def test_cglb_predict():
"""
Test that 1.) The predict method returns the same variance estimate as SGPR.
2.) The predict method returns the same mean as SGPR for v=0.
3.) The predict method returns a mean very similar to GPR when CG is run to low tolerance.
"""
rng: np.random.RandomState = np.random.RandomState(999)
train, z, xs = data(rng)
noise = 0.2
gpr = GPR(train, kernel=SquaredExponential(), noise_variance=noise)
sgpr = SGPR(train,
kernel=SquaredExponential(),
inducing_variable=z,
noise_variance=noise)
cglb = CGLB(
train,
kernel=SquaredExponential(),
inducing_variable=z,
noise_variance=noise,
)
gpr_mean, _ = gpr.predict_y(xs, full_cov=False)
sgpr_mean, sgpr_cov = sgpr.predict_y(xs, full_cov=False)
cglb_mean, cglb_cov = cglb.predict_y(
xs, full_cov=False,
cg_tolerance=1e6) # set tolerance high so v stays at 0.
assert np.allclose(sgpr_cov, cglb_cov)
assert np.allclose(sgpr_mean, cglb_mean)
cglb_mean, _ = cglb.predict_y(xs, full_cov=False, cg_tolerance=1e-12)
assert np.allclose(gpr_mean, cglb_mean)
def compute_residual_eig(Y: np.ndarray, Kx: np.ndarray) -> np.ndarray:
"""Residual of Y based on Kx, a kernel matrix of X"""
assert len(Y) == len(Kx)
eig_Kx, eix = truncated_eigen(*eigdec(Kx, min(100, len(Kx) // 4)))
phi_X = eix @ np.diag(np.sqrt(eig_Kx)) # X @ X.T is close to K_X
n_feats = phi_X.shape[1]
linear_kernel = Linear(n_feats, ARD=True)
gp_model = GPR(phi_X, Y, linear_kernel + White(n_feats))
gp_model.optimize()
new_Kx = linear_kernel.compute_K_symm(phi_X)
sigma_squared = gp_model.kern.white.variance.value[0]
return (pdinv(np.eye(len(Kx)) + new_Kx / sigma_squared) @ Y).squeeze()
def residual_kernel(K_Y: np.ndarray, K_X: np.ndarray, use_expectation=True, with_gp=True, sigma_squared=1e-3, return_learned_K_X=False):
"""Kernel matrix of residual of Y given X based on their kernel matrices, Y=f(X)"""
import gpflow
from gpflow.kernels import White, Linear
from gpflow.models import GPR
K_Y, K_X = centering(K_Y), centering(K_X)
T = len(K_Y)
if with_gp:
eig_Ky, eiy = truncated_eigen(*eigdec(K_Y, min(100, T // 4)))
eig_Kx, eix = truncated_eigen(*eigdec(K_X, min(100, T // 4)))
X = eix @ diag(sqrt(eig_Kx)) # X @ X.T is close to K_X
Y = eiy @ diag(sqrt(eig_Ky))
n_feats = X.shape[1]
linear = Linear(n_feats, ARD=True)
white = White(n_feats)
gp_model = GPR(X, Y, linear + white)
gpflow.train.ScipyOptimizer().minimize(gp_model)
K_X = linear.compute_K_symm(X)
sigma_squared = white.variance.value
P = pdinv(np.eye(T) + K_X / sigma_squared) # == I-K @ inv(K+Sigma) in Zhang et al. 2011
if use_expectation: # Flaxman et al. 2016 Gaussian Processes for Independence Tests with Non-iid Data in Causal Inference.
RK = (K_X + P @ K_Y) @ P
else: # Zhang et al. 2011. Kernel-based Conditional Independence Test and Application in Causal Discovery.
