def __init__(self, diff_parameters: DiffParameters):
super(Diffusion, self).__init__()
def get_bijector():
if gpflow.config.default_positive_bijector() == 'exp':
return tfp.bijectors.Exp()
elif gpflow.config.default_positive_bijector() == 'softplus':
return tfp.bijectors.Softplus()
else:
raise ValueError(
"Unexpected value in default_positive_bijector()")
assert len(diff_parameters.alphas) == len(
diff_parameters.betas), "len(alphas) != len(betas)"
self.dimension = len(diff_parameters.alphas)
alphas = diff_parameters.alphas
betas = diff_parameters.betas
self._alphas = gpflow.Parameter(
tf.ones_like(alphas, dtype=tf_floatx()),
# alphas,
transform=get_bijector(),
name='alphas')
self._betas = gpflow.Parameter(
# TODO
tf.ones_like(betas, dtype=tf_floatx()),
# betas,
transform=get_bijector(),
name='betas')
self.prior_distribution = tfd.Gamma(alphas, betas)
def test_construct_parameter_from_existing_parameter_override_trainable(
trainable):
initial_parameter = gpflow.Parameter([1.2, 1.1], trainable=trainable)
new_parameter = gpflow.Parameter(initial_parameter,
trainable=not trainable)
assert new_parameter.trainable is not trainable
def __init__(self,
eigenpairs,
kappa=4,
sigma_f=1,
vertex_dim=0,
point_kernel=None,
active_dims=None,
dtype=tf.float64):
self.eigenvectors, self.eigenvalues = eigenpairs
self.num_verticies = tf.cast(tf.shape(self.eigenvectors)[0],
dtype=dtype)
self.vertex_dim = vertex_dim
if vertex_dim != 0:
self.point_kernel = point_kernel
else:
self.point_kernel = None
self.dtype = dtype
self.kappa = gpflow.Parameter(kappa,
dtype=self.dtype,
transform=gpflow.utilities.positive(),
name='kappa')
self.sigma_f = gpflow.Parameter(sigma_f,
dtype=self.dtype,
transform=gpflow.utilities.positive(),
name='sigma_f')
super().__init__(active_dims=active_dims)
def update(self, dataset: Dataset, *, jitter: float = DEFAULTS.JITTER) -> None:
"""
Update the model given the specified ``dataset``. Does not train the model.
:param dataset: The data with which to update the model.
:param jitter: The size of the jitter to use when stabilizing the Cholesky decomposition of
the covariance matrix.
"""
model = self.model
x, y = self.model.data[0].value(), self.model.data[1].value()
assert_data_is_compatible(dataset, Dataset(x, y))
f_mu, f_cov = self.model.predict_f(dataset.query_points, full_cov=True) # [N, L], [L, N, N]
# GPflow's VGP model is hard-coded to use the whitened representation, i.e.
# q_mu and q_sqrt parametrise q(v), and u = f(X) = L v, where L = cholesky(K(X, X))
# Hence we need to back-transform from f_mu and f_cov to obtain the updated
# new_q_mu and new_q_sqrt:
Knn = model.kernel(dataset.query_points, full_cov=True) # [N, N]
jitter_mat = jitter * tf.eye(len(dataset), dtype=Knn.dtype)
Lnn = tf.linalg.cholesky(Knn + jitter_mat) # [N, N]
new_q_mu = tf.linalg.triangular_solve(Lnn, f_mu) # [N, L]
tmp = tf.linalg.triangular_solve(Lnn[None], f_cov) # [L, N, N], L⁻¹ f_cov
S_v = tf.linalg.triangular_solve(Lnn[None], tf.linalg.matrix_transpose(tmp)) # [L, N, N]
new_q_sqrt = tf.linalg.cholesky(S_v + jitter_mat) # [L, N, N]
model.data[0].assign(dataset.query_points)
model.data[1].assign(dataset.observations)
model.num_data = len(dataset)
model.q_mu = gpflow.Parameter(new_q_mu)
model.q_sqrt = gpflow.Parameter(new_q_sqrt, transform=gpflow.utilities.triangular())
def test_construct_parameter_from_existing_parameter_override_name():
initial_parameter = gpflow.Parameter([1.2, 1.1])
transform = tfp.bijectors.Sigmoid(tf.constant(0.0, dtype=tf.float64),
tf.constant(2.0, dtype=tf.float64))
new_parameter = gpflow.Parameter(initial_parameter, transform=transform)
assert new_parameter.name == transform.name
def __init__(self, variance=1.0, lengthscales=1.0, **kwargs):
super().__init__()
self.variance = gpflow.Parameter(variance,
transform=gpflow.utilities.positive())
self.lengthscales = gpflow.Parameter(
lengthscales, transform=gpflow.utilities.positive())
self._validate_ard_active_dims(self.lengthscales)
def test_construct_parameter_from_existing_parameter_override_prior():
initial_parameter = gpflow.Parameter([1.2, 1.1])
prior = tfp.distributions.Normal(0.0, 1.0)
new_parameter = gpflow.Parameter(initial_parameter, prior=prior)
assert new_parameter.prior == prior
def __init__(self, input_dim, Q=1, active_dims=None, name='sm'):
"""
- Q (int): The number of mixtures.
