From a5208f474ec0880eac02392c4d186fdd6b35d2d9 Mon Sep 17 00:00:00 2001
From: James Hensman <james.hensman@gmail.com>
Date: Thu, 6 Jun 2013 10:59:34 +0100
Subject: [PATCH 1/3] modified lengthscale gradients - demo works now.

---
 GPy/kern/rbf.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/GPy/kern/rbf.py b/GPy/kern/rbf.py
index 2d316234..d1e0797c 100644
--- a/GPy/kern/rbf.py
+++ b/GPy/kern/rbf.py
@@ -96,13 +96,13 @@ class rbf(Kernpart):
             var_len3 = self.variance / np.power(self.lengthscale, 3)
             if X2 is None:
                 # save computation for the symmetrical case
-                dvardLdK += dvardLdK.T
+                dvardLdK = dvardLdK + dvardLdK.T
                 code = """
                 int q,i,j;
                 double tmp;
                 for(q=0; q<input_dim; q++){
                   tmp = 0;
-                  for(i=0; i<N; i++){
+                  for(i=0; i<num_data; i++){
                     for(j=0; j<i; j++){
                       tmp += (X(i,q)-X(j,q))*(X(i,q)-X(j,q))*dvardLdK(i,j);
                     }
@@ -110,14 +110,15 @@ class rbf(Kernpart):
                   target(q+1) += var_len3(q)*tmp;
                 }
                 """
-                N, num_inducing, input_dim = X.shape[0], X.shape[0], self.input_dim
+                num_data, num_inducing, input_dim = X.shape[0], X.shape[0], self.input_dim
+                weave.inline(code, arg_names=['num_data','num_inducing','input_dim','X','X2','target','dvardLdK','var_len3'], type_converters=weave.converters.blitz, **self.weave_options)
             else:
                 code = """
                 int q,i,j;
                 double tmp;
                 for(q=0; q<input_dim; q++){
                   tmp = 0;
-                  for(i=0; i<N; i++){
+                  for(i=0; i<num_data; i++){
                     for(j=0; j<num_inducing; j++){
                       tmp += (X(i,q)-X2(j,q))*(X(i,q)-X2(j,q))*dvardLdK(i,j);
                     }
@@ -125,10 +126,9 @@ class rbf(Kernpart):
                   target(q+1) += var_len3(q)*tmp;
                 }
                 """
-                N, num_inducing, input_dim = X.shape[0], X2.shape[0], self.input_dim
-            # [np.add(target[1+q:2+q],var_len3[q]*np.sum(dvardLdK*np.square(X[:,q][:,None]-X2[:,q][None,:])),target[1+q:2+q]) for q in range(self.input_dim)]
-            weave.inline(code, arg_names=['N','num_inducing','input_dim','X','X2','target','dvardLdK','var_len3'],
-                 type_converters=weave.converters.blitz, **self.weave_options)
+                num_data, num_inducing, input_dim = X.shape[0], X2.shape[0], self.input_dim
+                #[np.add(target[1+q:2+q],var_len3[q]*np.sum(dvardLdK*np.square(X[:,q][:,None]-X2[:,q][None,:])),target[1+q:2+q]) for q in range(self.input_dim)]
+                weave.inline(code, arg_names=['num_data','num_inducing','input_dim','X','X2','target','dvardLdK','var_len3'], type_converters=weave.converters.blitz, **self.weave_options)
         else:
             target[1] += (self.variance / self.lengthscale) * np.sum(self._K_dvar * self._K_dist2 * dL_dK)
 

From 1238252a19a4195084c0384817e3977d53778f84 Mon Sep 17 00:00:00 2001
From: Nicolas <n.durrande@sheffield.ac.uk>
Date: Thu, 6 Jun 2013 11:24:00 +0100
Subject: [PATCH 2/3] removed visualize dependencies and added dKdiag_dX for
 linear

---
 GPy/kern/linear.py   | 3 +++
 GPy/util/__init__.py | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/GPy/kern/linear.py b/GPy/kern/linear.py
index b2aa29f9..402e6ead 100644
--- a/GPy/kern/linear.py
+++ b/GPy/kern/linear.py
@@ -100,6 +100,9 @@ class linear(Kernpart):
     def dK_dX(self, dL_dK, X, X2, target):
         target += (((X2[:, None, :] * self.variances)) * dL_dK[:, :, None]).sum(0)
 
+    def dKdiag_dX(self,dL_dKdiag,X,target):
+        target += 2.*self.variances*dL_dKdiag[:,None]*X
+
     #---------------------------------------#
     #             PSI statistics            #
     #---------------------------------------#
diff --git a/GPy/util/__init__.py b/GPy/util/__init__.py
index 27d25518..cbb5e250 100644
--- a/GPy/util/__init__.py
+++ b/GPy/util/__init__.py
@@ -11,6 +11,6 @@ import misc
 import warping_functions
 import datasets
 import mocap
-import visualize
+#import visualize
 import decorators
 import classification

From feb7b04c51f0a602834619c0b16eface8ff730b3 Mon Sep 17 00:00:00 2001
From: Ricardo <acq11ra@sheffield.ac.uk>
Date: Thu, 6 Jun 2013 14:02:42 +0100
Subject: [PATCH 3/3] removing unused link_functions

---
 GPy/likelihoods/link_functions.py | 40 ++++++-------------------------
 1 file changed, 7 insertions(+), 33 deletions(-)

diff --git a/GPy/likelihoods/link_functions.py b/GPy/likelihoods/link_functions.py
index cd5ae0c5..3b9a55b2 100644
--- a/GPy/likelihoods/link_functions.py
+++ b/GPy/likelihoods/link_functions.py
@@ -19,41 +19,15 @@ class LinkFunction(object):
     def __init__(self):
         pass
 
-class Identity(LinkFunction):
-    def transf(self,mu):
-        return mu
-
-    def inv_transf(self,f):
-        return f
-
-    def log_inv_transf(self,f):
-        return np.log(f)
-
-class Log(LinkFunction):
-
-    def transf(self,mu):
-        return np.log(mu)
-
-    def inv_transf(self,f):
-        return np.exp(f)
-
-    def log_inv_transf(self,f):
-        return f
-
-class Log_ex_1(LinkFunction):
-    def transf(self,mu):
-        return np.log(np.exp(mu) - 1)
-
-    def inv_transf(self,f):
-        return np.log(np.exp(f)+1)
-
-    def log_inv_tranf(self,f):
-        return np.log(np.log(np.exp(f)+1))
-
 class Probit(LinkFunction):
+    """
+    Probit link function: Squashes a likelihood between 0 and 1
+    """
+    def transf(self,mu):
+        pass
 
     def inv_transf(self,f):
-        return std_norm_cdf(f)
+        pass
 
     def log_inv_transf(self,f):
-        return np.log(std_norm_cdf(f))
+        pass