title: keras: predict_proba(), predict() and predict_classes() issues
body: <p>During the predicting phase of my keras model, when I print out predicted values and classes, I'm given different probabilities in <code>predict_proba()</code> and <code>predict()</code>.
  Also, output for <code>predict_classes()</code> doesn't correspond to the probabilities.
  Example of code and sample of printout below:</p>
  <p>Code:</p>
  <pre><code>p = pd.read_csv(&quot;test.csv&quot;, header=None)
  p = np.reshape(p.values, (50, seq_length))
  for i in range(len(p)):
      p[i] = scaler.fit_transform(p[i])
  
  p = np.reshape(p, (50, seq_length, 1))
  model.predict(p, batch_size=50)
  model.predict_classes(p, batch_size=50)
  model.predict_on_batch(p)
  model.predict_proba(p, batch_size=50)
  for i in zip(model.predict_proba(p, batch_size=50), model.predict_classes(p, batch_size=50), model.predict(p, batch_size=50)):
      print(&quot;model.predict_proba&quot;, &quot;--&quot;, i[0], &quot;model.predict&quot;,&quot;--&quot;, i[2], &quot;predict_clases&quot;, &quot;--&quot;, i[1])
  </code></pre>
  <p>Sample of output with different <code>predict_proba()</code> and <code>predict()</code></p>
  <pre><code>model.predict_proba -- [ 0.18768159  0.81231844]
  model.predict -- [ 0.18982948  0.81017047]
  predict_classes -- 1
  
  model.predict_proba -- [ 0.55918539  0.4408147 ]
  model.predict -- [ 0.78916383  0.2108362 ]
  predict_classes -- 1
  </code></pre>
  <p>The last one is also the case where the highest probability corresponds to the index = 0, but the predicted class is 1</p>
  <p>Below another example. The highest probability is for the index = 0, but predicted class is 1</p>
  <pre><code>model.predict_proba -- [ 0.55918539  0.4408147 ]
  model.predict -- [ 0.78916383  0.2108362 ]
  predict_classes -- 1  
  </code></pre>
  <p>But the majority of cases are like below, where <code>predict_proba()</code> and <code>predict()</code> show the same values and predicted class correctly corresponds to the index with highest probability</p>
  <pre><code>model.predict_proba -- [ 0.39802018  0.60197979]
  model.predict -- [ 0.39802018  0.60197979]
  predict_classes -- 1 
  </code></pre>
  <p>Maybe I don't understand how to read it?</p>