From fbbef3447ffbe233bc4edb620b484547311611a6 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sun, 21 May 2017 16:09:04 -0400
Subject: [PATCH] update
---
.../class1_neural_network.py | 11 +++++------
.../train_allele_specific_models_command.py | 1 +
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/mhcflurry/class1_affinity_prediction/class1_neural_network.py b/mhcflurry/class1_affinity_prediction/class1_neural_network.py
index df8e767c..a6d93d2e 100644
--- a/mhcflurry/class1_affinity_prediction/class1_neural_network.py
+++ b/mhcflurry/class1_affinity_prediction/class1_neural_network.py
@@ -73,13 +73,12 @@ class Class1NeuralNetwork(object):
self.hyperparameters = self.hyperparameter_defaults.with_defaults(
hyperparameters)
self.network = None
- self.fit_history = None
+ self.loss_history = None
self.fit_seconds = None
def __getstate__(self):
result = dict(self.__dict__)
del result['network']
- result['fit_history'] = None
result['network_json'] = self.network.to_json()
result['network_weights'] = self.get_weights()
return result
@@ -204,7 +203,7 @@ class Class1NeuralNetwork(object):
min_val_loss_iteration = None
min_val_loss = None
- self.fit_history = collections.defaultdict(list)
+ self.loss_history = collections.defaultdict(list)
start = time.time()
for i in range(self.hyperparameters['max_epochs']):
random_negative_peptides_list = []
@@ -243,17 +242,17 @@ class Class1NeuralNetwork(object):
sample_weight=sample_weights)
for (key, value) in fit_history.history.items():
- self.fit_history[key].extend(value)
+ self.loss_history[key].extend(value)
logging.info(
"Epoch %3d / %3d: loss=%g. Min val loss at epoch %s" % (
i,
self.hyperparameters['max_epochs'],
- self.fit_history['loss'][-1],
+ self.loss_history['loss'][-1],
min_val_loss_iteration))
if self.hyperparameters['validation_split']:
- val_loss = fit_history.history['val_loss'][-1]
+ val_loss = self.loss_history['val_loss'][-1]
val_losses.append(val_loss)
if min_val_loss is None or val_loss <= min_val_loss:
diff --git a/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py b/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py
index 4b420191..e3d7f715 100644
--- a/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py
+++ b/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py
@@ -16,6 +16,7 @@ import mhcnames
from .class1_neural_network import Class1NeuralNetwork
from ..common import configure_logging
+
def normalize_allele_name(s):
try:
return mhcnames.normalize_allele_name(s)
--
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