Graph-tool is a great open source tool for creating, using and analyzing graphs. It’s a python library with C++ bindings, uses boost::graph under the hood and seems to be pretty fast (http://graph-tool.skewed.de/).
Graph-tool Neural Networks (gtnn) is an implementation of ANN on top of graph-tool. It makes researching neural networks nice&easy. You can create custom nets, train, analyze and plot them.
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