From c9aa6743711846d7605cf712102db673e0c0d724 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sun, 23 Jun 2019 16:16:43 -0400
Subject: [PATCH] fix
---
mhcflurry/class1_neural_network.py | 10 ++++++++--
1 file changed, 8 insertions(+), 2 deletions(-)
diff --git a/mhcflurry/class1_neural_network.py b/mhcflurry/class1_neural_network.py
index e434e1b2..92cf8b27 100644
--- a/mhcflurry/class1_neural_network.py
+++ b/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:
--
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