corrected caching for psi derivatives

GPy/kern/_src/kern.py

@@ -58,12 +58,7 @@ class Kern(Parameterized):
 
         self._sliced_X = 0
         self.useGPU = self._support_GPU and useGPU
-        self._return_psi2_n_flag = ObsAr(np.zeros(1)).astype(bool)
+        self._return_psi2_n_flag = ObsAr(np.zeros(1).astype(bool))
-
-        #FIXME: temporary solution
-        from ...core.parameterization.lists_and_dicts import ObserverList
-        self._return_psi2_n_flag.observers = ObserverList()
-        self._return_psi2_n_flag._update_on = True
 
         from .psi_comp import PSICOMP_GH
         self.psicomp = PSICOMP_GH()

GPy/kern/_src/psi_comp/rbf_psi_comp.py

@@ -68,6 +68,7 @@ def __psi2computations(variance, lengthscale, Z, mu, S):
     _psi2 = variance*variance*np.exp(_psi2_logdenom[:,None,None]+_psi2_exp1[None,:,:]+_psi2_exp2)
     return _psi2
 
+@profile
 def psiDerivativecomputations(dL_dpsi0, dL_dpsi1, dL_dpsi2, variance, lengthscale, Z, variational_posterior,
                               psi0=None, psi1=None, psi2=None, Lpsi0=None, Lpsi1=None, Lpsi2=None):
     ARD = (len(lengthscale)!=1)
@@ -121,6 +122,7 @@ def __psi1compDer(dL_dpsi1, variance, lengthscale, Z, mu, S, psi1=None, Lpsi1=No
 
     return _dL_dvar, _dL_dl, _dL_dZ, _dL_dmu, _dL_dS
 
+@profile
 def __psi2compDer(dL_dpsi2, variance, lengthscale, Z, mu, S, psi2=None, Lpsi2=None):
     """
     Z - MxQ
@@ -156,8 +158,14 @@ def __psi2compDer(dL_dpsi2, variance, lengthscale, Z, mu, S, psi2=None, Lpsi2=No
     _dL_dvar = Lpsi2sum.sum()*2/variance
     _dL_dmu = (-2*denom) * (mu*Lpsi2sum[:,None]-Lpsi2Zhat)
     _dL_dS = (2*np.square(denom))*(np.square(mu)*Lpsi2sum[:,None]-2*mu*Lpsi2Zhat+Lpsi2Zhat2) - denom*Lpsi2sum[:,None]
-    _dL_dZ = -np.einsum('nmo,oq->oq',Lpsi2,Z)/lengthscale2+np.einsum('nmo,oq->mq',Lpsi2,Z)/lengthscale2+ \
+    _dL_dZ1 = -np.einsum('nmo,oq->oq',Lpsi2,Z)/lengthscale2
-             2*np.einsum('nmo,nq,nq->mq',Lpsi2,mu,denom) - np.einsum('nmo,nq,mq->mq',Lpsi2,denom,Z) - np.einsum('nmo,oq,nq->mq',Lpsi2,Z,denom)
+    _dL_dZ2 = np.einsum('nmo,oq->mq',Lpsi2,Z)/lengthscale2
+    _dL_dZ3 = 2*np.einsum('nmo,nq,nq->mq',Lpsi2,mu,denom)
+    _dL_dZ4 = - np.einsum('nmo,nq,mq->mq',Lpsi2,denom,Z)
+    _dL_dZ5 = - np.einsum('nmo,oq,nq->mq',Lpsi2,Z,denom)
+    _dL_dZ = _dL_dZ1 + _dL_dZ2 + _dL_dZ3 + _dL_dZ4 + _dL_dZ5
+    #_dL_dZ = -np.einsum('nmo,oq->oq',Lpsi2,Z)/lengthscale2+np.einsum('nmo,oq->mq',Lpsi2,Z)/lengthscale2+ \
+             #2*np.einsum('nmo,nq,nq->mq',Lpsi2,mu,denom) - np.einsum('nmo,nq,mq->mq',Lpsi2,denom,Z) - np.einsum('nmo,oq,nq->mq',Lpsi2,Z,denom)
     _dL_dl = 2*lengthscale* ((S/lengthscale2*denom+np.square(mu*denom))*Lpsi2sum[:,None]+(Lpsi2Z2-Lpsi2Z2p)/(2*np.square(lengthscale2))-
                              (2*mu*denom2)*Lpsi2Zhat+denom2*Lpsi2Zhat2).sum(axis=0)
 

GPy/models/bayesian_gplvm_minibatch.py

@@ -9,6 +9,7 @@ from ..inference.latent_function_inference.var_dtc_parallel import VarDTC_miniba
 import logging
 from GPy.models.sparse_gp_minibatch import SparseGPMiniBatch
 from GPy.core.parameterization.param import Param
+from GPy.core.parameterization.observable_array import ObsAr
 
 class BayesianGPLVMMiniBatch(SparseGPMiniBatch):
     """
@@ -134,17 +135,6 @@ class BayesianGPLVMMiniBatch(SparseGPMiniBatch):
             full_values['Xgrad'] = self.kern.gradients_X(full_values['dL_dKnm'], self.X, self.Z)
             full_values['Xgrad'] += self.kern.gradients_X_diag(full_values['dL_dKdiag'], self.X)
 
