From 9d197d67e47adb9ef691ea951e5bc0efe884ece9 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Thu, 5 Dec 2019 19:33:51 -0500
Subject: [PATCH] tests
---
mhcflurry/custom_loss.py | 5 +++--
test/test_class1_presentation_predictor.py | 18 ++++++++++--------
2 files changed, 13 insertions(+), 10 deletions(-)
diff --git a/mhcflurry/custom_loss.py b/mhcflurry/custom_loss.py
index 12b2c669..3660ae32 100644
--- a/mhcflurry/custom_loss.py
+++ b/mhcflurry/custom_loss.py
@@ -291,8 +291,9 @@ class MultiallelicMassSpecLoss(Loss):
pos_max = tf.reduce_max(pos, axis=1)
neg = tf.boolean_mask(y_pred, tf.math.equal(y_true, 0.0))
term = tf.reshape(neg, (-1, 1)) - pos_max + self.delta
- result = tf.reduce_sum(tf.maximum(0.0, term) ** 2) / tf.cast(
- tf.size(term), tf.float32) * self.multiplier
+ result = tf.math.divide_no_nan(
+ tf.reduce_sum(tf.maximum(0.0, term) ** 2),
+ tf.cast(tf.size(term), tf.float32)) * self.multiplier
return result
diff --git a/test/test_class1_presentation_predictor.py b/test/test_class1_presentation_predictor.py
index eeb574d3..37837571 100644
--- a/test/test_class1_presentation_predictor.py
+++ b/test/test_class1_presentation_predictor.py
@@ -91,7 +91,7 @@ def teardown():
cleanup()
-def test_basic():
+def Xtest_basic():
affinity_predictor = PAN_ALLELE_PREDICTOR_NO_MASS_SPEC
models = []
for affinity_network in affinity_predictor.class1_pan_allele_models:
@@ -485,9 +485,11 @@ def Xtest_real_data_multiallelic_refinement(max_epochs=10):
import ipdb ; ipdb.set_trace()
+def test_synthetic_allele_refinement_with_affinity_data():
+ test_synthetic_allele_refinement(include_affinities=True)
-def Xtest_synthetic_allele_refinement_with_affinity_data(
- max_epochs=10, include_affinities=False):
+
+def test_synthetic_allele_refinement(max_epochs=10, include_affinities=False):
refine_allele = "HLA-C*01:02"
alleles = [
"HLA-A*02:01", "HLA-B*27:01", "HLA-C*07:01",
@@ -508,11 +510,10 @@ def Xtest_synthetic_allele_refinement_with_affinity_data(
"curated_training_data.no_mass_spec.csv.bz2"))
def filter_df(df):
- df = df.loc[
+ return df.loc[
(df.allele.isin(alleles)) &
(df.peptide.str.len() == length)
]
- return df
train_with_ms = filter_df(train_with_ms)
train_no_ms = filter_df(train_no_ms)
@@ -560,12 +561,13 @@ def Xtest_synthetic_allele_refinement_with_affinity_data(
(affinity_model,) = PAN_ALLELE_PREDICTOR_NO_MASS_SPEC.class1_pan_allele_models
presentation_model = Class1PresentationNeuralNetwork(
auxiliary_input_features=["gene"],
+ batch_generator_batch_size=1024,
max_epochs=max_epochs,
- learning_rate=0.0001,
+ learning_rate=0.001,
patience=5,
min_delta=0.0,
- random_negative_rate=0.0,
- random_negative_constant=0) # WHY DOES THIS BREAK WITH RANDOM NEG?
+ random_negative_rate=1.0,
+ random_negative_constant=25)
presentation_model.load_from_class1_neural_network(affinity_model)
presentation_model = pickle.loads(pickle.dumps(presentation_model))
--
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