From c749b93089ddf950200ef9d6106443446855638c Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sat, 13 Jul 2019 12:58:34 -0400
Subject: [PATCH] fix
---
.../generate_hyperparameters.py | 3 ++
mhcflurry/class1_neural_network.py | 9 +++-
mhcflurry/train_pan_allele_models_command.py | 45 ++++++++++++++-----
test/test_train_pan_allele_models_command.py | 2 -
4 files changed, 43 insertions(+), 16 deletions(-)
diff --git a/downloads-generation/models_class1_pan_unselected/generate_hyperparameters.py b/downloads-generation/models_class1_pan_unselected/generate_hyperparameters.py
index ccffc6b0..4ed6e35c 100644
--- a/downloads-generation/models_class1_pan_unselected/generate_hyperparameters.py
+++ b/downloads-generation/models_class1_pan_unselected/generate_hyperparameters.py
@@ -24,6 +24,7 @@ base_hyperparameters = {
'optimizer': 'rmsprop',
'output_activation': 'sigmoid',
"patience": 20,
+ "min_delta": 0.0,
'peptide_encoding': {
'vector_encoding_name': 'BLOSUM62',
'alignment_method': 'left_pad_centered_right_pad',
@@ -44,6 +45,8 @@ base_hyperparameters = {
'pretrain_peptides_per_epoch': 1024,
'pretrain_steps_per_epoch': 16,
'pretrain_patience': 10,
+ 'pretrain_min_delta': 0.0001,
+ 'pretrain_max_val_loss': 0.10,
},
'validation_split': 0.1,
}
diff --git a/mhcflurry/class1_neural_network.py b/mhcflurry/class1_neural_network.py
index d1add2b7..3773f7d4 100644
--- a/mhcflurry/class1_neural_network.py
+++ b/mhcflurry/class1_neural_network.py
@@ -89,6 +89,7 @@ class Class1NeuralNetwork(object):
early_stopping_hyperparameter_defaults = HyperparameterDefaults(
patience=20,
+ min_delta=0.0,
)
"""
Hyperparameters for early stopping.
@@ -429,6 +430,7 @@ class Class1NeuralNetwork(object):
steps_per_epoch=10,
epochs=1000,
patience=10,
+ min_delta=0.0,
verbose=1):
"""
Fit using a generator. Does not support many of the features of fit(),
@@ -532,6 +534,7 @@ class Class1NeuralNetwork(object):
callbacks=[keras.callbacks.EarlyStopping(
monitor="val_loss",
patience=patience,
+ min_delta=min_delta,
verbose=verbose)]
)
for (key, value) in fit_history.history.items():
@@ -831,7 +834,8 @@ class Class1NeuralNetwork(object):
shuffle=True,
batch_size=self.hyperparameters['minibatch_size'],
verbose=verbose,
- epochs=1,
+ epochs=i + 1,
+ initial_epoch=i,
validation_split=self.hyperparameters['validation_split'],
sample_weight=sample_weights_with_random_negatives)
@@ -857,7 +861,8 @@ class Class1NeuralNetwork(object):
val_loss = fit_info['val_loss'][-1]
val_losses.append(val_loss)
- if min_val_loss is None or val_loss <= min_val_loss:
+ if min_val_loss is None or (
+ val_loss < min_val_loss - self.hyperparameters['min_delta']):
min_val_loss = val_loss
min_val_loss_iteration = i
diff --git a/mhcflurry/train_pan_allele_models_command.py b/mhcflurry/train_pan_allele_models_command.py
index b5aaf36e..1ab50a0f 100644
--- a/mhcflurry/train_pan_allele_models_command.py
+++ b/mhcflurry/train_pan_allele_models_command.py
@@ -332,7 +332,7 @@ def main(args):
'hyperparameters': hyperparameters,
'pretrain_data_filename': args.pretrain_data,
'verbose': args.verbosity,
- 'progress_print_interval': None if not serial_run else 5.0,
+ 'progress_print_interval': 60.0 if not serial_run else 5.0,
'predictor': predictor if serial_run else None,
'save_to': args.out_models_dir if serial_run else None,
}
@@ -484,22 +484,43 @@ def train_model(
generator = pretrain_data_iterator(pretrain_data_filename, allele_encoding)
pretrain_patience = hyperparameters["train_data"].get(
"pretrain_patience", 10)
+ pretrain_min_delta = hyperparameters["train_data"].get(
+ "pretrain_min_delta", 0.0)
pretrain_steps_per_epoch = hyperparameters["train_data"].get(
"pretrain_steps_per_epoch", 10)
pretrain_max_epochs = hyperparameters["train_data"].get(
"pretrain_max_epochs", 1000)
- model.fit_generator(
- generator,
- validation_peptide_encoding=train_peptides,
- validation_affinities=train_data.measurement_value.values,
- validation_allele_encoding=train_alleles,
- validation_inequalities=train_data.measurement_inequality.values,
- patience=pretrain_patience,
- steps_per_epoch=pretrain_steps_per_epoch,
- epochs=pretrain_max_epochs,
- verbose=verbose,
- )
+ max_val_loss = hyperparameters["train_data"].get("pretrain_max_val_loss")
+
+ attempt = 0
+ while True:
+ attempt += 1
+ print("Pre-training attempt %d" % attempt)
+ if attempt > 10:
+ print("Too many pre-training attempts! Stopping pretraining.")
+ break
+ model.fit_generator(
+ generator,
+ validation_peptide_encoding=train_peptides,
+ validation_affinities=train_data.measurement_value.values,
+ validation_allele_encoding=train_alleles,
+ validation_inequalities=train_data.measurement_inequality.values,
+ patience=pretrain_patience,
+ min_delta=pretrain_min_delta,
+ steps_per_epoch=pretrain_steps_per_epoch,
+ epochs=pretrain_max_epochs,
+ verbose=verbose,
+ )
+ if not max_val_loss:
+ break
+ if model.fit_info[-1]["val_loss"] >= max_val_loss:
+ print("Val loss %f >= max val loss %f. Pre-training again." % (
+ model.fit_info[-1]["val_loss"], max_val_loss))
+ else:
+ print("Val loss %f < max val loss %f. Done pre-training." % (
+ model.fit_info[-1]["val_loss"], max_val_loss))
+ break
# Use a smaller learning rate for training on real data
learning_rate = model.fit_info[-1]["learning_rate"]
diff --git a/test/test_train_pan_allele_models_command.py b/test/test_train_pan_allele_models_command.py
index 1ecbe85f..f4255f76 100644
--- a/test/test_train_pan_allele_models_command.py
+++ b/test/test_train_pan_allele_models_command.py
@@ -144,7 +144,6 @@ def run_and_check(n_jobs=0, delete=True, additional_args=[]):
print("Deleting: %s" % models_dir)
shutil.rmtree(models_dir)
-"""
if os.environ.get("KERAS_BACKEND") != "theano":
def test_run_parallel():
run_and_check(n_jobs=1)
@@ -153,7 +152,6 @@ if os.environ.get("KERAS_BACKEND") != "theano":
def test_run_serial():
run_and_check(n_jobs=0)
-"""
def test_run_cluster_parallelism():
--
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