References:
http://hips.seas.harvard.edu/files/wilson-extrapolation-icml-2013_0.pdf
http://www.cs.cmu.edu/~andrewgw/typo.pdf
"""
mixture_weights = np.random.random((Q))
mixture_means = np.random.random((Q, input_dim))
mixture_scales = np.random.random((input_dim, Q))
super().__init__(active_dims, name=name)
self.num_mixtures = int(Q)
self.mixture_weights = gpflow.Parameter(
mixture_weights,
transform=gpflow.utilities.positive(),
name='mixture_weights')
self.mixture_scales = gpflow.Parameter(
mixture_scales,
transform=gpflow.utilities.positive(),
name='mixture_scales')
self.mixture_means = gpflow.Parameter(
mixture_means,
transform=gpflow.utilities.positive(),
name='mixture_means')
def __init__(self, data, Y_var):
super().__init__(active_dims=[0])
self.Y_var = Y_var
self.num_genes = data.m_obs.shape[1]
# l_affine = tfb.AffineScalar(shift=tf.cast(1., tf.float64),
# scale=tf.cast(4-1., tf.float64))
# l_sigmoid = tfb.Sigmoid()
# l_logistic = tfb.Chain([l_affine, l_sigmoid])
self.lengthscale = gpflow.Parameter(1.414, transform=positive())
D_affine = tfb.AffineScalar(shift=tf.cast(0.1, tf.float64),
scale=tf.cast(1.5 - 0.1, tf.float64))
D_sigmoid = tfb.Sigmoid()
D_logistic = tfb.Chain([D_affine, D_sigmoid])
S_affine = tfb.AffineScalar(shift=tf.cast(0.1, tf.float64),
scale=tf.cast(4. - 0.1, tf.float64))
S_sigmoid = tfb.Sigmoid()
S_logistic = tfb.Chain([S_affine, S_sigmoid])
self.D = gpflow.Parameter(np.random.uniform(0.9, 1, self.num_genes),
transform=positive(),
dtype=tf.float64)
# self.D[3].trainable = False
# self.D[3].assign(0.8)
self.S = gpflow.Parameter(np.random.uniform(1, 1, self.num_genes),
transform=positive(),
dtype=tf.float64)
# self.S[3].trainable = False
# self.S[3].assign(1)
self.kervar = gpflow.Parameter(np.float64(1), transform=positive())
self.noise_term = gpflow.Parameter(
0.1353 * tf.ones(self.num_genes, dtype='float64'),
transform=positive())
def test_construct_parameter_from_existing_parameter_check_transform():
transform = tfp.bijectors.Sigmoid(tf.constant(0.0, dtype=tf.float64),
tf.constant(2.0, dtype=tf.float64))
initial_parameter = gpflow.Parameter([1.2, 1.1], transform=transform)
new_parameter = gpflow.Parameter(initial_parameter)
assert new_parameter.transform == transform
def __init__(self, a, b, M):
# [a, b] defining the interval of the Fourier representation:
self.a = gpflow.Parameter(a, dtype=gpflow.default_float())
self.b = gpflow.Parameter(b, dtype=gpflow.default_float())
# integer array defining the frequencies, ω_m = 2π (b - a)/m:
self.ms = np.arange(M)
self.omegas = 2.0 * np.pi * self.ms / (b - a)
def __init__(self, latent_dim: int,
input_dim: int,
network_dims: int,
activation_func: Optional[Callable] = None):
"""
Encoder that uses GPflow params to encode the features.
