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      <h1 data-toc-skip>autoencoder_variational</h1>
            
      
      <small class="dont-index">Source: <a href="https://github.com/fdavidcl/ruta/blob/HEAD/vignettes/examples/autoencoder_variational.Rmd" class="external-link"><code>vignettes/examples/autoencoder_variational.Rmd</code></a></small>
      <div class="hidden name"><code>autoencoder_variational.Rmd</code></div>

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<p><span class="source-caption">Example source:</span> <a href="https://github.com/fdavidcl/ruta/blob/master/vignettes/examples/autoencoder_variational.R" class="external-link uri">https://github.com/fdavidcl/ruta/blob/master/vignettes/examples/autoencoder_variational.R</a></p>
<hr>
<p><strong>This example demonstrates the use of variational autoencoders
with the Ruta package.</strong></p>
<p>Define a variational autoencoder with 3-variable latent space. The
encoding of a variational autoencoder is defined with
<code>variational_block</code>.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tensorflow.rstudio.com/" class="external-link">keras</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/fdavidcl/ruta" class="external-link">ruta</a></span><span class="op">)</span></span>
<span></span>
<span><span class="va">network</span> <span class="op">&lt;-</span></span>
<span>  <span class="fu"><a href="../../reference/input.html">input</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span>
<span>  <span class="fu"><a href="../../reference/dense.html">dense</a></span><span class="op">(</span><span class="fl">256</span>, <span class="st">"elu"</span><span class="op">)</span> <span class="op">+</span></span>
<span>  <span class="fu"><a href="../../reference/variational_block.html">variational_block</a></span><span class="op">(</span><span class="fl">3</span>, seed <span class="op">=</span> <span class="fl">42</span><span class="op">)</span> <span class="op">+</span></span>
<span>  <span class="fu"><a href="../../reference/dense.html">dense</a></span><span class="op">(</span><span class="fl">256</span>, <span class="st">"elu"</span><span class="op">)</span> <span class="op">+</span></span>
<span>  <span class="fu"><a href="../../reference/output.html">output</a></span><span class="op">(</span><span class="st">"sigmoid"</span><span class="op">)</span></span>
<span></span>
<span><span class="va">learner</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/autoencoder_variational.html">autoencoder_variational</a></span><span class="op">(</span><span class="va">network</span>, loss <span class="op">=</span> <span class="st">"binary_crossentropy"</span><span class="op">)</span></span></code></pre></div>
<p>Load MNIST and normalize</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">mnist</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/keras/man/dataset_mnist.html" class="external-link">dataset_mnist</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="va">x_train</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rstudio.github.io/reticulate/reference/array_reshape.html" class="external-link">array_reshape</a></span><span class="op">(</span></span>
<span>  <span class="va">mnist</span><span class="op">$</span><span class="va">train</span><span class="op">$</span><span class="va">x</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/dim.html" class="external-link">dim</a></span><span class="op">(</span><span class="va">mnist</span><span class="op">$</span><span class="va">train</span><span class="op">$</span><span class="va">x</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span>, <span class="fl">784</span><span class="op">)</span></span>
<span><span class="op">)</span></span>
<span><span class="va">x_train</span> <span class="op">&lt;-</span> <span class="va">x_train</span> <span class="op">/</span> <span class="fl">255.0</span></span>
<span><span class="va">x_test</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rstudio.github.io/reticulate/reference/array_reshape.html" class="external-link">array_reshape</a></span><span class="op">(</span></span>
<span>  <span class="va">mnist</span><span class="op">$</span><span class="va">test</span><span class="op">$</span><span class="va">x</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/dim.html" class="external-link">dim</a></span><span class="op">(</span><span class="va">mnist</span><span class="op">$</span><span class="va">test</span><span class="op">$</span><span class="va">x</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span>, <span class="fl">784</span><span class="op">)</span></span>
<span><span class="op">)</span></span>
<span><span class="va">x_test</span> <span class="op">&lt;-</span> <span class="va">x_test</span> <span class="op">/</span> <span class="fl">255.0</span></span></code></pre></div>
<p>Train</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">model</span> <span class="op">&lt;-</span> <span class="va">learner</span> <span class="op">|&gt;</span> <span class="fu"><a href="../../reference/train.ruta_autoencoder.html">train</a></span><span class="op">(</span><span class="va">x_train</span>, epochs <span class="op">=</span> <span class="fl">5</span><span class="op">)</span></span></code></pre></div>
<p>Sample the trained model</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">samples</span> <span class="op">&lt;-</span> <span class="va">model</span> <span class="op">|&gt;</span> <span class="fu"><a href="../../reference/generate.html">generate</a></span><span class="op">(</span>dimensions <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span>, fixed_values <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span></span></code></pre></div>
