From 33b1b5d4251c484c1d3eb2ed20460d28a6584547 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Tue, 28 Nov 2017 11:11:54 -0500
Subject: [PATCH] Add minibatch_size hyperparameter
---
downloads-generation/models_class1/hyperparameters.yaml | 3 ++-
.../class1_affinity_prediction/class1_neural_network.py | 7 ++-----
2 files changed, 4 insertions(+), 6 deletions(-)
diff --git a/downloads-generation/models_class1/hyperparameters.yaml b/downloads-generation/models_class1/hyperparameters.yaml
index c6c2c2b6..964cc7e5 100644
--- a/downloads-generation/models_class1/hyperparameters.yaml
+++ b/downloads-generation/models_class1/hyperparameters.yaml
@@ -8,9 +8,10 @@
# OPTIMIZATION
##########################################
"max_epochs": 500,
-"patience": 10,
+"patience": 20,
"early_stopping": true,
"validation_split": 0.2,
+"minibatch_size": 128,
##########################################
# RANDOM NEGATIVE PEPTIDES
diff --git a/mhcflurry/class1_affinity_prediction/class1_neural_network.py b/mhcflurry/class1_affinity_prediction/class1_neural_network.py
index 73a9670a..995a629f 100644
--- a/mhcflurry/class1_affinity_prediction/class1_neural_network.py
+++ b/mhcflurry/class1_affinity_prediction/class1_neural_network.py
@@ -50,11 +50,6 @@ class Class1NeuralNetwork(object):
batch_normalization=False,
embedding_init_method="glorot_uniform",
locally_connected_layers=[
- {
- "filters": 8,
- "activation": "tanh",
- "kernel_size": 3
- },
{
"filters": 8,
"activation": "tanh",
@@ -77,6 +72,7 @@ class Class1NeuralNetwork(object):
take_best_epoch=False, # currently unused
validation_split=0.2,
early_stopping=True,
+ minibatch_size=128,
random_negative_rate=0.0,
random_negative_constant=25,
random_negative_affinity_min=20000.0,
@@ -447,6 +443,7 @@ class Class1NeuralNetwork(object):
x_dict_with_random_negatives,
y_dict_with_random_negatives,
shuffle=True,
+ batch_size=self.hyperparameters['minibatch_size'],
verbose=verbose,
epochs=1,
validation_split=self.hyperparameters['validation_split'],
--
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