-        #kl_fctr = self.kl_factr
-        #if self.has_uncertain_inputs():
-            #self._log_marginal_likelihood -= kl_fctr*self.variational_prior.KL_divergence(self.X)
-
-            # Subsetting Variational Posterior objects, makes the gradients
-            # empty. We need them to be 0 though:
-            #self.X.mean.gradient[:] = 0
-            #self.X.variance.gradient[:] = 0
-
-            #self.variational_prior.update_gradients_KL(self.X)
-
         if self.has_uncertain_inputs():
             self.X.mean.gradient = full_values['meangrad']
             self.X.variance.gradient = full_values['vargrad']
@@ -155,13 +145,15 @@ class BayesianGPLVMMiniBatch(SparseGPMiniBatch):
         full_values = super(BayesianGPLVMMiniBatch, self)._outer_init_full_values()
         full_values['meangrad'] = np.zeros((self.X.shape[0], self.X.shape[1]))
         full_values['vargrad'] = np.zeros((self.X.shape[0], self.X.shape[1]))
-        full_values['dL_dpsi0'] = np.zeros(self.X.shape[0])
-        full_values['dL_dpsi1'] = np.zeros((self.X.shape[0], self.Z.shape[0]))
-        full_values['dL_dpsi2'] = np.zeros((self.Z.shape[0], self.Z.shape[0]))
 
-        full_values['Lpsi0'] = np.zeros(self.X.shape[0])
+        #FIXME Hack
-        full_values['Lpsi1'] = np.zeros((self.X.shape[0], self.Z.shape[0]))
+        full_values['dL_dpsi0'] = ObsAr(np.zeros(self.X.shape[0]))
-        full_values['Lpsi2'] = np.zeros((self.X.shape[0], self.Z.shape[0], self.Z.shape[0]))
+        full_values['dL_dpsi1'] = ObsAr(np.zeros((self.X.shape[0], self.Z.shape[0])))
+        full_values['dL_dpsi2'] = ObsAr(np.zeros((self.Z.shape[0], self.Z.shape[0])))
+
+        full_values['Lpsi0'] = ObsAr(np.zeros(self.X.shape[0]))
+        full_values['Lpsi1'] = ObsAr(np.zeros((self.X.shape[0], self.Z.shape[0])))
+        full_values['Lpsi2'] = ObsAr(np.zeros((self.X.shape[0], self.Z.shape[0], self.Z.shape[0])))
         return full_values
 
     def parameters_changed(self):

GPy/models/sparse_gp_minibatch.py

@@ -147,7 +147,11 @@ class SparseGPMiniBatch(SparseGP):
                 if np.isscalar(current_values[key]):
                     full_values[key] += current_values[key]
                 else:
-                    full_values[key][index] += current_values[key]
+                    from ..core.parameterization.observable_array import ObsAr
+                    if isinstance(full_values[key], ObsAr):
+                        full_values[key].values[index] += current_values[key]
+                    else:
+                        full_values[key][index] += current_values[key]
             else:
                 full_values[key] = current_values[key]
 
@@ -178,11 +182,6 @@ class SparseGPMiniBatch(SparseGP):
                                                 dL_dpsi2=full_values['dL_dpsi2'],
                                                 psi0=self.psi0, psi1=self.psi1, psi2=self.psi2,
                                                 Lpsi0=full_values['Lpsi0'], Lpsi1=full_values['Lpsi1'], Lpsi2=full_values['Lpsi2'])
-            #self.kern.update_gradients_expectations(variational_posterior=self.X,
-                                                    #Z=self.Z,
-                                                    #dL_dpsi0=full_values['dL_dpsi0'],
-                                                    #dL_dpsi1=full_values['dL_dpsi1'],
-                                                    #dL_dpsi2=full_values['dL_dpsi2'])
             full_values['kerngrad'] += self.kern.gradient
 
             #gradients wrt Z
@@ -251,9 +250,10 @@ class SparseGPMiniBatch(SparseGP):
         #Compute the psi statistics for N once, but don't sum out N in psi2
         if self.has_uncertain_inputs():
             self.kern.return_psi2_n = True
-            psi0 = self.kern.psi0(self.Z, self.X)
+            from ..core.parameterization.observable_array import ObsAr
-            psi1 = self.kern.psi1(self.Z, self.X)
+            psi0 = ObsAr(self.kern.psi0(self.Z, self.X))
-            psi2 = self.kern.psi2(self.Z, self.X)
+            psi1 = ObsAr(self.kern.psi1(self.Z, self.X))
+            psi2 = ObsAr(self.kern.psi2(self.Z, self.X))
         else:
             psi0 = self.kern.Kdiag(self.X)
             psi1 = self.kern.K(self.X, self.Z)