Creates an MLP with input dimensions `input_dim` and produces
2 * `latent_dim` outputs. Unlike the standard encoder, this
expects an input of NR shape, and converts that to an output which is
(N*R)L, where L is the latent dim.
:param latent_dim: dimension of the latent variable, i.e L
:param input_dim: the MLP acts on data of `input_dim` dimensions, i.e. R
:param network_dims: dimensions of inner MLPs, e.g. [10, 20, 10]
:param activation_func: TensorFlow operation that can be used
as non-linearity between the layers (default: tanh).
"""
super().__init__()
self.latent_dim = tf.convert_to_tensor([latent_dim], tf.int32)
self.activation_func = activation_func or tf.nn.tanh
self.layer_dims = [input_dim, *network_dims, latent_dim * 2]
Ws, bs = [], []
for input_dim, output_dim in zip(self.layer_dims[:-1], self.layer_dims[1:]):
xavier_std = (2. / (input_dim + output_dim)) ** 0.5
W = np.random.randn(input_dim, output_dim) * xavier_std
Ws.append(gpflow.Parameter(W, dtype=gpflow.config.default_float()))
bs.append(gpflow.Parameter(np.zeros(output_dim), dtype=gpflow.config.default_float()))
self.Ws, self.bs = Ws, bs
def __init__(self,
input_dim,
output_dim,
Rq,
active_dims=None,
name='csm'):
"""
- input_dim (int): The number of input dimensions.
- output_dim (int): The number of output dimensions.
- Rq (int): The number of subcomponents.
- active_dims (list of int): Apply kernel to specified dimensions only.
"""
constant = np.random.random((Rq, output_dim))
mean = np.random.random(input_dim)
variance = np.random.random(input_dim)
phase = np.zeros((Rq, output_dim))
MultiKernel.__init__(self,
input_dim,
output_dim,
active_dims,
name=name)
self.constant = gpflow.Parameter(constant,
transform=gpflow.utilities.positive(),
name="constant")
self.mean = gpflow.Parameter(mean,
transform=gpflow.utilities.positive(),
name="mean")
self.variance = gpflow.Parameter(variance,
transform=gpflow.utilities.positive(),
name="variance")
self.phase = gpflow.Parameter(phase, name="phase")
def __init__(self,
data: RegressionData,
kernel: Kernel,
mu_old: Optional[tf.Tensor],
Su_old: Optional[tf.Tensor],
Kaa_old: Optional[tf.Tensor],
Z_old: Optional[tf.Tensor],
inducing_variable: Union[InducingPoints, np.ndarray],
mean_function=Zero()):
"""
Z is a matrix of pseudo inputs, size M x D
kern, mean_function are appropriate gpflow objects
mu_old, Su_old are mean and covariance of old q(u)
Z_old is the old inducing inputs
This method only works with a Gaussian likelihood.
"""
X, Y = data
self.X = X
self.Y = Y
likelihood = Gaussian()
self.inducing_variable = gpflow.models.util.inducingpoint_wrapper(inducing_variable)
GPModel.__init__(self, kernel, likelihood, mean_function, inducing_variable.size)
self.num_data = X.shape[0]
self.num_latent = Y.shape[1]
self.mu_old = gpflow.Parameter(mu_old, trainable=False)
self.M_old = Z_old.shape[0]
self.Su_old = gpflow.Parameter(Su_old, trainable=False)
self.Kaa_old = gpflow.Parameter(Kaa_old, trainable=False)
self.Z_old = gpflow.Parameter(Z_old, trainable=False)
def update(self, dataset: Dataset):
model = self.model
x, y = model.data
assert dataset.query_points.shape[-1] == x.shape[-1]
assert dataset.observations.shape[-1] == y.shape[-1]
data = (dataset.query_points, dataset.observations)
num_data = data[0].shape[0]
f_mu, f_cov = self.model.predict_f(dataset.query_points, full_cov=True) # [N, L], [L, N, N]
