From a0b0a8a994de54c7c6f31fc60a7faa77221711b6 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Wed, 25 Sep 2019 18:09:28 -0400
Subject: [PATCH] add random negative peptide method
by_allele_equalize_nonbinders
---
.../generate_hyperparameters.py | 2 +-
mhcflurry/class1_neural_network.py | 72 ++++++++-
test/test_random_negative_peptides.py | 142 ++++++++++++++++++
3 files changed, 213 insertions(+), 3 deletions(-)
create mode 100644 test/test_random_negative_peptides.py
diff --git a/downloads-generation/models_class1_pan_unselected/generate_hyperparameters.py b/downloads-generation/models_class1_pan_unselected/generate_hyperparameters.py
index a6d3297e..08873dfc 100644
--- a/downloads-generation/models_class1_pan_unselected/generate_hyperparameters.py
+++ b/downloads-generation/models_class1_pan_unselected/generate_hyperparameters.py
@@ -41,7 +41,7 @@ base_hyperparameters = {
'random_negative_distribution_smoothing': 0.0,
'random_negative_match_distribution': True,
'random_negative_rate': 1.0,
- 'random_negative_method': 'by_allele',
+ 'random_negative_method': 'by_allele_equalize_nonbinders',
'train_data': {
'pretrain': True,
'pretrain_peptides_per_epoch': 64,
diff --git a/mhcflurry/class1_neural_network.py b/mhcflurry/class1_neural_network.py
index 8b8f19f8..e6d33a57 100644
--- a/mhcflurry/class1_neural_network.py
+++ b/mhcflurry/class1_neural_network.py
@@ -6,6 +6,7 @@ import itertools
import os
import logging
import random
+import math
import numpy
import pandas
@@ -696,7 +697,14 @@ class Class1NeuralNetwork(object):
df["inequality"] = "="
else:
df["inequality"] = inequalities
+ df_nonbinders = None
if self.hyperparameters['random_negative_binder_threshold']:
+ df_nonbinders = df.loc[
+ (df.inequality != "<") &
+ (df.affinity > self.hyperparameters[
+ 'random_negative_binder_threshold'
+ ])
+ ]
df = df.loc[
(df.inequality != ">") &
(df.affinity <= self.hyperparameters[
@@ -762,8 +770,8 @@ class Class1NeuralNetwork(object):
num_for_allele = len(sub_df) * (
self.hyperparameters['random_negative_rate']
) + self.hyperparameters['random_negative_constant']
- num_per_length = int(
- num_for_allele / len(random_negative_lengths))
+ num_per_length = int(math.ceil(
+ num_for_allele / len(random_negative_lengths)))
total_random_peptides_per_length += num_per_length
allele_to_num_per_length[allele] = num_per_length
@@ -792,6 +800,66 @@ class Class1NeuralNetwork(object):
