From 5d447dbb3ccb026c47de496ebad90bb2d1c241a7 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Wed, 11 Dec 2019 15:58:50 -0500
Subject: [PATCH] fix
---
.../models_class1_pan_refined/hyperparameters.yaml | 2 +-
mhcflurry/class1_presentation_neural_network.py | 2 +-
mhcflurry/downloads.yml | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/downloads-generation/models_class1_pan_refined/hyperparameters.yaml b/downloads-generation/models_class1_pan_refined/hyperparameters.yaml
index 9dbb9575..a1747f7a 100644
--- a/downloads-generation/models_class1_pan_refined/hyperparameters.yaml
+++ b/downloads-generation/models_class1_pan_refined/hyperparameters.yaml
@@ -2,7 +2,7 @@
# Batch generation
#########################
batch_generator_validation_split: 0.1
-batch_generator_batch_size: 10240
+batch_generator_batch_size: 1024
batch_generator_affinity_fraction: 0.5
max_epochs: 500
random_negative_rate: 1.0
diff --git a/mhcflurry/class1_presentation_neural_network.py b/mhcflurry/class1_presentation_neural_network.py
index 58be6813..2e1156e6 100644
--- a/mhcflurry/class1_presentation_neural_network.py
+++ b/mhcflurry/class1_presentation_neural_network.py
@@ -453,7 +453,7 @@ class Class1PresentationNeuralNetwork(object):
allele_representations_hash = self.set_allele_representations(
allele_representations)
- loss_reduction = "none"
+ loss_reduction = "sum_over_batch_size"
self.network.compile(
loss=[
affinities_loss.get_keras_loss(reduction=loss_reduction),
diff --git a/mhcflurry/downloads.yml b/mhcflurry/downloads.yml
index 5de672d9..286121fd 100644
--- a/mhcflurry/downloads.yml
+++ b/mhcflurry/downloads.yml
@@ -30,7 +30,7 @@ releases:
default: false
- name: models_class1_pan_refined
- url: https://github.com/openvax/mhcflurry/releases/download/1.4.0/models_class1_pan_refined.20191211.tar.bz2
+ url: https://github.com/openvax/mhcflurry/releases/download/1.4.0/models_class1_pan_refined.20191211b.tar.bz2
default: false
- name: models_class1_pan_variants
--
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