assert self.model.q_sqrt.shape.ndims == 3
# GPflow's VGP model is hard-coded to use the whitened representation, i.e.
# q_mu and q_sqrt parametrise q(v), and u = f(X) = L v, where L = cholesky(K(X, X))
# Hence we need to backtransform from f_mu and f_cov to obtain the updated
# new_q_mu and new_q_sqrt:
Knn = model.kernel(dataset.query_points, full_cov=True) # [N, N]
jitter_mat = gpflow.config.default_jitter() * tf.eye(num_data, dtype=Knn.dtype)
Lnn = tf.linalg.cholesky(Knn + jitter_mat) # [N, N]
new_q_mu = tf.linalg.triangular_solve(Lnn, f_mu) # [N, L]
tmp = tf.linalg.triangular_solve(Lnn[None], f_cov) # [L, N, N], L⁻¹ f_cov
S_v = tf.linalg.triangular_solve(Lnn[None], tf.linalg.matrix_transpose(tmp)) # [L, N, N]
new_q_sqrt = tf.linalg.cholesky(S_v + jitter_mat) # [L, N, N]
model.data = data
model.num_data = num_data
model.q_mu = gpflow.Parameter(new_q_mu)
model.q_sqrt = gpflow.Parameter(new_q_sqrt, transform=gpflow.utilities.triangular())
def test_construct_parameter_from_existing_parameter_value_becomes_invalid():
initial_parameter = gpflow.Parameter(0.0)
transform = tfp.bijectors.Reciprocal()
with pytest.raises(tf.errors.InvalidArgumentError) as exc:
gpflow.Parameter(initial_parameter, transform=transform)
assert "gpflow.Parameter" in exc.value.message
def test_parameter_assign_validation():
with pytest.raises(tf.errors.InvalidArgumentError):
param = gpflow.Parameter(0.0, transform=positive())
param = gpflow.Parameter(0.1, transform=positive())
param.assign(0.2)
with pytest.raises(tf.errors.InvalidArgumentError):
param.assign(0.0)
def __init__(self,
active_dims=[0],
gap_decay=0.1,
match_decay=0.9,
max_subsequence_length=3,
alphabet=[],
maxlen=0,
batch_size=1000):
super().__init__(active_dims=active_dims)
# constrain decay kernel params to between 0 and 1
self.logistic_gap = tfb.Chain([
tfb.Shift(tf.cast(0, tf.float64))(tfb.Scale(tf.cast(1,
tf.float64))),
tfb.Sigmoid()
])
self.logisitc_match = tfb.Chain([
tfb.AffineScalar(shift=tf.cast(0, tf.float64),
scale=tf.cast(1, tf.float64)),
tfb.Sigmoid()
])
self.gap_decay_param = gpflow.Parameter(gap_decay,
transform=self.logistic_gap,
name="gap_decay")
self.match_decay_param = gpflow.Parameter(
match_decay, transform=self.logisitc_match, name="match_decay")
# use will use copies of the kernel params to stop building expensive computation graph
# we instead efficientely calculate gradients using dynamic programming
# These params are updated at every call to K and K_diag (to check if parameters have been updated)
self.match_decay = self.match_decay_param.numpy()
self.gap_decay = self.gap_decay_param.numpy()
self.match_decay_unconstrained = self.match_decay_param.unconstrained_variable.numpy(
)
self.gap_decay_unconstrained = self.gap_decay_param.unconstrained_variable.numpy(
)
self.order_coefs = tf.ones(max_subsequence_length, dtype=tf.float64)
# store additional kernel parameters
self.max_subsequence_length = tf.constant(max_subsequence_length)
self.alphabet = tf.constant(alphabet)
self.alphabet_size = tf.shape(self.alphabet)[0]
self.maxlen = tf.constant(maxlen)
self.batch_size = tf.constant(batch_size)
# build a lookup table of the alphabet to encode input strings
self.table = tf.lookup.StaticHashTable(
initializer=tf.lookup.KeyValueTensorInitializer(
keys=tf.constant(["PAD"] + alphabet),
values=tf.constant(range(0,
len(alphabet) + 1)),
),
default_value=0)
# initialize helful construction matricies to be lazily computed once needed
self.D = None
self.dD_dgap = None
def __init__(self, a, b, M, jitter=None):
self.length = M
# [a, b] defining the interval of the Fourier representation:
self.a = gpflow.Parameter(a, dtype=gpflow.default_float())
self.b = gpflow.Parameter(b, dtype=gpflow.default_float())
self.jitter = jitter
self.phis = gpflow.Parameter(np.random.uniform(0, 2 * np.pi, size=M))
self.omegas = gpflow.Parameter(np.random.uniform(0, 0.5 * M, size=M))
def __init__(self, a, b, M):
"""
`a` and `b` define the interval [a, b] of the Fourier representation.