RK = P @ K_Y @ P
if return_learned_K_X:
return RK, K_X
else:
return RK
def residualize(Y, X=None, gp_kernel=None):
"""Residual of Y given X. Y_i - E[Y_i|X_i]"""
import gpflow
from gpflow.models import GPR
if X is None:
return Y - np.mean(Y) # nothing is residualized!
if gp_kernel is None:
gp_kernel = default_gp_kernel(X)
m = GPR(X, Y, gp_kernel)
gpflow.train.ScipyOptimizer().minimize(m)
Yhat, _ = m.predict_y(X)
return Y - Yhat
def regression_distance_k(Kx: np.ndarray, Ky: np.ndarray):
warnings.warn('not tested yet!')
import gpflow
from gpflow.kernels import White, Linear
from gpflow.models import GPR
T = len(Kx)
eig_Ky, eiy = truncated_eigen(*eigdec(Ky, min(100, T // 4)))
eig_Kx, eix = truncated_eigen(*eigdec(Kx, min(100, T // 4)))
X = eix @ diag(sqrt(eig_Kx)) # X @ X.T is close to K_X
Y = eiy @ diag(sqrt(eig_Ky))
n_feats = X.shape[1]
linear = Linear(n_feats, ARD=True)
white = White(n_feats)
gp_model = GPR(X, Y, linear + white)
gpflow.train.ScipyOptimizer().minimize(gp_model)
Kx = linear.compute_K_symm(X)
sigma_squared = white.variance.value
P = Kx @ pdinv(Kx + sigma_squared * np.eye(T))
M = P @ Ky @ P
O = np.ones((T, 1))
N = O @ np.diag(M).T
D = np.sqrt(N + N.T - 2 * M)
return D
def _test_cg_gpr(config: ConfigDense,
model: GPR,
Xnew: tf.Tensor) -> tf.Tensor:
"""
Sample generation subroutine common to each unit test
"""
# Prepare preconditioner for CG
X, y = model.data
Kff = model.kernel(X, full_cov=True)
max_rank = config.num_cond//(2 if config.num_cond > 1 else 1)
preconditioner = get_default_preconditioner(Kff,
diag=model.likelihood.variance,
max_rank=max_rank)
count = 0
L_joint = None
samples = []
while count < config.num_samples:
# Sample $u ~ N(q_mu, q_sqrt q_sqrt^{T})$
size = min(config.shard_size, config.num_samples - count)
# Generate draws from the joint distribution $p(f(X), f(Xnew))$
(f, fnew), L_joint = common.sample_joint(model.kernel,
X,
Xnew,
num_samples=size,
L=L_joint)
# Solve for update functions
update_fns = cg_update(model.kernel,
X,
y,
f + model.mean_function(X),
tol=1e-6,
diag=model.likelihood.variance,
max_iter=config.num_cond,
preconditioner=preconditioner)
samples.append(fnew + update_fns(Xnew))
count += size
samples = tf.concat(samples, axis=0)
if model.mean_function is not None:
samples += model.mean_function(Xnew)
return samples
def _test_exact_gpr(config: ConfigDense, model: GPR,
Xnew: tf.Tensor) -> tf.Tensor:
"""
Sample generation subroutine common to each unit test
"""
# Precompute Cholesky factor (optional)
X, y = model.data
Kyy = model.kernel(X, full_cov=True)
Kyy = tf.linalg.set_diag(
Kyy,
tf.linalg.diag_part(Kyy) + model.likelihood.variance)
Lyy = tf.linalg.cholesky(Kyy)
count = 0
L_joint = None
samples = []
while count < config.num_samples:
# Sample $u ~ N(q_mu, q_sqrt q_sqrt^{T})$
size = min(config.shard_size, config.num_samples - count)
# Generate draws from the joint distribution $p(f(X), f(Xnew))$
(f, fnew), L_joint = common.sample_joint(model.kernel,
X,
Xnew,
num_samples=size,
L=L_joint)
# Solve for update functions
update_fns = exact_update(model.kernel,
X,
y,
f + model.mean_function(X),
L=Lyy,
diag=model.likelihood.variance)
samples.append(fnew + update_fns(Xnew))
count += size
samples = tf.concat(samples, axis=0)
if model.mean_function is not None:
samples += model.mean_function(Xnew)
return samples
def main(config):
assert config is not None, ValueError
tf.random.set_seed(config.seed)
gpflow_config.set_default_float(config.floatx)
gpflow_config.set_default_jitter(config.jitter)
X = tf.random.uniform([config.num_cond, config.input_dims],
dtype=floatx())
Xnew = tf.random.uniform([config.num_test, config.input_dims],
dtype=floatx())
for cls in SupportedBaseKernels:
minval = config.rel_lengthscales_min * (config.input_dims**0.5)
maxval = config.rel_lengthscales_max * (config.input_dims**0.5)
lenscales = tf.random.uniform(shape=[config.input_dims],
minval=minval,
maxval=maxval,
dtype=floatx())
kern = cls(lengthscales=lenscales,
variance=config.kernel_variance)
const = tf.random.normal([1], dtype=floatx())
K = kern(X, full_cov=True)
K = tf.linalg.set_diag(
K,
tf.linalg.diag_part(K) + config.noise_variance)
L = tf.linalg.cholesky(K)
y = L @ tf.random.normal([L.shape[-1], 1],
dtype=floatx()) + const
model = GPR(kernel=kern,
noise_variance=config.noise_variance,
data=(X, y),
mean_function=mean_functions.Constant(c=const))
mf, Sff = subroutine(config, model, Xnew)
mg, Sgg = model.predict_f(Xnew, full_cov=True)
tol = config.error_tol
assert allclose(mf, mg, tol, tol)
assert allclose(Sff, Sgg, tol, tol)
def compute_analytic_GP_predictions(X, y, kernel, noise_variance, X_star):
"""
Identify the mean and covariance of an analytic GPR posterior for test point locations.
:param X: The train point locations, with a shape of [N x D].
:param y: The train targets, with a shape of [N x 1].
:param kernel: The kernel object.
:param noise_variance: The variance of the observation model.
:param X_star: The test point locations, with a shape of [N* x D].
:return: The mean and covariance of the noise-free predictions,
with a shape of [N*] and [N* x N*] respectively.
"""
gpr_model = GPR(data=(X, y), kernel=kernel, noise_variance=noise_variance)
f_mean, f_var = gpr_model.predict_f(X_star, full_cov=True)
f_mean, f_var = f_mean[..., 0], f_var[0]
assert f_mean.shape == (X_star.shape[0], )
assert f_var.shape == (X_star.shape[0], X_star.shape[0])
return f_mean, f_var
def test_single_layer(self):
kern = RBF(1, lengthscales=0.1)
layers = init_layers_linear(self.X, self.Y, self.X, [kern])
lik = Gaussian()
lik.variance = self.lik_var
last_layer = SGPR_Layer(layers[-1].kern,
layers[-1].feature.Z.read_value(), self.D_Y,
layers[-1].mean_function)
layers = layers[:-1] + [last_layer]
m_dgp = DGP_Collapsed(self.X, self.Y, lik, layers)
L_dgp = m_dgp.compute_log_likelihood()
mean_dgp, var_dgp = m_dgp.predict_f_full_cov(self.Xs, 1)
m_exact = GPR(self.X, self.Y, kern)
m_exact.likelihood.variance = self.lik_var
L_exact = m_exact.compute_log_likelihood()
mean_exact, var_exact = m_exact.predict_f_full_cov(self.Xs)
assert_allclose(L_dgp, L_exact, atol=1e-5, rtol=1e-5)
assert_allclose(mean_dgp[0], mean_exact, atol=1e-5, rtol=1e-5)
assert_allclose(var_dgp[0], var_exact, atol=1e-5, rtol=1e-5)