# important NOT to shuffle peptides, since they correspond with
# specific alleles.
return EncodableSequences.create(peptides)
+ elif self.hyperparameters["random_negative_method"] == "by_allele_equalize_nonbinders":
+ assert df_nonbinders is not None
+
+ allele_and_length_to_num_random_negative = {}
+
+ # First pass
+ allele_to_num_per_length_first_pass = {}
+ for (allele, sub_df) in df.groupby("allele"):
+ num_for_allele = len(sub_df) * (
+ self.hyperparameters['random_negative_rate']
+ ) + self.hyperparameters['random_negative_constant']
+ num_per_length = int(math.ceil(
+ num_for_allele / len(random_negative_lengths)))
+ allele_to_num_per_length_first_pass[allele] = num_per_length
+
+ # Second pass
+ for (allele, sub_df) in df_nonbinders.groupby("allele"):
+ nonbinders_by_length = sub_df.peptide.str.len().value_counts()
+ nonbinders_by_length = nonbinders_by_length.reindex(
+ random_negative_lengths
+ ).fillna(0)
+
+ total_nonbinders_by_length = (
+ nonbinders_by_length +
+ allele_to_num_per_length_first_pass[allele])
+ max_total_nonbinders_by_length = total_nonbinders_by_length.max()
+ for (length, total) in total_nonbinders_by_length.items():
+ allele_and_length_to_num_random_negative[
+ (allele, length)
+ ] = math.ceil(
+ allele_to_num_per_length_first_pass[allele] +
+ max_total_nonbinders_by_length -
+ total)
+
+ plan_df = []
+ for (
+ (allele, length), num_random_negative) in (
+ allele_and_length_to_num_random_negative.items()):
+ plan_df.append((allele, length, num_random_negative))
+ plan_df = pandas.DataFrame(
+ plan_df, columns=["allele", "length", "num"])
+
+ logging.info("Random negative plan:\n%s", plan_df)
+
+ if allele_encoding is not None:
+ random_negative_alleles = []
+ for _, row in plan_df.iterrows():
+ random_negative_alleles.extend([row.allele] * int(row.num))
+
+ def sample_peptides():
+ peptides = []
+ for _, row in plan_df.iterrows():
+ peptides.extend(
+ random_peptides(
+ row.num,
+ length=row.length,
+ distribution=aa_distribution))
+ # important NOT to shuffle peptides, since they correspond with
+ # specific alleles.
+ return EncodableSequences.create(peptides)
else:
raise NotImplementedError(
self.hyperparameters["random_negative_method"])
diff --git a/test/test_random_negative_peptides.py b/test/test_random_negative_peptides.py
new file mode 100644
index 00000000..c3c978f2
--- /dev/null
+++ b/test/test_random_negative_peptides.py
@@ -0,0 +1,142 @@
+from mhcflurry import amino_acid
+from nose.tools import eq_
+from numpy.testing import assert_equal
+import numpy
+import pandas
+import math
+
+from mhcflurry import Class1NeuralNetwork
+from mhcflurry.encodable_sequences import EncodableSequences
+from mhcflurry.allele_encoding import AlleleEncoding
+from mhcflurry.common import random_peptides
+
+
+def test_random_negative_peptides_by_allele():
+ network = Class1NeuralNetwork(
+ random_negative_method="by_allele",
+ random_negative_binder_threshold=500,
+ random_negative_rate=1.0,
+ random_negative_constant=2)
+
+ allele_to_sequence = {
+ "HLA-A*02:01": "AAAAA",
+ "HLA-B*44:02": "CCCCC",
+ "HLA-C*07:02": "EEEEE",
+ }
+ data_rows = [
+ ("HLA-A*02:01", "SIINFEKL", 400, "="),
+ ("HLA-A*02:01", "SIINFEKLL", 300, "="),
+ ("HLA-A*02:01", "SIINFEKLL", 300, "="),
+ ("HLA-A*02:01", "SIINFEKLQ", 1000, "="),
+ ("HLA-A*02:01", "SIINFEKLZZ", 12000, ">"),
+ ]
+ for peptide in random_peptides(1000, length=9):
+ data_rows.append(("HLA-B*44:02", peptide, 100, "="))
+ for peptide in random_peptides(1000, length=9):
+ data_rows.append(("HLA-B*44:02", peptide, 1000, "="))
+ for peptide in random_peptides(5, length=10):
+ data_rows.append(("HLA-B*44:02", peptide, 100, "="))
+
+ data = pandas.DataFrame(
+ data_rows,
