apunkt/GPy
1
0
Fork 0
mirror of https://github.com/SheffieldML/GPy.git synced 2026-04-30 15:26:23 +02:00
Code Issues Projects Releases Packages Wiki Activity Actions

[gradxx] not working with X,X...

Browse source
This commit is contained in:
mzwiessele 2016-05-06 16:02:53 +01:00
parent b16d57f560
commit 17bfccb457
4 changed files with 41 additions and 23 deletions
Download patch file Download diff file Expand all files Collapse all files

2
GPy/core/gp.py
View file

@ -419,7 +419,7 @@ class GP(Model):
mumuT = np.einsum('iqd,ipd->iqp', mu_jac, mu_jac) mumuT = np.einsum('iqd,ipd->iqp', mu_jac, mu_jac)
Sigma = np.zeros(mumuT.shape) Sigma = np.zeros(mumuT.shape)
if var_jac.ndim == 4: # Missing data if var_jac.ndim == 4: # Missing data
Sigma[(slice(None), )+np.diag_indices(Xnew.shape[1], 2)] = var_jac.sum(-1) Sigma = var_jac.sum(-1)
else: else:
Sigma = self.output_dim*var_jac Sigma = self.output_dim*var_jac

42
GPy/kern/src/stationary.py
View file

@ -237,29 +237,37 @@ class Stationary(Kern):
# d2K_dXdX2 = dK_dr*d2r_dXdX2 + d2K_drdr * dr_dX * dr_dX2: # d2K_dXdX2 = dK_dr*d2r_dXdX2 + d2K_drdr * dr_dX * dr_dX2:
invdist = self._inv_dist(X, X2) invdist = self._inv_dist(X, X2)
invdist2 = invdist**2 invdist2 = invdist**2
dL_dr = self.dK_dr_via_X(X, X2) * dL_dK # we perofrm this product later dL_dr = self.dK_dr_via_X(X, X2) * dL_dK # we perform this product later
tmp1 = dL_dr * invdist tmp1 = dL_dr * invdist
dL_drdr = self.dK2_drdr_via_X(X, X2) * dL_dK # we perofrm this product later dL_drdr = self.dK2_drdr_via_X(X, X2) * dL_dK # we perofrm this product later
tmp2 = dL_drdr * invdist2 tmp2 = dL_drdr
l2 = np.ones(X.shape[1])*self.lengthscale**2 #np.multiply(np.ones(X.shape[1]) ,self.lengthscale**2) l2 = np.ones(X.shape[1])*self.lengthscale**2 #np.multiply(np.ones(X.shape[1]) ,self.lengthscale**2)
if X2 is None: tmp1[invdist2==0.] -= self.variance
X2 = X
tmp1 -= np.eye(X.shape[0])*self.variance
else:
#tmp1[X==X2.T] -= self.variance # Old version, to be removed
# (seems to have a bug: it is subtracted to the first X1 anyway)
tmp1[invdist2==0.] -= self.variance
tmp3 = (tmp1*invdist2 - tmp2) tmp3 = (tmp1 - tmp2)*invdist2
#tmp3 = (tmp1 - tmp2)*invdist2
#tmp3 = tmp3
# This is not quite right yet, I need the maths to fully understand what is going on....
#else:
if cov: # full covariance if cov: # full covariance
dist = X[:,None,:] - X2[None,:,:] if X2 is None:
t2 = (tmp3[:,:,None,None]*(dist[:,:,:,None]*dist[:,:,None,:]))/l2[None,None,:,None] #tmp3 = tmp3+tmp3.T
dist = X[:,None,:] - X[None,:,:]
#dist = dist+dist.swapaxes(0,1)
else:
dist = X[:,None,:] - X2[None,:,:]
dist = (dist[:,:,:,None]*dist[:,:,None,:])
t2 = (tmp3[:,:,None,None]*dist)/l2[None,None,:,None]
t2.T[np.diag_indices(self.input_dim)] -= tmp1.T[None,:,:] t2.T[np.diag_indices(self.input_dim)] -= tmp1.T[None,:,:]
grad = t2/l2[None,None,None,:] grad = t2/l2[None,None,None,:]
#grad_old = np.empty((X.shape[0], X2.shape[0], X2.shape[1], X.shape[1]), dtype=np.float64) #grad_old = np.empty((X.shape[0], X2.shape[0], X2.shape[1], X.shape[1]), dtype=np.float64)
#
#for q in range(self.input_dim): #for q in range(self.input_dim):
# tmpdist = (X[:,[q]]-X2[:,[q]].T) # tmpdist = (X[:,[q]]-X2[:,[q]].T)
# for r in range(self.input_dim): # for r in range(self.input_dim):
@ -268,13 +276,17 @@ class Stationary(Kern):
# grad_old[:, :, q, r] = ((tmp3 * tmpdist2)/l2[r] - tmp1)/l2[q] # grad_old[:, :, q, r] = ((tmp3 * tmpdist2)/l2[r] - tmp1)/l2[q]
# else: # else:
# grad_old[:, :, q, r] = (((tmp3 * tmpdist2)/l2[r])/l2[q]) # grad_old[:, :, q, r] = (((tmp3 * tmpdist2)/l2[r])/l2[q])
#import ipdb;ipdb.set_trace()
if X2 is None:
grad += tmp1[:,:,None,None]
else: else:
# Diagonal covariance, old code # Diagonal covariance, old code
grad = np.empty((X.shape[0], X2.shape[0], X.shape[1]), dtype=np.float64) grad = np.empty((X.shape[0], X2.shape[0], X.shape[1]), dtype=np.float64)
#grad = np.empty(X.shape, dtype=np.float64) #grad = np.empty(X.shape, dtype=np.float64)
for q in range(self.input_dim): for q in range(self.input_dim):
tmpdist2 = (X[:,[q]]-X2[:,[q]].T) ** 2 tmpdist2 = (X[:,[q]]-X2[:,[q]].T) ** 2
grad[:, :, q] = np.multiply(dL_dK,(np.multiply((tmp1*invdist2 - tmp2),tmpdist2)/l2[q] - tmp1)/l2[q]) grad[:, :, q] = ((np.multiply((tmp1*invdist2 - tmp2),tmpdist2)/l2[q] - tmp1)/l2[q])
#grad[:, :, q] = ((tmp1*invdist2 - tmp2)*tmpdist2/l2[q] - tmp1)/l2[q] #grad[:, :, q] = ((tmp1*invdist2 - tmp2)*tmpdist2/l2[q] - tmp1)/l2[q]
#grad[:, :, q] = ((tmp1*(((tmpdist2)*invdist2/l2[q])-1)) - (tmp2*(tmpdist2))/l2[q])/l2[q] #grad[:, :, q] = ((tmp1*(((tmpdist2)*invdist2/l2[q])-1)) - (tmp2*(tmpdist2))/l2[q])/l2[q]
#np.sum(((tmp1*(((tmpdist2)*invdist2/l2[q])-1)) - (tmp2*(tmpdist2))/l2[q])/l2[q], axis=1, out=grad[:,q]) #np.sum(((tmp1*(((tmpdist2)*invdist2/l2[q])-1)) - (tmp2*(tmpdist2))/l2[q])/l2[q], axis=1, out=grad[:,q])
@ -293,7 +305,7 @@ class Stationary(Kern):
""" """
if cov: if cov:
tmp = np.ones(X.shape+(X.shape[1],)) tmp = np.ones(X.shape+(X.shape[1],))
return tmp * d2L_dK * self.variance/self.lengthscale**2# np.zeros(X.shape+(X.shape[1],)) return tmp * (d2L_dK * self.variance/self.lengthscale**2)[:,None,None]# np.zeros(X.shape+(X.shape[1],))
return np.ones(X.shape) * d2L_dK * self.variance/self.lengthscale**2 # np.zeros(X.shape) return np.ones(X.shape) * d2L_dK * self.variance/self.lengthscale**2 # np.zeros(X.shape)
def _gradients_X_pure(self, dL_dK, X, X2=None): def _gradients_X_pure(self, dL_dK, X, X2=None):