def residual_kernel_matrix_kernel_real(Kx, Z, num_eig, ARD=True):
"""K_X|Z"""
assert len(Kx) == len(Z)
assert num_eig <= len(Kx)
T = len(Kx)
D = Z.shape[1]
I = eye(T)
eig_Kx, eix = truncated_eigen(*eigdec(Kx, num_eig))
rbf = RBF(D, ARD=ARD)
white = White(D)
gp_model = GPR(Z, 2 * sqrt(T) * eix @ diag(sqrt(eig_Kx)) / sqrt(eig_Kx[0]),
rbf + white)
gpflow.train.ScipyOptimizer().minimize(gp_model)
sigma_squared = white.variance.value
Kz_x = rbf.compute_K_symm(Z)
P = I - Kz_x @ pdinv(Kz_x + sigma_squared * I)
return P @ Kx @ P.T
def test_vs_single_layer(self):
lik = Gaussian()
lik_var = 0.01
lik.variance = lik_var
N, Ns, D_Y, D_X = self.X.shape[0], self.Xs.shape[
0], self.D_Y, self.X.shape[1]
Y = np.random.randn(N, D_Y)
Ys = np.random.randn(Ns, D_Y)
kern = Matern52(self.X.shape[1], lengthscales=0.5)
# mf = Linear(A=np.random.randn(D_X, D_Y), b=np.random.randn(D_Y))
mf = Zero()
m_gpr = GPR(self.X, Y, kern, mean_function=mf)
m_gpr.likelihood.variance = lik_var
mean_gpr, var_gpr = m_gpr.predict_y(self.Xs)
test_lik_gpr = m_gpr.predict_density(self.Xs, Ys)
pred_m_gpr, pred_v_gpr = m_gpr.predict_f(self.Xs)
pred_mfull_gpr, pred_vfull_gpr = m_gpr.predict_f_full_cov(self.Xs)
kerns = []
kerns.append(
Matern52(self.X.shape[1], lengthscales=0.5, variance=1e-1))
kerns.append(kern)
layer0 = GPMC_Layer(kerns[0], self.X.copy(), D_X, Identity())
layer1 = GPR_Layer(kerns[1], mf, D_Y)
m_dgp = DGP_Heinonen(self.X, Y, lik, [layer0, layer1])
mean_dgp, var_dgp = m_dgp.predict_y(self.Xs, 1)
test_lik_dgp = m_dgp.predict_density(self.Xs, Ys, 1)
pred_m_dgp, pred_v_dgp = m_dgp.predict_f(self.Xs, 1)
pred_mfull_dgp, pred_vfull_dgp = m_dgp.predict_f_full_cov(
self.Xs, 1)
tol = 1e-4
assert_allclose(mean_dgp[0], mean_gpr, atol=tol, rtol=tol)
assert_allclose(test_lik_dgp, test_lik_gpr, atol=tol, rtol=tol)
assert_allclose(pred_m_dgp[0], pred_m_gpr, atol=tol, rtol=tol)
assert_allclose(pred_mfull_dgp[0],
pred_mfull_gpr,
atol=tol,
rtol=tol)
assert_allclose(pred_vfull_dgp[0],
pred_vfull_gpr,
atol=tol,
rtol=tol)
def get_model(model_enum,
data,
noise_variance,
covariance_function,
max_parallel=10000):
if not isinstance(model_enum, ModelEnum):
model_enum = ModelEnum(model_enum)
if model_enum == ModelEnum.GP:
gp_model = GPR(data, covariance_function, None, noise_variance)
elif model_enum == ModelEnum.SSGP:
gp_model = StateSpaceGP(data,
covariance_function,
noise_variance,
parallel=False)
elif model_enum == ModelEnum.PSSGP:
gp_model = StateSpaceGP(data,
covariance_function,
noise_variance,
parallel=True,
max_parallel=max_parallel)
else:
raise ValueError("model not supported")
return gp_model
def generate_gp_models(
model_or_kernel: Union[GPModel, Kernel],
data_list: List[RegressionData]
):
"""
Generates a list of GPModel objects with the same length as data_list.
If a GPModel object was passed, the list will consist of deep copies of the GPModel, with the data reassigned.
If a Kernel was passed, the list will consist of GPR (all containing the Kernel) instead.
:param model_or_kernel: GPModel or Kernel object used to generate the list of models
:param data_list: List of RegressionData. Each model will get one element.