<p>Utility functions for plotting</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">plot_digit</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="va">digit</span>, <span class="va">...</span><span class="op">)</span> <span class="op">{</span></span>
<span>  <span class="fu"><a href="https://rdrr.io/r/graphics/image.html" class="external-link">image</a></span><span class="op">(</span><span class="fu"><a href="https://rstudio.github.io/reticulate/reference/array_reshape.html" class="external-link">array_reshape</a></span><span class="op">(</span><span class="va">digit</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">28</span>, <span class="fl">28</span><span class="op">)</span>, <span class="st">"F"</span><span class="op">)</span><span class="op">[</span>, <span class="fl">28</span><span class="op">:</span><span class="fl">1</span><span class="op">]</span>, xaxt <span class="op">=</span> <span class="st">"n"</span>, yaxt <span class="op">=</span> <span class="st">"n"</span>, col<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/grDevices/gray.html" class="external-link">gray</a></span><span class="op">(</span><span class="op">(</span><span class="fl">255</span><span class="op">:</span><span class="fl">0</span><span class="op">)</span><span class="op">/</span><span class="fl">255</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="op">}</span></span>
<span></span>
<span><span class="va">plot_matrix</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="va">digits</span><span class="op">)</span> <span class="op">{</span></span>
<span>  <span class="va">n</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/dim.html" class="external-link">dim</a></span><span class="op">(</span><span class="va">digits</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span></span>
<span>  <span class="fu"><a href="https://rdrr.io/r/graphics/layout.html" class="external-link">layout</a></span><span class="op">(</span></span>
<span>    <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="va">n</span>, byrow <span class="op">=</span> <span class="cn">F</span>, nrow <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="va">n</span><span class="op">)</span><span class="op">)</span></span>
<span>  <span class="op">)</span></span>
<span></span>
<span>  <span class="kw">for</span> <span class="op">(</span><span class="va">i</span> <span class="kw">in</span> <span class="fl">1</span><span class="op">:</span><span class="va">n</span><span class="op">)</span> <span class="op">{</span></span>
<span>    <span class="fu"><a href="https://rdrr.io/r/graphics/par.html" class="external-link">par</a></span><span class="op">(</span>mar <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>,<span class="fl">0</span>,<span class="fl">0</span>,<span class="fl">0</span><span class="op">)</span> <span class="op">+</span> <span class="fl">.2</span><span class="op">)</span></span>
<span>    <span class="fu">plot_digit</span><span class="op">(</span><span class="va">digits</span><span class="op">[</span><span class="va">i</span>, <span class="op">]</span><span class="op">)</span></span>
<span>  <span class="op">}</span></span>
<span><span class="op">}</span></span></code></pre></div>
<p>Plot samples</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu">plot_matrix</span><span class="op">(</span><span class="va">samples</span><span class="op">)</span></span></code></pre></div>
<p>Creating an animation from a sampling</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://yihui.org/animation/" class="external-link">animation</a></span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/graphics/par.html" class="external-link">par</a></span><span class="op">(</span>bg <span class="op">=</span> <span class="st">"white"</span><span class="op">)</span>  <span class="co"># ensure the background color is white</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="op">)</span>, type <span class="op">=</span> <span class="st">"n"</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">ani.record</span><span class="op">(</span>reset <span class="op">=</span> <span class="cn">T</span><span class="op">)</span></span>
<span></span>
<span><span class="kw">for</span> <span class="op">(</span><span class="va">t</span> <span class="kw">in</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span>from <span class="op">=</span> <span class="fl">0.001</span>, to <span class="op">=</span> <span class="fl">0.999</span>, length.out <span class="op">=</span> <span class="fl">180</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
<span>  <span class="va">model</span> <span class="op">|&gt;</span> <span class="fu"><a href="../../reference/generate.html">generate</a></span><span class="op">(</span>dimensions <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span>, from <span class="op">=</span> <span class="fl">0.001</span>, to <span class="op">=</span> <span class="fl">0.999</span>, fixed_values <span class="op">=</span> <span class="va">t</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu">plot_matrix</span><span class="op">(</span><span class="op">)</span></span>
<span>  <span class="fu">ani.record</span><span class="op">(</span><span class="op">)</span></span>
<span><span class="op">}</span></span>
<span></span>
<span><span class="fu">saveHTML</span><span class="op">(</span><span class="fu">ani.replay</span><span class="op">(</span><span class="op">)</span>, img.name <span class="op">=</span> <span class="st">"record_plot"</span><span class="op">)</span></span></code></pre></div>
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