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Merge branch 'devel' of github.com:SheffieldML/GPy into devel

Browse source 
Conflicts:
	GPy/inference/latent_function_inference/inferenceX.py
This commit is contained in:
Max Zwiessele 2014-11-14 11:28:19 +00:00
commit 118ed2733e
2 changed files with 23 additions and 27 deletions
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6
GPy/core/parameterization/variational.py
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@ -169,7 +169,7 @@ class SpikeAndSlabPosterior(VariationalPosterior):
def gamma_probabilities(self): def gamma_probabilities(self):
prob = np.zeros_like(param_to_array(self.gamma)) prob = np.zeros_like(param_to_array(self.gamma))
prob[self.gamma>-710] = 1./(1.+np.exp(-self.gamma[self.gamma>-710])) prob[self.gamma>-710] = 1./(1.+np.exp(-self.gamma[self.gamma>-710]))
prob1 = np.zeros_like(param_to_array(self.gamma)) prob1 = -np.zeros_like(param_to_array(self.gamma))
prob1[self.gamma<710] = 1./(1.+np.exp(self.gamma[self.gamma<710])) prob1[self.gamma<710] = 1./(1.+np.exp(self.gamma[self.gamma<710]))
return prob, prob1 return prob, prob1
@ -177,8 +177,8 @@ class SpikeAndSlabPosterior(VariationalPosterior):
def gamma_log_prob(self): def gamma_log_prob(self):
loggamma = param_to_array(self.gamma).copy() loggamma = param_to_array(self.gamma).copy()
loggamma[loggamma>-40] = -np.log1p(np.exp(-loggamma[loggamma>-40])) loggamma[loggamma>-40] = -np.log1p(np.exp(-loggamma[loggamma>-40]))
loggamma1 = param_to_array(self.gamma).copy() loggamma1 = -param_to_array(self.gamma).copy()
loggamma1[loggamma1<40] = -np.log1p(np.exp(loggamma1[loggamma1<40])) loggamma1[loggamma1>-40] = -np.log1p(np.exp(-loggamma1[loggamma1>-40]))
return loggamma,loggamma1 return loggamma,loggamma1
def set_gradients(self, grad): def set_gradients(self, grad):