:return:
"""
assert isinstance(model_or_kernel, (Kernel, GPModel)), \
"The regression_source object needs to be an instance of either a Kernel or a GPModel, "
assert all(map(lambda data: type(data) is tuple and len(data) is 2, data_list)), \
"data_list should be a list of tuples of length 2 (i.e. a list of RegressionData)"
is_kernel = isinstance(model_or_kernel, Kernel)
models = list()
for data in data_list:
# Ensures both the InputData and OutputData are in a format usable by tensorflow
data = tuple(map(util.ensure_tf_matrix, data))
if is_kernel:
# Appends a GPR object to the list of models if a Kernel was passed instead of a GPModel
models.append(GPR(data, model_or_kernel))
else:
# Appends a deepcopy of the passed GPModel to the list of models
model = gf.utilities.deepcopy(model_or_kernel)
model.data = data
models.append(model)
return models
def regression_distance(Y: np.ndarray, Z: np.ndarray, ard=True):
"""d(z,z') = |f(z)-f(z')| where Y=f(Z) + noise and f ~ GP"""
import gpflow
from gpflow.kernels import White, RBF
from gpflow.models import GPR
n, dims = Z.shape
rbf = RBF(dims, ARD=ard)
rbf_white = rbf + White(dims)
gp_model = GPR(Z, Y, rbf_white)
gpflow.train.ScipyOptimizer().minimize(gp_model)
Kz_y = rbf.compute_K_symm(Z)
Ry = pdinv(rbf_white.compute_K_symm(Z))
Fy = Y.T @ Ry @ Kz_y # F(z)
M = Fy.T @ Fy
O = np.ones((n, 1))
N = O @ (np.diag(M)[:, None]).T
D = np.sqrt(N + N.T - 2 * M)
return D, Kz_y
data = (x, y)
inducing_variable = tf.random.uniform((M, D))
adam_learning_rate = 0.01
iterations = ci_niter(5)
# %% [markdown]
# ### VGP is a GPR
# %% [markdown]
# The following section demonstrates how natural gradients can turn VGP into GPR *in a single step, if the likelihood is Gaussian*.
# %% [markdown]
# Let's start by first creating a standard GPR model with Gaussian likelihood:
# %%
gpr = GPR(data, kernel=gpflow.kernels.Matern52())
# %% [markdown]
# The log marginal likelihood of the exact GP model is:
# %%
gpr.log_marginal_likelihood().numpy()
# %% [markdown]
# Now we will create an approximate model which approximates the true posterior via a variational Gaussian distribution.<br>We initialize the distribution to be zero mean and unit variance.
# %%
vgp = VGP(data,
kernel=gpflow.kernels.Matern52(),
likelihood=gpflow.likelihoods.Gaussian())
def _gpr(x: tf.Tensor, y: tf.Tensor) -> GPR:
return GPR((x, y), gpflow.kernels.Linear())
# %% [markdown]
# The CGLB model introduces less bias in comparison to SGPR model.
# We can show empirically that CGLB has a lower bias by plotting the objective landscape with respect to different values of the lengthscale hyperparameters.
# %%
x, y = data
n = x.shape[0]
m = 10
iv_indices = np.random.choice(range(n), size=m, replace=False)
iv = x[iv_indices, :]
noise = 0.1
gpr = GPR(data, kernel=SquaredExponential(), noise_variance=noise)
cglb = CGLB(data,
kernel=SquaredExponential(),
noise_variance=noise,
inducing_variable=iv)
sgpr = SGPR(data,
kernel=SquaredExponential(),
noise_variance=noise,
inducing_variable=iv)
def loss_with_changed_parameter(model, parameter, value: float):
original = parameter.numpy()
parameter.assign(value)
loss = model.training_loss()
parameter.assign(original)
def build_model(data, mean_function):
model = GPR(data, kernel=RBF(), mean_function=mean_function)
set_trainable(model.kernel, False)
model.likelihood.variance.assign(1e-2)
set_trainable(model.likelihood, False)
return model
def __init__(self, X, Y, kern):
GPR.__init__(self, X, Y, kern)
def __init__(self, *args, paths: AbstractSampler = None, **kwargs): GPR.__init__(self, *args, **kwargs) self._paths = paths
