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<div class="section" id="demo-of-affinity-propagation-clustering-algorithm">
<span id="example-cluster-plot-affinity-propagation-py"></span><h1>Demo of affinity propagation clustering algorithm<a class="headerlink" href="#demo-of-affinity-propagation-clustering-algorithm" title="Permalink to this headline">ΒΆ</a></h1>
<p>Reference:
Brendan J. Frey and Delbert Dueck, “Clustering by Passing Messages
Between Data Points”, Science Feb. 2007</p>
<img alt="auto_examples/cluster/images/plot_affinity_propagation.png" class="align-center" src="auto_examples/cluster/images/plot_affinity_propagation.png" />
<p><strong>Python source code:</strong> <a class="reference download internal" href="../../_downloads/plot_affinity_propagation.py"><tt class="xref download docutils literal"><span class="pre">plot_affinity_propagation.py</span></tt></a></p>
<div class="highlight-python"><div class="highlight"><pre><span class="k">print</span> <span class="n">__doc__</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
<span class="kn">from</span> <span class="nn">scikits.learn.cluster</span> <span class="kn">import</span> <span class="n">AffinityPropagation</span>
<span class="c">################################################################################</span>
<span class="c"># Generate sample data</span>
<span class="c">################################################################################</span>
<span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">seed</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
<span class="n">n_points_per_cluster</span> <span class="o">=</span> <span class="mi">100</span>
<span class="n">n_clusters</span> <span class="o">=</span> <span class="mi">3</span>
<span class="n">n_points</span> <span class="o">=</span> <span class="n">n_points_per_cluster</span><span class="o">*</span><span class="n">n_clusters</span>
<span class="n">means</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">1</span><span class="p">,</span><span class="mi">1</span><span class="p">],[</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">],[</span><span class="mi">1</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">]])</span>
<span class="n">std</span> <span class="o">=</span> <span class="o">.</span><span class="mi">5</span>
<span class="n">X</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">empty</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">))</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">n_clusters</span><span class="p">):</span>
<span class="n">X</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">r_</span><span class="p">[</span><span class="n">X</span><span class="p">,</span> <span class="n">means</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">+</span> <span class="n">std</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randn</span><span class="p">(</span><span class="n">n_points_per_cluster</span><span class="p">,</span> <span class="mi">2</span><span class="p">)]</span>
<span class="c">################################################################################</span>
<span class="c"># Compute similarities</span>
<span class="c">################################################################################</span>
<span class="n">X_norms</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">X</span><span class="o">*</span><span class="n">X</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">S</span> <span class="o">=</span> <span class="o">-</span> <span class="n">X_norms</span><span class="p">[:,</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">]</span> <span class="o">-</span> <span class="n">X_norms</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">,:]</span> <span class="o">+</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">X</span><span class="o">.</span><span class="n">T</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="mi">10</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">median</span><span class="p">(</span><span class="n">S</span><span class="p">)</span>
<span class="c">################################################################################</span>
<span class="c"># Compute Affinity Propagation</span>
<span class="c">################################################################################</span>
<span class="n">af</span> <span class="o">=</span> <span class="n">AffinityPropagation</span><span class="p">()</span>
<span class="n">af</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">S</span><span class="p">,</span> <span class="n">p</span><span class="p">)</span>
<span class="n">cluster_centers_indices</span> <span class="o">=</span> <span class="n">af</span><span class="o">.</span><span class="n">cluster_centers_indices_</span>
<span class="n">labels</span> <span class="o">=</span> <span class="n">af</span><span class="o">.</span><span class="n">labels_</span>
<span class="n">n_clusters_</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">cluster_centers_indices</span><span class="p">)</span>
<span class="k">print</span> <span class="s">'Estimated number of clusters: </span><span class="si">%d</span><span class="s">'</span> <span class="o">%</span> <span class="n">n_clusters_</span>
<span class="c">################################################################################</span>
<span class="c"># Plot result</span>
<span class="c">################################################################################</span>
<span class="kn">import</span> <span class="nn">pylab</span> <span class="kn">as</span> <span class="nn">pl</span>
<span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">cycle</span>
<span class="n">pl</span><span class="o">.</span><span class="n">close</span><span class="p">(</span><span class="s">'all'</span><span class="p">)</span>
<span class="n">pl</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="n">pl</span><span class="o">.</span><span class="n">clf</span><span class="p">()</span>
<span class="n">colors</span> <span class="o">=</span> <span class="n">cycle</span><span class="p">(</span><span class="s">'bgrcmykbgrcmykbgrcmykbgrcmyk'</span><span class="p">)</span>
<span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">col</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="n">n_clusters_</span><span class="p">),</span> <span class="n">colors</span><span class="p">):</span>
<span class="n">class_members</span> <span class="o">=</span> <span class="n">labels</span> <span class="o">==</span> <span class="n">k</span>
<span class="n">cluster_center</span> <span class="o">=</span> <span class="n">X</span><span class="p">[</span><span class="n">cluster_centers_indices</span><span class="p">[</span><span class="n">k</span><span class="p">]]</span>
<span class="n">pl</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">X</span><span class="p">[</span><span class="n">class_members</span><span class="p">,</span><span class="mi">0</span><span class="p">],</span> <span class="n">X</span><span class="p">[</span><span class="n">class_members</span><span class="p">,</span><span class="mi">1</span><span class="p">],</span> <span class="n">col</span><span class="o">+</span><span class="s">'.'</span><span class="p">)</span>
<span class="n">pl</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">cluster_center</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">cluster_center</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">'o'</span><span class="p">,</span> <span class="n">markerfacecolor</span><span class="o">=</span><span class="n">col</span><span class="p">,</span>
<span class="n">markeredgecolor</span><span class="o">=</span><span class="s">'k'</span><span class="p">,</span> <span class="n">markersize</span><span class="o">=</span><span class="mi">14</span><span class="p">)</span>
<span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">X</span><span class="p">[</span><span class="n">class_members</span><span class="p">]:</span>
<span class="n">pl</span><span class="o">.</span><span class="n">plot</span><span class="p">([</span><span class="n">cluster_center</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]],</span> <span class="p">[</span><span class="n">cluster_center</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]],</span> <span class="n">col</span><span class="p">)</span>
<span class="n">pl</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s">'Estimated number of clusters: </span><span class="si">%d</span><span class="s">'</span> <span class="o">%</span> <span class="n">n_clusters_</span><span class="p">)</span>
<span class="n">pl</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
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