4
GPy/plotting/__init__.py
View file

@ -50,6 +50,8 @@ def inject_plotting():
GP.plot_samples = gpy_plot.gp_plots.plot_samples GP.plot_samples = gpy_plot.gp_plots.plot_samples
GP.plot = gpy_plot.gp_plots.plot GP.plot = gpy_plot.gp_plots.plot
GP.plot_f = gpy_plot.gp_plots.plot_f GP.plot_f = gpy_plot.gp_plots.plot_f
GP.plot_latent = gpy_plot.gp_plots.plot_f
GP.plot_noiseless = gpy_plot.gp_plots.plot_f
GP.plot_magnification = gpy_plot.latent_plots.plot_magnification GP.plot_magnification = gpy_plot.latent_plots.plot_magnification
from ..models import StateSpace from ..models import StateSpace
@ -62,6 +64,8 @@ def inject_plotting():
StateSpace.plot_samples = gpy_plot.gp_plots.plot_samples StateSpace.plot_samples = gpy_plot.gp_plots.plot_samples
StateSpace.plot = gpy_plot.gp_plots.plot StateSpace.plot = gpy_plot.gp_plots.plot
StateSpace.plot_f = gpy_plot.gp_plots.plot_f StateSpace.plot_f = gpy_plot.gp_plots.plot_f
StateSpace.plot_latent = gpy_plot.gp_plots.plot_f
StateSpace.plot_noiseless = gpy_plot.gp_plots.plot_f
from ..core import SparseGP from ..core import SparseGP
SparseGP.plot_inducing = gpy_plot.data_plots.plot_inducing SparseGP.plot_inducing = gpy_plot.data_plots.plot_inducing

8
GPy/testing/kernel_tests.py
View file

@ -112,13 +112,15 @@ class Kern_check_d2K_dXdX_cov(Kern_check_model):
self.link_parameter(self.X) self.link_parameter(self.X)
def log_likelihood(self): def log_likelihood(self):
return np.sum(self.kernel.gradients_X(self.dL_dK,self.X, self.X2)) return self.kernel.gradients_X(self.dL_dK, self.X, self.X2).sum()
def parameters_changed(self): def parameters_changed(self):
#if self.kernel.name == 'rbf': #if self.kernel.name == 'rbf':
# import ipdb;ipdb.set_trace() # import ipdb;ipdb.set_trace()
grads = self.kernel.gradients_XX(self.dL_dK, self.X, self.X2, cov=True) if self.X2 is None: X2 = self.X
self.X.gradient[:] = grads.sum(-1).sum(1) else: X2 = self.X2
grads = self.kernel.gradients_XX(self.dL_dK.T, X2, self.X, cov=True)
self.X.gradient[:] = grads.sum(-1).sum(0)
class Kern_check_d2Kdiag_dXdX_cov(Kern_check_model): class Kern_check_d2Kdiag_dXdX_cov(Kern_check_model):
"""This class allows gradient checks for the second derivative of a kernel with respect to X. """ """This class allows gradient checks for the second derivative of a kernel with respect to X. """