_model=gpy_model)
return VanillaBayesianQuadrature(base_gp=basegp,
X=gpy_model.X,
Y=gpy_model.Y)
def model():
rng = np.random.RandomState(42)
x_init = rng.rand(5, 2)
y_init = rng.rand(5, 1)
gpy_kernel = GPy.kern.RBF(input_dim=x_init.shape[1])
gpy_model = GPy.models.GPRegression(X=x_init, Y=y_init, kernel=gpy_kernel)
qrbf = QuadratureRBFLebesgueMeasure(RBFGPy(gpy_kernel), integral_bounds=x_init.shape[1] * [(-3, 3)])
basegp = BaseGaussianProcessGPy(kern=qrbf, gpy_model=gpy_model)
model = VanillaBayesianQuadrature(base_gp=basegp, X=x_init, Y=y_init)
return model
def test_vanilla_bq_shapes():
X = np.array([[-1, 1], [0, 0], [-2, 0.1]])
Y = np.array([[1], [2], [3]])
x = np.array([[-1, 1], [0, 0], [-2, 0.1], [-3, 4]])
D = X.shape[1]
# integral bounds
lb = -3
ub = 3
gpy_model = GPy.models.GPRegression(X=X,
Y=Y,
kernel=GPy.kern.RBF(input_dim=D))
emukit_qrbf = QuadratureRBF(RBFGPy(gpy_model.kern),
integral_bounds=D * [(lb, ub)])
emukit_model = BaseGaussianProcessGPy(kern=emukit_qrbf,
gpy_model=gpy_model)
vanilla_bq = VanillaBayesianQuadrature(base_gp=emukit_model)
# integrate
res = vanilla_bq.integrate()
assert len(res) == 2
assert isinstance(res[0], float)
assert isinstance(res[1], float)
# transformations
assert vanilla_bq.transform(Y).shape == Y.shape
assert vanilla_bq.inverse_transform(Y).shape == Y.shape
# predictions base
res = vanilla_bq.predict_base(x)
assert len(res) == 4
for i in range(4):
assert res[i].shape == (x.shape[0], 1)
# predictions base full covariance
res = vanilla_bq.predict_base_with_full_covariance(x)
assert len(res) == 4
assert res[0].shape == (x.shape[0], 1)
assert res[1].shape == (x.shape[0], x.shape[0])
assert res[2].shape == (x.shape[0], 1)
assert res[3].shape == (x.shape[0], x.shape[0])
# predictions
res = vanilla_bq.predict(x)
assert len(res) == 2
assert res[0].shape == (x.shape[0], 1)
assert res[1].shape == (x.shape[0], 1)
# predictions full covariance
res = vanilla_bq.predict_with_full_covariance(x)
assert len(res) == 2
assert res[0].shape == (x.shape[0], 1)
assert res[1].shape == (x.shape[0], x.shape[0])
def _wrap_emukit(self, gpy_gp: GPy.core.GP):
"""
Wrap GPy GP around Emukit interface to enable subsequent quadrature
:param gpy_gp:
:return:
"""
# gpy_gp.optimize()
rbf = RBFGPy(gpy_gp.kern)
qrbf = QuadratureRBF(rbf, integral_bounds=[(-4, 8)] * self.dimensions)
model = BaseGaussianProcessGPy(kern=qrbf, gpy_model=gpy_gp)
method = VanillaBayesianQuadrature(base_gp=model)
return method
def model_with_density():
rng = np.random.RandomState(42)
x_init = rng.rand(5, 2)
y_init = rng.rand(5, 1)
gpy_kernel = GPy.kern.RBF(input_dim=x_init.shape[1])
gpy_model = GPy.models.GPRegression(X=x_init, Y=y_init, kernel=gpy_kernel)
measure = IsotropicGaussianMeasure(mean=np.arange(x_init.shape[1]), variance=2.)
qrbf = QuadratureRBFIsoGaussMeasure(RBFGPy(gpy_kernel), measure=measure)
basegp = BaseGaussianProcessGPy(kern=qrbf, gpy_model=gpy_model)
model = VanillaBayesianQuadrature(base_gp=basegp, X=x_init, Y=y_init)
return model
def qrbf_iso_gauss_infinite():
x1 = np.array([[-1, 1], [0, 0], [-2, 0.1]])
x2 = np.array([[-1, 1], [0, 0], [-2, 0.1], [-3, 3]])
M1 = x1.shape[0]
M2 = x2.shape[0]
D = x1.shape[1]
gpy_kernel = GPy.kern.RBF(input_dim=D)
emukit_rbf = RBFGPy(gpy_kernel)
measure = IsotropicGaussianMeasure(mean=np.arange(D), variance=2.)