+ columns=["allele", "peptide", "affinity", "inequality"])
+ data["length"] = data.peptide.str.len()
+
+ peptides = EncodableSequences.create(data.peptide.values)
+ allele_encoding = AlleleEncoding(data.allele.values, allele_to_sequence)
+
+ results = network.random_negatives_generator(
+ peptides,
+ data.affinity.values,
+ allele_encoding,
+ data.inequality.values
+ )
+ result_allele_encoding = next(results)
+ first_peptide_sample = next(results)
+ second_peptide_sample = next(results)
+
+ result_df1 = pandas.DataFrame({
+ "allele": result_allele_encoding.alleles,
+ "peptide": first_peptide_sample.sequences,
+ })
+ result_df1["length"] = result_df1.peptide.str.len()
+ random_negatives = result_df1.groupby(["allele", "length"]).peptide.count().unstack()
+ real_data = data.groupby(["allele", "length"]).peptide.count().unstack().fillna(0)
+ real_binders = data.loc[
+ data.affinity <= 500
+ ].groupby(["allele", "length"]).peptide.count().unstack().fillna(0)
+ real_nonbinders = data.loc[
+ data.affinity > 500
+ ].groupby(["allele", "length"]).peptide.count().unstack().fillna(0)
+ total_nonbinders = random_negatives + real_nonbinders
+
+ assert (random_negatives.loc["HLA-A*02:01"] == 1.0).all()
+ assert (random_negatives.loc["HLA-B*44:02"] == math.ceil(1007 / 8)).all(), (
+ random_negatives.loc["HLA-B*44:02"], math.ceil(1007 / 8))
+
+
+
+def test_random_negative_peptides_by_allele():
+ network = Class1NeuralNetwork(
+ random_negative_method="by_allele_equalize_nonbinders",
+ random_negative_binder_threshold=500,
+ random_negative_rate=1.0,
+ random_negative_constant=2)
+
+ allele_to_sequence = {
+ "HLA-A*02:01": "AAAAA",
+ "HLA-B*44:02": "CCCCC",
+ "HLA-C*07:02": "EEEEE",
+ }
+ data_rows = [
+ ("HLA-A*02:01", "SIINFEKL", 400, "="),
+ ("HLA-A*02:01", "SIINFEKLL", 300, "="),
+ ("HLA-A*02:01", "SIINFEKLL", 300, "="),
+ ("HLA-A*02:01", "SIINFEKLQ", 1000, "="),
+ ("HLA-A*02:01", "SIINFEKLZZ", 12000, ">"),
+ ]
+ for peptide in random_peptides(1000, length=9):
+ data_rows.append(("HLA-B*44:02", peptide, 100, "="))
+ for peptide in random_peptides(1000, length=9):
+ data_rows.append(("HLA-B*44:02", peptide, 1000, "="))
+ for peptide in random_peptides(5, length=10):
+ data_rows.append(("HLA-B*44:02", peptide, 100, "="))
+
+ data = pandas.DataFrame(
+ data_rows,
+ columns=["allele", "peptide", "affinity", "inequality"])
+ data["length"] = data.peptide.str.len()
+
+ peptides = EncodableSequences.create(data.peptide.values)
+ allele_encoding = AlleleEncoding(data.allele.values, allele_to_sequence)
+
+ results = network.random_negatives_generator(
+ peptides,
+ data.affinity.values,
+ allele_encoding,
+ data.inequality.values
+ )
+ result_allele_encoding = next(results)
+ first_peptide_sample = next(results)
+ second_peptide_sample = next(results)
+
+ result_df1 = pandas.DataFrame({
+ "allele": result_allele_encoding.alleles,
+ "peptide": first_peptide_sample.sequences,
+ })
+ result_df1["length"] = result_df1.peptide.str.len()
+ random_negatives = result_df1.groupby(["allele", "length"]).peptide.count().unstack()
+ real_data = data.groupby(["allele", "length"]).peptide.count().unstack().fillna(0)
+ real_binders = data.loc[
+ data.affinity <= 500
+ ].groupby(["allele", "length"]).peptide.count().unstack().fillna(0)
+ real_nonbinders = data.loc[
+ data.affinity > 500
+ ].groupby(["allele", "length"]).peptide.count().unstack().fillna(0)
+ for length in random_negatives.columns:
+ if length not in real_nonbinders.columns:
+ real_nonbinders[length] = 0
+ total_nonbinders = random_negatives + real_nonbinders
+
+ assert (total_nonbinders.loc["HLA-A*02:01"] == 2.0).all()
+ assert (total_nonbinders.loc["HLA-B*44:02"] == 1126).all()
--
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