Modified log_like_gradients to make it _log_like_gradients and moved extract_gradient to _log_like_gradients_transformed.

GPy/core/model.py

@@ -25,7 +25,7 @@ class model(parameterised):
         raise NotImplementedError, "this needs to be implemented to utilise the model class"
     def log_likelihood(self):
         raise NotImplementedError, "this needs to be implemented to utilise the model class"
-    def log_likelihood_gradients(self):
+    def _log_likelihood_gradients(self):
         raise NotImplementedError, "this needs to be implemented to utilise the model class"
 
     def set_prior(self,which,what):
@@ -108,7 +108,7 @@ class model(parameterised):
         """evaluate the prior"""
         return np.sum([p.lnpdf(x) for p, x in zip(self.priors,self._get_params()) if p is not None])
 
-    def log_prior_gradients(self):
+    def _log_prior_gradients(self):
         """evaluate the gradients of the priors"""
         x = self._get_params()
         ret = np.zeros(x.size)
@@ -120,7 +120,7 @@ class model(parameterised):
         Use self.log_likelihood_gradients and self.prior_gradients to get the gradients of the model.
         Adjust the gradient for constraints and ties, return.
         """
-        g = self.log_likelihood_gradients() + self.log_prior_gradients()
+        g = self._log_likelihood_gradients() + self._log_prior_gradients()
         x = self._get_params()
         g[self.constrained_positive_indices] = g[self.constrained_positive_indices]*x[self.constrained_positive_indices]
         g[self.constrained_negative_indices] = g[self.constrained_negative_indices]*x[self.constrained_negative_indices]

GPy/inference/likelihoods.py

@@ -99,6 +99,6 @@ class probit(likelihood):
     def predictive_mean(self,mu,variance):
         return stats.norm.cdf(mu/np.sqrt(1+variance))
 
-    def log_likelihood_gradients():
+    def _log_likelihood_gradients():
         raise NotImplementedError
 

GPy/models/GPLVM.py

@@ -44,7 +44,7 @@ class GPLVM(GP_regression):
         self.X = x[:self.X.size].reshape(self.N,self.Q).copy()
         GP_regression._set_params(self, x[self.X.size:])
 
-    def log_likelihood_gradients(self):
+    def _log_likelihood_gradients(self):
         dL_dK = self.dL_dK()
 
         dL_dtheta = self.kern.dK_dtheta(dL_dK,self.X)

GPy/models/GP_EP.py

@@ -78,7 +78,7 @@ class GP_EP(model):
         L3 = sum(np.log(self.ep_approx.Z_hat))
         return L1 + L2A + L2B + L3
 
-    def log_likelihood_gradients(self):
+    def _log_likelihood_gradients(self):
         dK_dp = self.kernel.dK_dtheta(self.X)
         self.dK_dp = dK_dp
         aux1,info_1 = linalg.flapack.dtrtrs(self.L,np.dot(self.Sroot_tilde_K,self.ep_approx.v_tilde),lower=1)

GPy/models/GP_regression.py

@@ -103,7 +103,7 @@ class GP_regression(model):
 
         return dL_dK
 
-    def log_likelihood_gradients(self):
+    def _log_likelihood_gradients(self):
         return self.kern.dK_dtheta(partial=self.dL_dK(),X=self.X)
 
     def predict(self,Xnew, slices=None, full_cov=False):

GPy/models/generalized_FITC.py

@@ -99,7 +99,7 @@ class generalized_FITC(model):
         E = .5*np.sum((self.ep_approx.v_/self.ep_approx.tau_ - self.mu_tilde.flatten())**2/(1./self.ep_approx.tau_ + 1./self.ep_approx.tau_tilde))
         return  A + B + C + D + E
 
-    def log_likelihood_gradients(self):
+    def _log_likelihood_gradients(self):
         dKmm_dtheta = self.kernel.dK_dtheta(self.Z)
         dKnn_dtheta = self.kernel.dK_dtheta(self.X)
         dKmn_dtheta = self.kernel.dK_dtheta(self.Z,self.X)

GPy/models/sparse_GPLVM.py

@@ -49,8 +49,8 @@ class sparse_GPLVM(sparse_GP_regression, GPLVM):
 
         return dL_dX
 
-    def log_likelihood_gradients(self):
+    def _log_likelihood_gradients(self):
-        return np.hstack((self.dL_dX().flatten(), sparse_GP_regression.log_likelihood_gradients(self)))
+        return np.hstack((self.dL_dX().flatten(), sparse_GP_regression._log_likelihood_gradients(self)))
 
     def plot(self):
         GPLVM.plot(self)

GPy/models/sparse_GP_regression.py

@@ -168,7 +168,7 @@ class sparse_GP_regression(GP_regression):
             dL_dZ += self.kern.dK_dX(dL_dpsi1,self.Z,self.X)
         return dL_dZ
 
-    def log_likelihood_gradients(self):
+    def _log_likelihood_gradients(self):
         return np.hstack([self.dL_dZ().flatten(), self.dL_dbeta(), self.dL_dtheta()])
 
     def _raw_predict(self, Xnew, slices, full_cov=False):

GPy/models/warped_GP.py

@@ -59,8 +59,8 @@ class warpedGP(GP_regression):
         jacobian = self.warping_function.fgrad_y(self.Z, self.warping_params)
         return ll + np.log(jacobian).sum()
 
-    def log_likelihood_gradients(self):
+    def _log_likelihood_gradients(self):
-        ll_grads = GP_regression.log_likelihood_gradients(self)
+        ll_grads = GP_regression._log_likelihood_gradients(self)
         alpha = np.dot(self.Ki, self.Y.flatten())
         warping_grads = self.warping_function_gradients(alpha)
         return np.hstack((warping_grads.flatten(), ll_grads.flatten()))