--- a/deep/stacked_dae/v_sylvain/stacked_dae.py	Wed Apr 21 14:50:59 2010 -0400
+++ b/deep/stacked_dae/v_sylvain/stacked_dae.py	Wed Apr 21 14:51:14 2010 -0400
@@ -153,23 +153,23 @@
     # note  : y is stored as an attribute of the class so that it can be 
     #         used later when stacking dAs. 
     
-    self.y   = T.nnet.sigmoid(T.dot(self.tilde_x, self.W      ) + self.b)
-        
-    # Equation (3)
-    #self.z   = T.nnet.sigmoid(T.dot(self.y, self.W_prime) + self.b_prime)
-    # Equation (4)
-    # note : we sum over the size of a datapoint; if we are using minibatches,
-    #        L will  be a vector, with one entry per example in minibatch
-    #self.L = - T.sum( self.x*T.log(self.z) + (1-self.x)*T.log(1-self.z), axis=1 ) 
-    #self.L = binary_cross_entropy(target=self.x, output=self.z, sum_axis=1)
-
-    # bypassing z to avoid running to log(0)
-    z_a = T.dot(self.y, self.W_prime) + self.b_prime
-    log_sigmoid = T.log(1.) - T.log(1.+T.exp(-z_a))
-    # log(1-sigmoid(z_a))
-    log_1_sigmoid = -z_a - T.log(1.+T.exp(-z_a))
-    self.L = -T.sum( self.x * (log_sigmoid) \
-                    + (1.0-self.x) * (log_1_sigmoid), axis=1 )
+##    self.y   = T.nnet.sigmoid(T.dot(self.tilde_x, self.W      ) + self.b)
+##        
+##    # Equation (3)
+##    #self.z   = T.nnet.sigmoid(T.dot(self.y, self.W_prime) + self.b_prime)
+##    # Equation (4)
+##    # note : we sum over the size of a datapoint; if we are using minibatches,
+##    #        L will  be a vector, with one entry per example in minibatch
+##    #self.L = - T.sum( self.x*T.log(self.z) + (1-self.x)*T.log(1-self.z), axis=1 ) 
+##    #self.L = binary_cross_entropy(target=self.x, output=self.z, sum_axis=1)
+##
+##    # bypassing z to avoid running to log(0)
+##    z_a = T.dot(self.y, self.W_prime) + self.b_prime
+##    log_sigmoid = T.log(1.) - T.log(1.+T.exp(-z_a))
+##    # log(1-sigmoid(z_a))
+##    log_1_sigmoid = -z_a - T.log(1.+T.exp(-z_a))
+##    self.L = -T.sum( self.x * (log_sigmoid) \
+##                    + (1.0-self.x) * (log_1_sigmoid), axis=1 )
 
     # I added this epsilon to avoid getting log(0) and 1/0 in grad
     # This means conceptually that there'd be no probability of 0, but that
@@ -183,19 +183,19 @@
     #        minibatch. We need to compute the average of all these to get 
     #        the cost of the minibatch
     
-##    #Or use a Tanh everything is always between 0 and 1, the range is 
-##    #changed so it remain the same as when sigmoid is used
-##    self.y   = (T.tanh(T.dot(self.tilde_x, self.W      ) + self.b)+1.0)/2.0
-##    
-##    z_a = T.dot(self.y, self.W_prime) + self.b_prime
-##    self.z =  (T.tanh(z_a + self.b_prime)+1.0) / 2.0
-##    #To ensure to do not have a log(0) operation
-##    if self.z <= 0:
-##        self.z = 0.000001
-##    if self.z >= 1:
-##        self.z = 0.999999
-##        
-##    self.L = - T.sum( self.x*T.log(self.z) + (1-self.x)*T.log(1-self.z), axis=1 )
+    #Or use a Tanh everything is always between 0 and 1, the range is 
+    #changed so it remain the same as when sigmoid is used
+    self.y   = (T.tanh(T.dot(self.tilde_x, self.W      ) + self.b)+1.0)/2.0
+    
+    z_a = T.dot(self.y, self.W_prime) + self.b_prime
+    self.z =  (T.tanh(z_a + self.b_prime)+1.0) / 2.0
+    #To ensure to do not have a log(0) operation
+    if self.z <= 0:
+        self.z = 0.000001
+    if self.z >= 1:
+        self.z = 0.999999
+        
+    self.L = - T.sum( self.x*T.log(self.z) + (1-self.x)*T.log(1-self.z), axis=1 )
     
     self.cost = T.mean(self.L)
 
@@ -241,6 +241,7 @@
         self.y  = T.ivector('y') # the labels are presented as 1D vector of 
                                  # [int] labels
         self.finetune_lr = T.fscalar('finetune_lr') #To get a dynamic finetune learning rate
+        self.pretrain_lr = T.fscalar('pretrain_lr') #To get a dynamic pretrain learning rate
 
         for i in xrange( self.n_layers ):
             # construct the sigmoidal layer
@@ -261,11 +262,11 @@
                 layer_input = self.layers[-1].output
             #We have to choose between sigmoidal layer or tanh layer !
 
-            layer = SigmoidalLayer(rng, layer_input, input_size, 
-                                   hidden_layers_sizes[i] )
+##            layer = SigmoidalLayer(rng, layer_input, input_size, 
+##                                   hidden_layers_sizes[i] )
                                 
-##            layer = TanhLayer(rng, layer_input, input_size, 
-##                                   hidden_layers_sizes[i] )
+            layer = TanhLayer(rng, layer_input, input_size, 
+                                   hidden_layers_sizes[i] )
             # add the layer to the 
             self.layers += [layer]
             self.params += layer.params
@@ -285,10 +286,10 @@
             # compute the list of updates
             updates = {}
             for param, gparam in zip(dA_layer.params, gparams):
-                updates[param] = param - gparam * pretrain_lr
+                updates[param] = param - gparam * self.pretrain_lr
             
             # create a function that trains the dA
-            update_fn = theano.function([self.x], dA_layer.cost, \
+            update_fn = theano.function([self.x, self.pretrain_lr], dA_layer.cost, \
                   updates = updates)#,
             #     givens = { 
             #         self.x : ensemble})