def __init__(self, input_dim, energy=np.asarray([1.]), frequency=np.asarray([2*np.pi]), variance=1.,
lengthscales=1., len_fixed=False):
gpflow.kernels.Stationary.__init__(self, input_dim, variance=variance, lengthscales=lengthscales,
active_dims=None, ARD=False)
# self.variance = Param(variance, transforms.positive())
# self.lengthscale = Param(lengthscale, transforms.positive())
self.num_partials = len(frequency)
energy_list = []
frequency_list = []
for i in range(self.num_partials):
energy_list.append(Param(energy[i], transforms.positive))
frequency_list.append(Param(frequency[i], transforms.positive))
self.energy = ParamList(energy_list)
self.frequency = ParamList(frequency_list)
# self.energy.fixed = True
# self.frequency.fixed = True
# self.energy = energy
# self.frequency = frequency
if len_fixed:
self.lengthscales.fixed = True
def __init__(self,
input_dim,
num_partials,
lengthscales=None,
variances=None,
frequencies=None):
gpflow.kernels.Kern.__init__(self, input_dim, active_dims=None)
len_l = []
var_l = []
freq_l = []
self.ARD = False
self.num_partials = num_partials
if lengthscales.all() == None:
lengthscales = 1. * np.ones((num_partials, 1))
variances = 0.125 * np.ones((num_partials, 1))
frequencies = 1. * (1. + np.arange(num_partials))
for i in range(self.num_partials):
len_l.append(Param(lengthscales[i], transforms.Logistic(0., 2.)))
var_l.append(Param(variances[i], transforms.Logistic(0., 1.)))
freq_l.append(Param(frequencies[i], transforms.positive))
self.lengthscales = ParamList(len_l)
self.variance = ParamList(var_l)
self.frequency = ParamList(freq_l)
def __init__(self,
input_dim,
energy=np.asarray([1.]),
frequency=np.asarray([2 * np.pi]),
variance=1.0,
features_as_params=False):
"""
- input_dim is the dimension of the input to the kernel
- variance is the (initial) value for the variance parameter(s)
if ARD=True, there is one variance per input
- active_dims is a list of length input_dim which controls
which columns of X are used.
"""
gpflow.kernels.Kern.__init__(self, input_dim, active_dims=None)
self.num_features = len(frequency)
self.variance = Param(variance, transforms.Logistic(0., 0.25))
if features_as_params:
energy_list = []
frequency_list = []
for i in range(energy.size):
energy_list.append(Param(energy[i], transforms.positive))
frequency_list.append(Param(frequency[i], transforms.positive))
self.energy = ParamList(energy_list)
self.frequency = ParamList(frequency_list)
else:
self.energy = energy
self.frequency = frequency
def __init__(self,
input_dim,
variance=1.,
lengthscales=None,
energy=None,
frequencies=None,
len_fixed=True):
gpflow.kernels.Kern.__init__(self, input_dim, active_dims=None)
energy_l = []
freq_l = []
self.ARD = False
self.num_partials = len(energy)
for i in range(self.num_partials):
energy_l.append(Param(energy[i], transforms.positive))
freq_l.append(Param(frequencies[i], transforms.positive))
self.energy = ParamList(energy_l)
self.frequency = ParamList(freq_l)
self.variance = Param(variance, transforms.positive)
self.lengthscales = Param(lengthscales, transforms.positive)
self.vars_n_freqs_fixed(fix_energy=True, fix_freq=True)
if len_fixed:
self.lengthscales.fixed = True
def __init__(self, kern, q_mu, q_sqrt, Z, mean_function):
Parameterized.__init__(self)
nodes = []
for n_kern, n_q_mu, n_q_s in zip(kern, q_mu, q_sqrt):
nodes.append(Node(n_kern, n_q_mu, n_q_s, Z))
self.nodes = ParamList(nodes)
self.mean_function = mean_function
def __init__(self, operands, oper):
"""
:param operands: list of acquisition objects
:param oper: a tf.reduce operation (e.g., tf.reduce_sum) for aggregating the returned scores of each operand.
"""
super(AcquisitionAggregation, self).__init__()
assert (all([isinstance(x, Acquisition) for x in operands]))
self.operands = ParamList(operands)
self._oper = oper
def __init__(self,
X,
Y,
inducing_points,
final_inducing_points,
hidden_units,
units,
share_inducing_inputs=True):
Model.__init__(self)
assert X.shape[0] == Y.shape[0]
self.num_data, D_X = X.shape
self.D_Y = 1
self.num_samples = 100
kernels = []
for l in range(hidden_units + 1):
ks = []
if (l > 0):
D = units
else:
D = D_X
if (l < hidden_units):
for w in range(units):
ks.append(
RBF(D, lengthscales=1., variance=1.) +
White(D, variance=1e-5))
else:
ks.append(RBF(D, lengthscales=1., variance=1.))
kernels.append(ks)
self.dims_in = [D_X] + [units] * hidden_units
self.dims_out = [units] * hidden_units + [1]
q_mus, q_sqrts, Zs, mean_functions = init_layers(
X, self.dims_in, self.dims_out, inducing_points,
final_inducing_points, share_inducing_inputs)
layers = []
for q_mu, q_sqrt, Z, mean_function, kernel in zip(
q_mus, q_sqrts, Zs, mean_functions, kernels):
layers.append(Layer(kernel, q_mu, q_sqrt, Z, mean_function))
self.layers = ParamList(layers)
for layer in self.layers[:-1]: # fix the inner layer mean functions
layer.mean_function.fixed = True
self.likelihood = Gaussian()
minibatch_size = 10000 if X.shape[0] > 10000 else None
if minibatch_size is not None:
self.X = MinibatchData(X, minibatch_size)
self.Y = MinibatchData(Y, minibatch_size)
else:
self.X = DataHolder(X)
self.Y = DataHolder(Y)
def __init__(self, models=[], optimize_restarts=5):
"""
:param models: list of GPflow models representing our beliefs about the problem
:param optimize_restarts: number of optimization restarts to use when training the models
"""
super(Acquisition, self).__init__()
models = np.atleast_1d(models)
assert all(isinstance(model, (Model, ModelWrapper)) for model in models)
self._models = ParamList([DataScaler(m) for m in models])
assert (optimize_restarts >= 0)
self.optimize_restarts = optimize_restarts
self._needs_setup = True
def _optimize_models(self):
# Optimize model #1
self.operands[0]._optimize_models()
# Copy it again if needed due to changed free state
if self._needs_new_copies:
new_copies = [copy.deepcopy(self.operands[0]) for _ in range(len(self.operands) - 1)]
for c in new_copies:
c.optimize_restarts = 0
self.operands = ParamList([self.operands[0]] + new_copies)
self._needs_new_copies = False
# Draw samples using HMC
# Sample each model of the acquisition function - results in a list of 2D ndarrays.
hypers = np.hstack([model.sample(len(self.operands), **self._sample_opt) for model in self.models])
# Now visit all acquisition copies, and set state
for idx, draw in enumerate(self.operands):
draw.set_state(hypers[idx, :])
def __init__(self,
X,
Y,
Z,
kernels,
likelihood,
num_latent_Y=None,
minibatch_size=None,
num_samples=1,
mean_function=Zero()):
Model.__init__(self)
assert X.shape[0] == Y.shape[0]
assert Z.shape[1] == X.shape[1]
assert kernels[0].input_dim == X.shape[1]
self.num_data, D_X = X.shape
self.num_samples = num_samples
self.D_Y = num_latent_Y or Y.shape[1]
self.dims = [k.input_dim for k in kernels] + [
self.D_Y,
]
q_mus, q_sqrts, Zs, mean_functions = init_layers(
X, Z, self.dims, mean_function)
layers = []
for q_mu, q_sqrt, Z, mean_function, kernel in zip(
q_mus, q_sqrts, Zs, mean_functions, kernels):
layers.append(Layer(kernel, q_mu, q_sqrt, Z, mean_function))
self.layers = ParamList(layers)
for layer in self.layers[:-1]: # fix the inner layer mean functions
layer.mean_function.fixed = True
self.likelihood = likelihood
if minibatch_size is not None:
self.X = MinibatchData(X, minibatch_size)
self.Y = MinibatchData(Y, minibatch_size)
else:
self.X = DataHolder(X)
self.Y = DataHolder(Y)
def __init__(self, X_variational_mean, X_variational_var, Y, kern, t, kern_t, M , Z=None):
"""
Initialization of Bayesian Gaussian Process Dynamics Model. This method only works with Gaussian likelihood.
:param X_variational_mean: initial latent positions, size N (number of points) x Q (latent dimensions).
:param X_variational_var: variance of latent positions (N x Q), for the initialisation of the latent space.
:param Y: data matrix, size N (number of points) x D (dimensions).
:param kern: kernel specification, by default RBF.
:param t: time stamps.
:param kern_t: dynamics kernel specification, by default RBF.
:param M: number of inducing points.
:param Z: matrix of inducing points, size M (inducing points) x Q (latent dimensions), By default
random permutation of X_mean.
"""
super(BayesianDGPLVM, self).__init__(name='BayesianDGPLVM')
self.kern = kern
assert len(X_variational_mean) == len(X_variational_var), 'must be same amount of time series'
self.likelihood = likelihoods.Gaussian()
# multiple sequences
series = []
for i in range(len(X_variational_mean)):
series.append(GPTimeSeries(X_variational_mean[i], X_variational_var[i], t[i]))
self.series = ParamList(series)
# inducing points
if Z is None:
# By default we initialize by permutation of initial
Z = np.random.permutation(np.concatenate(X_variational_mean, axis=0).copy())[:M]
else:
assert Z.shape[0] == M
self.Z = Param(Z)
self.kern_t = kern_t
self.Y = DataHolder(Y)
self.M = M
self.n_s = 0
def __init__(self,
prev_ind_list,
cur_ind_list,
X_grid,
kerns_list,
name='collaborative_pref_gps'):
Model.__init__(self, name)
total_shape = total_all_actions(prev_ind_list)
Y = np.ones(total_shape)[:, None]
self.Y = DataHolder(Y)
# Introducing Paramlist to define kernels for latent GPs H
self.kerns_list = ParamList(kerns_list)
self.X_grid = DataHolder(X_grid[:, None])
self.prev_ind_list = prev_ind_list
self.cur_ind_list = cur_ind_list
# define likelihood
self.likelihood = gpflow.likelihoods.Bernoulli()