From d39b3269c3816ad993e79d2bb57b9b3a8a1804b1 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Tue, 19 Jun 2018 14:54:23 -0400
Subject: [PATCH] fix
---
mhcflurry/class1_neural_network.py | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/mhcflurry/class1_neural_network.py b/mhcflurry/class1_neural_network.py
index bbf3e18e..c38a0b77 100644
--- a/mhcflurry/class1_neural_network.py
+++ b/mhcflurry/class1_neural_network.py
@@ -790,9 +790,11 @@ class Class1NeuralNetwork(object):
self.prediction_cache[peptides] = result
return result
- @staticmethod
+ def make_allele_subnetwork(allele_sequence_layer):
+ return allele_sequence_layer
+
def make_network(
- allele_representations,
+ self,
kmer_size,
peptide_amino_acid_encoding,
embedding_input_dim,
@@ -810,7 +812,8 @@ class Class1NeuralNetwork(object):
dropout_probability,
batch_normalization,
embedding_init_method,
- locally_connected_layers):
+ locally_connected_layers,
+ allele_representations=None):
"""
Helper function to make a keras network for class1 affinity prediction.
"""
@@ -889,6 +892,9 @@ class Class1NeuralNetwork(object):
allele_layer = Reshape(
target_shape=allele_representations.shape[1:],
name="allele_reshaped")(allele_representation)
+
+ allele_layer = self.make_allele_subnetwork(allele_layer)
+
allele_layer = Flatten(name="allele_flat")(allele_layer)
for (i, layer_size) in enumerate(allele_dense_layer_sizes):
--
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