emukit_qrbf = QuadratureRBFIsoGaussMeasure(rbf_kernel=emukit_rbf,
measure=measure)
return emukit_qrbf, x1, x2, M1, M2, D
def vanilla_bq():
X = np.array([[-1, 1], [0, 0], [-2, 0.1]])
Y = np.array([[1], [2], [3]])
D = X.shape[1]
integral_bounds = [(-1, 2), (-3, 3)]
gpy_model = GPy.models.GPRegression(X=X,
Y=Y,
kernel=GPy.kern.RBF(input_dim=D))
qrbf = QuadratureRBFLebesgueMeasure(RBFGPy(gpy_model.kern),
integral_bounds=integral_bounds)
model = BaseGaussianProcessGPy(kern=qrbf, gpy_model=gpy_model)
vanilla_bq = VanillaBayesianQuadrature(base_gp=model, X=X, Y=Y)
return vanilla_bq
def qrbf_lebesgue_finite():
x1 = np.array([[-1, 1], [0, 0], [-2, 0.1]])
x2 = np.array([[-1, 1], [0, 0], [-2, 0.1], [-3, 3]])
M1 = x1.shape[0]
M2 = x2.shape[0]
D = x1.shape[1]
# integral bounds
bounds = [(-1, 2), (-3, 3)]
gpy_kernel = GPy.kern.RBF(input_dim=D)
emukit_rbf = RBFGPy(gpy_kernel)
emukit_qrbf = QuadratureRBFLebesgueMeasure(emukit_rbf,
integral_bounds=bounds)
return emukit_qrbf, x1, x2, M1, M2, D
def qrbf_uniform_infinite():
x1 = np.array([[-1, 1], [0, 0], [-2, 0.1]])
x2 = np.array([[-1, 1], [0, 0], [-2, 0.1], [-3, 3]])
M1 = x1.shape[0]
M2 = x2.shape[0]
D = x1.shape[1]
# measure
measure_bounds = [(0, 2), (-4, 3)]
measure = UniformMeasure(bounds=measure_bounds)
gpy_kernel = GPy.kern.RBF(input_dim=D)
emukit_rbf = RBFGPy(gpy_kernel)
emukit_qrbf = QuadratureRBFUniformMeasure(rbf_kernel=emukit_rbf,
integral_bounds=None,
measure=measure)
return emukit_qrbf, x1, x2, M1, M2, D
def test_vanilla_bq_loop_initial_state():
x_init = np.random.rand(5, 2)
y_init = np.random.rand(5, 1)
bounds = [(-1, 1), (0, 1)]
gpy_model = GPy.models.GPRegression(X=x_init,
Y=y_init,
kernel=GPy.kern.RBF(
input_dim=x_init.shape[1],
lengthscale=1.,
variance=1.))
emukit_qrbf = QuadratureRBF(RBFGPy(gpy_model.kern), integral_bounds=bounds)
emukit_model = BaseGaussianProcessGPy(kern=emukit_qrbf,
gpy_model=gpy_model)
emukit_method = VanillaBayesianQuadrature(base_gp=emukit_model)
emukit_loop = VanillaBayesianQuadratureLoop(model=emukit_method)
assert_array_equal(emukit_loop.loop_state.X, x_init)
assert_array_equal(emukit_loop.loop_state.Y, y_init)
assert emukit_loop.loop_state.iteration == 0
def loop():
init_size = 5
x_init = np.random.rand(init_size, 2)
y_init = np.random.rand(init_size, 1)
bounds = [(-1, 1), (0, 1)]
gpy_model = GPy.models.GPRegression(X=x_init,
Y=y_init,
kernel=GPy.kern.RBF(
input_dim=x_init.shape[1],
lengthscale=1.,
variance=1.))
emukit_qrbf = QuadratureRBFLebesgueMeasure(RBFGPy(gpy_model.kern),
integral_bounds=bounds)
emukit_model = BaseGaussianProcessGPy(kern=emukit_qrbf,
gpy_model=gpy_model)
emukit_method = VanillaBayesianQuadrature(base_gp=emukit_model,
X=x_init,
Y=y_init)
emukit_loop = VanillaBayesianQuadratureLoop(model=emukit_method)
return emukit_loop, init_size, x_init, y_init
def test_rbf_qkernel_shapes():
x1 = np.array([[-1, 1], [0, 0], [-2, 0.1]])
x2 = np.array([[-1, 1], [0, 0], [-2, 0.1], [-3, 3]])
M1 = x1.shape[0]
M2 = x2.shape[0]
D = x1.shape[1]
# integral bounds
lb = -3
ub = 3
gpy_kernel = GPy.kern.RBF(input_dim=D)
emukit_rbf = RBFGPy(gpy_kernel)
emukit_qrbf = QuadratureRBF(emukit_rbf, integral_bounds=D * [(lb, ub)])
# kernel shapes
assert emukit_qrbf.K(x1, x2).shape == (M1, M2)
assert emukit_qrbf.qK(x2).shape == (1, M2)
assert emukit_qrbf.Kq(x1).shape == (M1, 1)
assert isinstance(emukit_qrbf.qKq(), float)
# gradient shapes
assert emukit_qrbf.dKq_dx(x1).shape == (M1, D)
assert emukit_qrbf.dqK_dx(x2).shape == (D, M2)
if __name__ == "__main__":
np.random.seed(0)
METHOD = "Vanilla BQ"
X = np.array([[-1, 1], [0, 0], [-2, 0.1]])
Y = np.array([[1], [2], [3]])
D = X.shape[1]
integral_bounds = [(-1, 2), (-3, 3)]
gpy_model = GPy.models.GPRegression(X=X,
Y=Y,
kernel=GPy.kern.RBF(input_dim=D))
qrbf = QuadratureRBFLebesgueMeasure(RBFGPy(gpy_model.kern),
integral_bounds=integral_bounds)
model = BaseGaussianProcessGPy(kern=qrbf, gpy_model=gpy_model)
vanilla_bq = VanillaBayesianQuadrature(base_gp=model, X=X, Y=Y)
print()
print("method: {}".format(METHOD))
print("no dimensions: {}".format(D))
print()
# === mean =============================================================
num_runs = 100
num_samples = 1e6
num_std = 3
def get_base_gp():
gpy_model, dat = get_gpy_model()
measure = GaussianMeasure(mean=dat.measure_mean, variance=dat.measure_var)
qrbf = QuadratureRBFGaussianMeasure(RBFGPy(gpy_model.kern),
measure=measure)
return BaseGaussianProcessGPy(kern=qrbf, gpy_model=gpy_model), dat
def base_gp_wrong_kernel(gpy_model):
integral_bounds = [(-1, 2), (-3, 3)]
qrbf = QuadratureRBFLebesgueMeasure(RBFGPy(gpy_model.kern),
integral_bounds=integral_bounds)
return BaseGaussianProcessGPy(kern=qrbf, gpy_model=gpy_model)
def base_gp(gpy_model):
measure = IsotropicGaussianMeasure(mean=np.array([0.1, 1.8]), variance=0.8)
qrbf = QuadratureRBFIsoGaussMeasure(RBFGPy(gpy_model.kern),
measure=measure)
return BaseGaussianProcessGPy(kern=qrbf, gpy_model=gpy_model)
# METHOD = 'WSABI-l adapt'
METHOD = "WSABI-l fixed"
# the GPy model
X = np.array([[-1, 1], [0, 0], [-2, 0.1]])
Y = np.array([[1], [2], [3]])
D = X.shape[1]
gpy_model = GPy.models.GPRegression(X=X,
Y=Y,
kernel=GPy.kern.RBF(input_dim=D))
# the measure
measure = IsotropicGaussianMeasure(mean=np.array([0.1, 1.8]), variance=0.8)
# the emukit base GP
qrbf = QuadratureRBFIsoGaussMeasure(RBFGPy(gpy_model.kern),
measure=measure)
base_gp = BaseGaussianProcessGPy(kern=qrbf, gpy_model=gpy_model)
# the emukit bounded BQ model
if METHOD == "Bounded BQ lower":
bound = np.min(base_gp.Y) - 0.5
model = BoundedBayesianQuadrature(base_gp=base_gp,
X=X,
Y=Y,
bound=bound,
is_lower_bounded=True)
elif METHOD == "Bounded BQ upper":
bound = np.max(base_gp.Y) + 0.5
model = BoundedBayesianQuadrature(base_gp=base_gp,
X=X,
if __name__ == "__main__":
np.random.seed(0)
# === Choose MEASURE BELOW ======
# MEASURE_INTBOUNDS = 'Lebesgue-finite'
# MEASURE_INTBOUNDS = 'GaussIso-infinite'
# MEASURE_INTBOUNDS = 'Uniform-infinite'
MEASURE_INTBOUNDS = "Uniform-finite"
# === CHOOSE MEASURE ABOVE ======
x1 = np.array([[-1, 1], [0, 0], [-2, 0.1]])
x2 = np.array([[-1, 1], [0, 0], [-2, 0.1], [-3, 3]])
D = x1.shape[1]
gpy_kernel = GPy.kern.RBF(input_dim=D)
emukit_rbf = RBFGPy(gpy_kernel)
if MEASURE_INTBOUNDS == "Lebesgue-finite":
emukit_qrbf = QuadratureRBFLebesgueMeasure(emukit_rbf,
integral_bounds=[(-1, 2),
(-3, 3)])
elif MEASURE_INTBOUNDS == "GaussIso-infinite":
measure = IsotropicGaussianMeasure(mean=np.arange(D), variance=2.0)
emukit_qrbf = QuadratureRBFIsoGaussMeasure(rbf_kernel=emukit_rbf,
measure=measure)
elif MEASURE_INTBOUNDS == "Uniform-infinite":
measure = UniformMeasure(bounds=[(0, 2), (-4, 3)])
emukit_qrbf = QuadratureRBFUniformMeasure(emukit_rbf,
integral_bounds=None,
measure=measure)
elif MEASURE_INTBOUNDS == "Uniform-finite":
