<p>Implement HyperNEAT algorithm and tests.</p>
<hr>
<h4>You can view, comment on, or merge this pull request online at:</h4>
<p> <a href='https://github.com/mlpack/mlpack/pull/754'>https://github.com/mlpack/mlpack/pull/754</a></p>
<h4>Commit Summary</h4>
<ul>
<li>change .gitignore to ignore .DS_Store</li>
<li>create gene.hpp, add ne_test.cpp, and created or modified multiple CMakeLists.txt.</li>
<li>Created gene.happ, add tests and changed or created CMakeLists.txt</li>
<li>Add aDepth to NeuronGene.</li>
<li>implement CNE, haven't finish.</li>
<li>delete blank files</li>
<li>finished genome.hpp, revised gene.hpp</li>
<li>modified gene.hpp</li>
<li>implemented CNE skeleton; more genome and population functions.</li>
<li>implemented XOR test case; need debugging; one heart function -- CNE::Evolve() remains to fulfill.</li>
<li>solved most bugs for testing XOR</li>
<li>further solved some bugs in code.</li>
<li>Solved bugs. Need to fulfill Reproduce() to finish CNE.</li>
<li>CNE algorithm finished. XOR test passes. Need to revise coding style and some TODOs. Then continue other algorithms.</li>
<li>Create Species class.</li>
<li>Revised LinkGene and related file for NEAT</li>
<li>revised sortSpecies()</li>
<li>add aAdjustedFitness to genome</li>
<li>fix bug in CNE Reproduce()</li>
<li>Implemented neat mutations, replace size_t by ssize_t</li>
<li>Implemented crossover, some bug exist</li>
<li>Revise Crossover, solve bugs, more functions implementations.</li>
<li>revised neat functions. In paper,disabled links also consider for crossover and calc distance.</li>
<li>neat almost finished. Need debugging,need revise coding style, need testing.</li>
<li>NEAT finished, but has bugs. XOR not pass.</li>
<li>In progress of debugging. Add lots of printf ... Will clear them after debugging</li>
<li>seems bugs solved. keep printf. Seems information such as species size, numSpecies are not updated when things changed, that is why so many bugs.</li>
<li>solve more bugs</li>
<li>solved more. But still have problem.</li>
<li>solved CalcAverageRank bug. Still have more.</li>
<li>currently seems no bug. Previously we removed stale species even when species number is small, leads to species disappear.</li>
<li>revised WeightDiff</li>
<li>Removed redundant members in species, population. haven't remove in genome, as it caused some bug. Still need checking.</li>
<li>Further cleaned some code.</li>
<li>changed the place where we should set the childGenome's NumInput, NumOutput, GenomeDepth. However, seems calculate genome depth is quite slow.</li>
<li>changed neuron_gene, genome's activation. Still need to revise neat.</li>
<li>Revised MutateAddLink.</li>
<li>solved some bugs about activation.</li>
<li>Add Cart Pole test. Result not good. Fitness doesn't improve.</li>
<li>Solved more bugs.</li>
<li>Fixed a bug in task. Removed adjustFitness. Problems maybe the parameter setting.</li>
<li>further revised something.</li>
<li>Passed Cart Pole problem. Revised neat, task.</li>
<li>Implemented test MountainCar, not pass yet.</li>
<li>Seems passed Mountain Car.. in 1 iteration</li>
<li>Revised a bug in TaskMountainCar Action()</li>
<li>added Success() for tasks.</li>
<li>Finished double pole. Non-Markov have bug.</li>
<li>revised non-markov, still have bug</li>
<li>revised neat MutateAddLink. Non-Markov still have bug.</li>
<li>revised neat, clean genome before evaluate.</li>
<li>Merge pull request #1 from mlpack/master</li>
<li>revised a bug in Activate()</li>
<li>fix conflict</li>
<li>changed header file in ne_test</li>
</ul>
<h4>File Changes</h4>
<ul>
<li>
<strong>M</strong>
<a href="https://github.com/mlpack/mlpack/pull/754/files#diff-0">.gitignore</a>
(2)
</li>
<li>
<strong>M</strong>
<a href="https://github.com/mlpack/mlpack/pull/754/files#diff-1">src/mlpack/methods/CMakeLists.txt</a>
(1)
</li>
<li>
<strong>A</strong>
<a href="https://github.com/mlpack/mlpack/pull/754/files#diff-2">src/mlpack/methods/ne/CMakeLists.txt</a>
(23)
</li>
<li>
<strong>A</strong>
<a href="https://github.com/mlpack/mlpack/pull/754/files#diff-3">src/mlpack/methods/ne/cne.hpp</a>
(186)
</li>
<li>
<strong>A</strong>
<a href="https://github.com/mlpack/mlpack/pull/754/files#diff-4">src/mlpack/methods/ne/genome.hpp</a>
(334)
</li>
<li>
<strong>A</strong>
<a href="https://github.com/mlpack/mlpack/pull/754/files#diff-5">src/mlpack/methods/ne/link_gene.hpp</a>
(111)
</li>
<li>
<strong>A</strong>
<a href="https://github.com/mlpack/mlpack/pull/754/files#diff-6">src/mlpack/methods/ne/neat.hpp</a>
(976)
</li>
<li>
<strong>A</strong>
<a href="https://github.com/mlpack/mlpack/pull/754/files#diff-7">src/mlpack/methods/ne/neuron_gene.hpp</a>
(174)
</li>
<li>
<strong>A</strong>
<a href="https://github.com/mlpack/mlpack/pull/754/files#diff-8">src/mlpack/methods/ne/parameters.hpp</a>
(96)
</li>
<li>
<strong>A</strong>
<a href="https://github.com/mlpack/mlpack/pull/754/files#diff-9">src/mlpack/methods/ne/population.hpp</a>
(154)
</li>
<li>
<strong>A</strong>
<a href="https://github.com/mlpack/mlpack/pull/754/files#diff-10">src/mlpack/methods/ne/species.hpp</a>
(141)
</li>
<li>
<strong>A</strong>
<a href="https://github.com/mlpack/mlpack/pull/754/files#diff-11">src/mlpack/methods/ne/tasks.hpp</a>
(692)
</li>
<li>
<strong>A</strong>
<a href="https://github.com/mlpack/mlpack/pull/754/files#diff-12">src/mlpack/methods/ne/utils.hpp</a>
(88)
</li>
<li>
<strong>M</strong>
<a href="https://github.com/mlpack/mlpack/pull/754/files#diff-13">src/mlpack/tests/CMakeLists.txt</a>
(5)
</li>
<li>
<strong>A</strong>
<a href="https://github.com/mlpack/mlpack/pull/754/files#diff-14">src/mlpack/tests/ne_test.cpp</a>
(691)
</li>
</ul>
<h4>Patch Links:</h4>
<ul>
<li><a href='https://github.com/mlpack/mlpack/pull/754.patch'>https://github.com/mlpack/mlpack/pull/754.patch</a></li>
<li><a href='https://github.com/mlpack/mlpack/pull/754.diff'>https://github.com/mlpack/mlpack/pull/754.diff</a></li>
</ul>
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