44
GPy/inference/latent_function_inference/inferenceX.py
View file

@ -7,38 +7,37 @@ from ...core.parameterization import variational
def infer_newX(model, Y_new, optimize=True, init='L2'): def infer_newX(model, Y_new, optimize=True, init='L2'):
""" """
Infer the distribution of X for the new observed data *Y_new*. Infer the distribution of X for the new observed data *Y_new*.
:param model: the GPy model used in inference :param model: the GPy model used in inference
:type model: GPy.core.Model :type model: GPy.core.Model
:param Y_new: the new observed data for inference :param Y_new: the new observed data for inference
:type Y_new: numpy.ndarray :type Y_new: numpy.ndarray
:param optimize: whether to optimize the location of new X (True by default) :param optimize: whether to optimize the location of new X (True by default)
:type optimize: boolean :type optimize: boolean
:return: a tuple containing the estimated posterior distribution of X and the model that optimize X :return: a tuple containing the estimated posterior distribution of X and the model that optimize X
:rtype: (GPy.core.parameterization.variational.VariationalPosterior, GPy.core.Model) :rtype: (GPy.core.parameterization.variational.VariationalPosterior, GPy.core.Model)
""" """
infr_m = InferenceX(model, Y_new, init=init) infr_m = InferenceX(model, Y_new, init=init)
if optimize: if optimize:
infr_m.optimize() infr_m.optimize()
return infr_m.X, infr_m return infr_m.X, infr_m
class InferenceX(Model): class InferenceX(Model):
""" """
The class for inference of new X with given new Y. (do_test_latent) The class for inference of new X with given new Y. (do_test_latent)
:param model: the GPy model used in inference :param model: the GPy model used in inference
:type model: GPy.core.Model :type model: GPy.core.Model
:param Y: the new observed data for inference :param Y: the new observed data for inference
:type Y: numpy.ndarray :type Y: numpy.ndarray
""" """
def __init__(self, model, Y, name='inferenceX', init='L2'): def __init__(self, model, Y, name='inferenceX', init='L2'):
if np.isnan(Y).any() or getattr(model, 'missing_data', False): if np.isnan(Y).any():
assert Y.shape[0]==1, "The current implementation of inference X only support one data point at a time with missing data!" assert Y.shape[0]==1, "The current implementation of inference X only support one data point at a time with missing data!"
self.missing_data = True self.missing_data = True
self.valid_dim = np.logical_not(np.isnan(Y[0])) self.valid_dim = np.logical_not(np.isnan(Y[0]))
self.ninan = getattr(model, 'ninan', None)
else: else:
self.missing_data = False self.missing_data = False
super(InferenceX, self).__init__(name) super(InferenceX, self).__init__(name)
@ -67,12 +66,12 @@ class InferenceX(Model):
self.Y = Y self.Y = Y
self.X = self._init_X(model, Y, init=init) self.X = self._init_X(model, Y, init=init)
self.compute_dL() self.compute_dL()
self.link_parameter(self.X) self.link_parameter(self.X)
def _init_X(self, model, Y_new, init='L2'): def _init_X(self, model, Y_new, init='L2'):
# Initialize the new X by finding the nearest point in Y space. # Initialize the new X by finding the nearest point in Y space.
Y = model.Y Y = model.Y
if self.missing_data: if self.missing_data:
Y = Y[:,self.valid_dim] Y = Y[:,self.valid_dim]
@ -86,7 +85,7 @@ class InferenceX(Model):
elif init=='rand': elif init=='rand':
dist = np.random.rand(Y_new.shape[0],Y.shape[0]) dist = np.random.rand(Y_new.shape[0],Y.shape[0])
idx = dist.argmin(axis=1) idx = dist.argmin(axis=1)
from ...models import SSGPLVM from ...models import SSGPLVM
from ...util.misc import param_to_array from ...util.misc import param_to_array
if isinstance(model, SSGPLVM): if isinstance(model, SSGPLVM):
@ -99,9 +98,9 @@ class InferenceX(Model):
else: else:
from ...core import Param from ...core import Param
X = Param('latent mean',param_to_array(model.X[idx]).copy()) X = Param('latent mean',param_to_array(model.X[idx]).copy())
return X return X
def compute_dL(self): def compute_dL(self):
# Common computation # Common computation
beta = 1./np.fmax(self.likelihood.variance, 1e-6) beta = 1./np.fmax(self.likelihood.variance, 1e-6)
@ -109,18 +108,15 @@ class InferenceX(Model):
wv = self.posterior.woodbury_vector wv = self.posterior.woodbury_vector
if self.missing_data: if self.missing_data:
wv = wv[:,self.valid_dim] wv = wv[:,self.valid_dim]
if self.ninan is not None: output_dim = self.valid_dim.sum()
self.dL_dpsi2 = beta/2.*(self.posterior.woodbury_inv[:, :, self.valid_dim] - np.einsum('md,od->mo',wv, wv)[:, :, None]) self.dL_dpsi2 = beta*(output_dim*self.posterior.woodbury_inv - np.einsum('md,od->mo',wv, wv))/2.
self.dL_dpsi2 = self.dL_dpsi2.sum(-1)
else:
self.dL_dpsi2 = beta/2.*(self.valid_dim.sum() * self.posterior.woodbury_inv - np.einsum('md,od->mo',wv, wv))
self.dL_dpsi1 = beta*np.dot(self.Y[:,self.valid_dim], wv.T) self.dL_dpsi1 = beta*np.dot(self.Y[:,self.valid_dim], wv.T)
self.dL_dpsi0 = - beta/2.* np.ones(self.Y.shape[0]) self.dL_dpsi0 = - beta/2.* np.ones(self.Y.shape[0])
else: else:
self.dL_dpsi2 = beta/2.*(output_dim*self.posterior.woodbury_inv - np.einsum('md,od->mo',wv, wv)) self.dL_dpsi2 = beta*(output_dim*self.posterior.woodbury_inv - np.einsum('md,od->mo',wv, wv))/2.
self.dL_dpsi1 = beta*np.dot(self.Y, wv.T) self.dL_dpsi1 = beta*np.dot(self.Y, wv.T)
self.dL_dpsi0 = -beta/2.* np.ones(self.Y.shape[0]) self.dL_dpsi0 = -beta/2.*output_dim* np.ones(self.Y.shape[0])
def parameters_changed(self): def parameters_changed(self):
if self.uncertain_input: if self.uncertain_input:
psi0 = self.kern.psi0(self.Z, self.X) psi0 = self.kern.psi0(self.Z, self.X)
@ -132,7 +128,7 @@ class InferenceX(Model):
psi2 = np.dot(psi1.T,psi1) psi2 = np.dot(psi1.T,psi1)
self._log_marginal_likelihood = (self.dL_dpsi2*psi2).sum()+(self.dL_dpsi1*psi1).sum()+(self.dL_dpsi0*psi0).sum() self._log_marginal_likelihood = (self.dL_dpsi2*psi2).sum()+(self.dL_dpsi1*psi1).sum()+(self.dL_dpsi0*psi0).sum()
if self.uncertain_input: if self.uncertain_input:
X_grad = self.kern.gradients_qX_expectations(variational_posterior=self.X, Z=self.Z, dL_dpsi0=self.dL_dpsi0, dL_dpsi1=self.dL_dpsi1, dL_dpsi2=self.dL_dpsi2) X_grad = self.kern.gradients_qX_expectations(variational_posterior=self.X, Z=self.Z, dL_dpsi0=self.dL_dpsi0, dL_dpsi1=self.dL_dpsi1, dL_dpsi2=self.dL_dpsi2)
self.X.set_gradients(X_grad) self.X.set_gradients(X_grad)
@ -141,7 +137,7 @@ class InferenceX(Model):
X_grad = self.kern.gradients_X_diag(self.dL_dpsi0, self.X) X_grad = self.kern.gradients_X_diag(self.dL_dpsi0, self.X)
X_grad += self.kern.gradients_X(dL_dpsi1, self.X, self.Z) X_grad += self.kern.gradients_X(dL_dpsi1, self.X, self.Z)
self.X.gradient = X_grad self.X.gradient = X_grad
if self.uncertain_input: if self.uncertain_input:
from ...core.parameterization.variational import SpikeAndSlabPrior from ...core.parameterization.variational import SpikeAndSlabPrior
if isinstance(self.variational_prior, SpikeAndSlabPrior): if isinstance(self.variational_prior, SpikeAndSlabPrior):
@ -155,7 +151,7 @@ class InferenceX(Model):
# update for the KL divergence # update for the KL divergence
self.variational_prior.update_gradients_KL(self.X) self.variational_prior.update_gradients_KL(self.X)
self._log_marginal_likelihood += -KL_div self._log_marginal_likelihood += -KL_div
def log_likelihood(self): def log_likelihood(self):
return self._log_marginal_likelihood return self._log_marginal_likelihood