`M` specifies the number of frequencies to use.
"""
# [a, b] defining the interval of the Fourier representation:
self.a = gpflow.Parameter(a, dtype=gpflow.default_float())
self.b = gpflow.Parameter(b, dtype=gpflow.default_float())
# integer array defining the frequencies, ω_m = 2π (b - a)/m:
self.ms = np.arange(M)
def __init__(self, args):
super().__init__(active_dims=[0])
self.var = gpflow.Parameter(10.0, transform=positive())
self.mag = gpflow.Parameter(1.0, transform=positive())
self.args = args
self.re = REMatchKernel(metric="polynomial",
degree=3,
gamma=1,
coef0=0,
alpha=0.5,
threshold=1e-6,
normalize_kernel=True)
def __init__(self, X, Y, name=None):
super().__init__(name=name)
self.X = X.copy() # Contains the covariates and decision point
self.Y = Y.copy() # Y is the minute-level step counts
self.num_data, self.input_dim = X.shape
_, self.num_classes = Y.shape
# Parameters
self.W = gpflow.Parameter(
np.random.randn(self.input_dim, self.num_classes))
self.b = gpflow.Parameter(np.random.rand(self.num_classes))
def __init__(self, state_dim, W=None, t=None):
Reward.__init__(self)
self.state_dim = state_dim
if W is not None:
self.W = gpflow.Parameter(
np.reshape(W, (state_dim, state_dim)), trainable=False
)
else:
self.W = gpflow.Parameter(np.eye(state_dim), trainable=False)
if t is not None:
self.t = gpflow.Parameter(np.reshape(t, (1, state_dim)), trainable=False)
else:
self.t = gpflow.Parameter(np.zeros((1, state_dim)), trainable=False)
def __init__(self, input_dim, output_dim, active_dims=None, name='conv'):
"""
- input_dim (int): The number of input dimensions.
- output_dim (int): The number of output dimensions.
- active_dims (list of int): Apply kernel to specified dimensions only.
"""
constant = np.random.random((output_dim))
variance = np.ones((input_dim, output_dim)) * 10
MultiKernel.__init__(self, input_dim, output_dim, active_dims, name=name)
self.constant = gpflow.Parameter(constant, transform=gpflow.utilities.positive(), name="constant")
self.variance = gpflow.Parameter(variance, transform=gpflow.utilities.positive(), name="variance")
def update(self, dataset: Dataset):
model = self.model
x, y = model.data
assert dataset.query_points.shape[-1] == x.shape[-1]
assert dataset.observations.shape[-1] == y.shape[-1]
data = (dataset.query_points, dataset.observations)
num_data = data[0].shape[0]
num_latent_gps = model.num_latent_gps
model.data = data
model.num_data = num_data
model.q_mu = gpflow.Parameter(np.zeros((num_data, num_latent_gps)))
q_sqrt = np.eye(num_data)
q_sqrt = np.repeat(q_sqrt[None], num_latent_gps, axis=0)
model.q_sqrt = gpflow.Parameter(q_sqrt, transform=gpflow.utilities.triangular())
def __init__(self, X, Y, name=None):
super().__init__(name=name) # always call the parent constructor
self.X = X.copy() # X is a NumPy array of inputs
self.Y = Y.copy(
) # Y is a 1-of-k (one-hot) representation of the labels
self.num_data, self.input_dim = X.shape
_, self.num_classes = Y.shape
# make some parameters
self.W = gpflow.Parameter(
np.random.randn(self.input_dim, self.num_classes))
self.b = gpflow.Parameter(np.random.randn(self.num_classes))
def __init__(self, data, latent_data, x_data_mean, kernel):
super().__init__()
print("HGPLVM")
self.iter = 0
self.kernel0 = kernel[0]
self.kernel1 = kernel[1]
self.mean_function = Zero()
self.likelihood0 = gpflow.likelihoods.Gaussian(1.0)
self.likelihood1 = gpflow.likelihoods.Gaussian(1.0)
# make some parameters
self.data = (gpflow.Parameter(x_data_mean),
gpflow.Parameter(latent_data), data)
print("gpr_data", np.shape(self.data[0]), np.shape(self.data[1]),
np.shape(self.data[2]))
def test_cast_to_dtype_precision_issue():
"""
TensorFlow's tf.cast(value, dtype) implicitly does a tf.convert_to_tensor(value)
*before* the cast when the value is not a tensor already. When value is a python float,
this results in the following behaviour:
>>> tf.cast(0.2, tf.float64)
<tf.Tensor: id=37, shape=(), dtype=float64, numpy=0.20000000298023224>
instead of the expected expansion of 0.2 to float64 precision that you get when
passing in an object that already carries dtype information, such as a numpy array
(which has float64 precision by default):
>>> tf.cast(np.array(0.2), tf.float64)
<tf.Tensor: id=40, shape=(), dtype=float64, numpy=0.2>
This affected *all* gpflow.Parameter objects, resulting in numerical discrepancies
between GPflow 1 and 2, due to the pass through _cast_to_dtype, which is now fixed.
This is the corresponding regression test.
"""
p = gpflow.Parameter(0.2, dtype=np.float64)
actual_value = p.numpy()
assert actual_value.dtype == np.float64
expected_value = np.float64(0.2)
assert actual_value == expected_value
def test_find_best_model_initialization_changes_params_with_sigmoid_bijectors(
gpflow_interface_factory: ModelFactoryType, dim: int
) -> None:
x = tf.constant(
np.arange(1, 1 + 10 * dim).reshape(-1, dim), dtype=gpflow.default_float()
) # shape: [10, dim]
model, _ = gpflow_interface_factory(x, fnc_3x_plus_10(x)[:, 0:1])
model.model.kernel = gpflow.kernels.RBF(lengthscales=[0.2] * dim)
if isinstance(model, (VariationalGaussianProcess, SparseVariational)):
pytest.skip("find_best_model_initialization is only implemented for the GPR models.")
upper = tf.cast([10.0] * dim, dtype=tf.float64)
lower = upper / 100
model.model.kernel.lengthscales = gpflow.Parameter(
model.model.kernel.lengthscales, transform=tfp.bijectors.Sigmoid(low=lower, high=upper)
)
model.find_best_model_initialization(2)
npt.assert_allclose(1.0, model.model.kernel.variance)
npt.assert_array_equal(dim, model.model.kernel.lengthscales.shape)
npt.assert_raises(
AssertionError, npt.assert_allclose, [0.2, 0.2], model.model.kernel.lengthscales
)
def test_find_best_model_initialization_improves_likelihood(
gpflow_interface_factory: ModelFactoryType, dim: int
) -> None:
x = tf.constant(
np.arange(1, 1 + 10 * dim).reshape(-1, dim), dtype=gpflow.default_float()
) # shape: [10, dim]
model, _ = gpflow_interface_factory(x, fnc_3x_plus_10(x)[:, 0:1])
model.model.kernel = gpflow.kernels.RBF(variance=1.0, lengthscales=[0.2] * dim)
if isinstance(model, (VariationalGaussianProcess, SparseVariational)):
pytest.skip("find_best_model_initialization is only implemented for the GPR models.")
model.model.kernel.variance.prior = tfp.distributions.LogNormal(
loc=np.float64(-2.0), scale=np.float64(1.0)
)
upper = tf.cast([10.0] * dim, dtype=tf.float64)
lower = upper / 100
model.model.kernel.lengthscales = gpflow.Parameter(
model.model.kernel.lengthscales, transform=tfp.bijectors.Sigmoid(low=lower, high=upper)
)
pre_init_loss = model.model.training_loss()
model.find_best_model_initialization(100)
post_init_loss = model.model.training_loss()
npt.assert_array_less(post_init_loss, pre_init_loss)