From 0a45437f67f71f32ebdef7f150ed976e7fa39178 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Wed, 11 Dec 2019 14:15:52 -0500
Subject: [PATCH] fix
---
mhcflurry/__init__.py | 5 +++++
.../class1_presentation_neural_network.py | 22 ++++++++++++++++++-
mhcflurry/custom_loss.py | 6 ++++-
mhcflurry/downloads.yml | 2 +-
...test_class1_presentation_neural_network.py | 2 +-
5 files changed, 33 insertions(+), 4 deletions(-)
diff --git a/mhcflurry/__init__.py b/mhcflurry/__init__.py
index 5d7ceb0f..525ce6a1 100644
--- a/mhcflurry/__init__.py
+++ b/mhcflurry/__init__.py
@@ -4,10 +4,15 @@ Class I MHC ligand prediction package
from .class1_affinity_predictor import Class1AffinityPredictor
from .class1_neural_network import Class1NeuralNetwork
+from .class1_presentation_predictor import Class1PresentationPredictor
+from .class1_presentation_neural_network import Class1PresentationNeuralNetwork
+
from .version import __version__
__all__ = [
"__version__",
"Class1AffinityPredictor",
"Class1NeuralNetwork",
+ "Class1PresentationPredictor",
+ "Class1PresentationNeuralNetwork",
]
diff --git a/mhcflurry/class1_presentation_neural_network.py b/mhcflurry/class1_presentation_neural_network.py
index a1c495fa..58be6813 100644
--- a/mhcflurry/class1_presentation_neural_network.py
+++ b/mhcflurry/class1_presentation_neural_network.py
@@ -554,6 +554,26 @@ class Class1PresentationNeuralNetwork(object):
"peptide"
][:num_random_negatives] = random_negative_peptides_encoding
+ if i == 0:
+ (train_generator, test_generator) = (
+ batch_generator.get_train_and_test_generators(
+ x_dict=x_dict_with_random_negatives,
+ y_list=[encoded_y1, encoded_y2],
+ epochs=1))
+ pairs = [
+ ("train", train_generator, batch_generator.num_train_batches),
+ ("test", test_generator, batch_generator.num_test_batches),
+ ]
+ for (kind, generator, steps) in pairs:
+ self.assert_allele_representations_hash(
+ allele_representations_hash)
+ metrics = self.network.evaluate_generator(
+ generator=generator,
+ steps=steps,
+ workers=0,
+ use_multiprocessing=False)
+ for (key, val) in zip(self.network.metrics_names, metrics):
+ fit_info["pre_fit_%s_%s" % (kind, key)] = val
(train_generator, test_generator) = (
batch_generator.get_train_and_test_generators(
x_dict=x_dict_with_random_negatives,
@@ -631,7 +651,7 @@ class Class1PresentationNeuralNetwork(object):
return {
'batch_generator': batch_generator,
'last_x': x_dict_with_random_negatives,
- 'last_y': [encoded_y1, encoded_y2, encoded_y2],
+ 'last_y': [encoded_y1, encoded_y2],
'fit_info': fit_info,
}
diff --git a/mhcflurry/custom_loss.py b/mhcflurry/custom_loss.py
index 6cec8a8b..53574a96 100644
--- a/mhcflurry/custom_loss.py
+++ b/mhcflurry/custom_loss.py
@@ -183,10 +183,14 @@ class MSEWithInequalities(Loss):
diff3 *= K.cast(y_true >= 4.0, "float32")
diff3 *= K.cast(diff3 > 0.0, "float32")
+ denominator = K.maximum(
+ K.sum(K.cast(K.not_equal(y_true, 2.0), "float32"), 0),
+ 1.0)
+
result = (
K.sum(K.square(diff1)) +
K.sum(K.square(diff2)) +
- K.sum(K.square(diff3))) / K.cast(K.shape(y_pred)[0], "float32")
+ K.sum(K.square(diff3))) / denominator
return result
diff --git a/mhcflurry/downloads.yml b/mhcflurry/downloads.yml
index 5899f29a..5de672d9 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.20191210.tar.bz2
+ url: https://github.com/openvax/mhcflurry/releases/download/1.4.0/models_class1_pan_refined.20191211.tar.bz2
default: false
- name: models_class1_pan_variants
diff --git a/test/test_class1_presentation_neural_network.py b/test/test_class1_presentation_neural_network.py
index 91799922..75cd751d 100644
--- a/test/test_class1_presentation_neural_network.py
+++ b/test/test_class1_presentation_neural_network.py
@@ -91,7 +91,7 @@ def make_motif(presentation_predictor, allele, peptides, frac=0.01):
# TESTS
###################################################
-def test_synthetic_allele_refinement(include_affinities=False):
+def test_synthetic_allele_refinement(include_affinities=True):
"""
Test that in a synthetic example the model is able to learn that HLA-C*01:02
prefers P at position 3.
--
GitLab