From 9788ec5b53d6b58bfb1f87ba6c2be071d02828ec Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Wed, 19 Sep 2018 14:34:23 -0400
Subject: [PATCH] fixes
---
mhcflurry/class1_neural_network.py | 21 +++++++--------------
1 file changed, 7 insertions(+), 14 deletions(-)
diff --git a/mhcflurry/class1_neural_network.py b/mhcflurry/class1_neural_network.py
index ad1c85f8..adeb0850 100644
--- a/mhcflurry/class1_neural_network.py
+++ b/mhcflurry/class1_neural_network.py
@@ -30,6 +30,7 @@ class Class1NeuralNetwork(object):
network_hyperparameter_defaults = HyperparameterDefaults(
kmer_size=15,
peptide_amino_acid_encoding="BLOSUM62",
+ allele_amino_acid_encoding="BLOSUM62",
embedding_input_dim=21,
embedding_output_dim=8,
allele_dense_layer_sizes=[],
@@ -418,11 +419,12 @@ class Class1NeuralNetwork(object):
Returns
-------
- numpy.array
+ (numpy.array, numpy.array)
"""
return (
allele_encoding.indices,
- allele_encoding.allele_representations("BLOSUM62"))
+ allele_encoding.allele_representations(
+ self.hyperparameters['allele_amino_acid_encoding']))
def fit(
self,
@@ -790,13 +792,10 @@ class Class1NeuralNetwork(object):
self.prediction_cache[peptides] = result
return result
- def make_allele_subnetwork(self, allele_sequence_layer):
- from keras.layers.core import Flatten
- return Flatten(name="allele_flat")(allele_sequence_layer)
-
def make_network(
self,
kmer_size,
+ allele_amino_acid_encoding,
peptide_amino_acid_encoding,
embedding_input_dim,
embedding_output_dim,
@@ -883,19 +882,13 @@ class Class1NeuralNetwork(object):
name='allele')
inputs.append(allele_input)
- allele_representation = Embedding(
+ allele_layer = Embedding(
name="allele_representation",
input_dim=allele_representations.shape[0],
- output_dim=allele_representations.shape[1] * allele_representations.shape[2],
+ output_dim=numpy.product(allele_representations.shape[1:], dtype=int),
input_length=1,
trainable=False)(allele_input)
- allele_layer = Reshape(
- target_shape=allele_representations.shape[1:],
- name="allele_reshaped")(allele_representation)
-
- allele_layer = self.make_allele_subnetwork(allele_layer)
-
for (i, layer_size) in enumerate(allele_dense_layer_sizes):
allele_layer = Dense(
layer_size,
--
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