Fix failing tests

theano/scan_module/scan_opt.py

@@ -612,6 +612,11 @@ class PushOutScanOutput(gof.Optimizer):
 
         op = node.op
 
+        # Obtain the list containing the indices, in clean_outputs, of the
+        # scan op's outputs that are nit_sot (not fed back to the inner fct.)
+        nitsot_outs = op.inner_nitsot_outs(node.outputs)
+        idx_nitsot_outs = [node.outputs.index(i) for i in nitsot_outs]
+
         # Construct the list of non_sequences to simplify a few things
         inner_non_seqs = op.inner_non_seqs(clean_inputs)
         outer_non_seqs = op.outer_non_seqs(node.inputs)
@@ -621,6 +626,7 @@ class PushOutScanOutput(gof.Optimizer):
         assert len(inner_seqs) == len(outer_seqs)
 
         new_scan_node = None
+
         for nd in local_fgraph.toposort():
 
             if (isinstance(nd.op, theano.tensor.Dot) and
@@ -637,12 +643,29 @@ class PushOutScanOutput(gof.Optimizer):
                 concatenating the vectors into a matrix.
                 """
 
-                # Ensure that the output of the Dot is used somewhere
-                # in the outer graph
-                idx_dot_output = clean_outputs.index(nd.out)
-                if len(node.outputs[idx_dot_output].clients) == 0:
-                    # The Dot's output is not used. It is not worth performing
-                    # the optimization. Move on to the next node
+                # Go through clean_outputs and pick one that is
+                # - Equal to the output of the tensor.Dot
+                # - Nit_sot : not fed back to the inner graph because applying
+                #   the optimization in that case would alter the results of
+                #   the function
+                # - Used by something outside of the graph to avoid applying
+                #   the optimization needlessly
+                idx_dot_output = -1
+                for i in range(len(clean_outputs)):
+
+                    is_dot_output = (nd.out == clean_outputs[i])
+                    is_nitsot_output = i in idx_nitsot_outs
+                    used_in_outer_graph = (len(node.outputs[i].clients) > 0)
+
+                    if (is_dot_output and is_nitsot_output and
+                        used_in_outer_graph):
+
+                        idx_dot_output = i
+                        break
+
+                if idx_dot_output == -1:
+                    # The dot has no output that fits the requirements for
+                    # this optimization. Move on to the next node.
                     continue
 
                 """
@@ -710,7 +733,8 @@ class PushOutScanOutput(gof.Optimizer):
                     # Perform the Dot on the new scan output.
                     if idx_matrix_input == 0:
                         outer_dot_inputs = [outer_matrix_input,
-                                            new_outer_output]
+                                            new_outer_output.transpose()]
+                        outer_dot_output = theano.tensor.dot(*outer_dot_inputs).transpose()
                     else: # idx_matrix_input == 1
                         outer_dot_inputs = [new_outer_output,
                                             outer_matrix_input]
@@ -736,8 +760,8 @@ class PushOutScanOutput(gof.Optimizer):
         """
 
         # Compute the index at which to insert the new output. For a scan Op,
-        # the outputs the ordering : mit_mot, mit_sot, sis_sot, nit_sot and
-        # shared_outs
+        # the outputs follow the ordering : mit_mot, mit_sot, sis_sot, nit_sot
+        # and shared_outs
         output_insert_idx = (scan_node.op.info['n_mit_mot'] +
                              scan_node.op.info['n_mit_sot'] +
                              scan_node.op.info['n_sit_sot'] +