title: dealing with noise in hdbscan
body: <p>I have been testing hdbscan from the scikit learn package with a small instance of (x,y) points "point_coord" and the resulting clusters do not really make sense to me. Given the small size of the sample, I am allowing a single cluster.</p>
  
  <p>I would expect two clusters: 4th and 5th point clustered together versus the rest the points.</p>
  
  <pre><code>point_coord=[[0,0],[1,1],[0,1],[50,40],[50,45],[2,3],[1,2]]
  
  test=pairwise_distances(point_coord)
  
  clusterer= hdbscan.HDBSCAN( allow_single_cluster=True,                
  metric='precomputed')
  
  clusterer.fit(test)
  </code></pre>
  
  <p>However, the resulting clusterer.labels are:</p>
  
  <p>[-1, 0, 0, 0, -1, 0, 0]</p>