fix

mhcflurry/class1_neural_network.py

@@ -82,7 +82,8 @@ class Class1NeuralNetwork(object):
         random_negative_affinity_min=20000.0,
         random_negative_affinity_max=50000.0,
         random_negative_match_distribution=True,
-        random_negative_distribution_smoothing=0.0)
+        random_negative_distribution_smoothing=0.0,
+        random_negative_output_indices=None)
     """
     Hyperparameters for neural network training.
     """
@@ -725,8 +726,13 @@ class Class1NeuralNetwork(object):
             sample_weights_with_random_negatives = None
 
         if output_indices is not None:
+            random_negative_output_indices = (
+                self.hyperparameters['random_negative_output_indices']
+                if self.hyperparameters['random_negative_output_indices']
+                else list(range(0, self.hyperparameters['num_outputs'])))
             output_indices_with_random_negatives = numpy.concatenate([
-                numpy.zeros(int(num_random_negative.sum()), dtype=int),
+                pandas.Series(random_negative_output_indices, dtype=int).sample(
+                    n=int(num_random_negative.sum()), replace=True).values,
                 output_indices
             ])
         else: