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Managed to get it to save by forcing the tf.graph to be complete. I just added a custom loss_out lambda function that included the variables that weren't being used.
but now have issues getting it to load the save due to the loss=None
File "/Users/rob/py27/lib/python2.7/site-packages/keras/engine/topology.py", line 2370, in get_config
new_node_index = node_conversion_map[node_key]
KeyError: 'labels_ib-0'
This is the same common error that saving / loading unusual graph shapes get
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