From 21dc2918db86c6b9937f7caecb1bad480c031dbe Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Tue, 16 Jul 2019 12:23:28 -0400
Subject: [PATCH] fix
---
.../GENERATE.WITH_HPC_CLUSTER.sh | 2 +-
.../cluster_submit_script_header.mssm_hpc.lsf | 1 +
.../generate_hyperparameters.py | 4 +-
mhcflurry/class1_neural_network.py | 96 +++++++++++++------
mhcflurry/train_pan_allele_models_command.py | 30 +++---
test/expensive_test_pretrain_optimizable.py | 5 +-
6 files changed, 91 insertions(+), 47 deletions(-)
diff --git a/downloads-generation/models_class1_pan_unselected/GENERATE.WITH_HPC_CLUSTER.sh b/downloads-generation/models_class1_pan_unselected/GENERATE.WITH_HPC_CLUSTER.sh
index 84801026..2e4dc910 100755
--- a/downloads-generation/models_class1_pan_unselected/GENERATE.WITH_HPC_CLUSTER.sh
+++ b/downloads-generation/models_class1_pan_unselected/GENERATE.WITH_HPC_CLUSTER.sh
@@ -42,7 +42,7 @@ do
--hyperparameters hyperparameters.yaml \
--out-models-dir models.${kind} \
--worker-log-dir "$SCRATCH_DIR/$DOWNLOAD_NAME" \
- --verbosity 1 \
+ --verbosity 0 \
--cluster-parallelism \
--cluster-submit-command bsub \
--cluster-results-workdir ~/mhcflurry-scratch \
diff --git a/downloads-generation/models_class1_pan_unselected/cluster_submit_script_header.mssm_hpc.lsf b/downloads-generation/models_class1_pan_unselected/cluster_submit_script_header.mssm_hpc.lsf
index 16a8411d..f312bb07 100644
--- a/downloads-generation/models_class1_pan_unselected/cluster_submit_script_header.mssm_hpc.lsf
+++ b/downloads-generation/models_class1_pan_unselected/cluster_submit_script_header.mssm_hpc.lsf
@@ -2,6 +2,7 @@
#BSUB -J mhcf-{work_item_num} # Job name
#BSUB -P acc_nkcancer # allocation account or Unix group
#BSUB -q gpu # queue
+#BSUB -R rusage[ngpus_excl_p=1] # 1 exclusive GPU
#BSUB -R span[hosts=1] # one node
#BSUB -n 1 # number of compute cores
#BSUB -W 36:00 # walltime in HH:MM
diff --git a/downloads-generation/models_class1_pan_unselected/generate_hyperparameters.py b/downloads-generation/models_class1_pan_unselected/generate_hyperparameters.py
index 12d5748c..47101408 100644
--- a/downloads-generation/models_class1_pan_unselected/generate_hyperparameters.py
+++ b/downloads-generation/models_class1_pan_unselected/generate_hyperparameters.py
@@ -44,9 +44,11 @@ base_hyperparameters = {
'pretrain': True,
'pretrain_peptides_per_epoch': 64,
'pretrain_steps_per_epoch': 256,
- 'pretrain_patience': 5,
+ 'pretrain_patience': 2,
'pretrain_min_delta': 0.0001,
'pretrain_max_val_loss': 0.10,
+ 'pretrain_max_epochs': 50,
+ 'pretrain_min_epochs': 5,
},
'validation_split': 0.1,
'data_dependent_initialization_method': "lsuv",
diff --git a/mhcflurry/class1_neural_network.py b/mhcflurry/class1_neural_network.py
index 40efdbc2..55729a44 100644
--- a/mhcflurry/class1_neural_network.py
+++ b/mhcflurry/class1_neural_network.py
@@ -457,9 +457,13 @@ class Class1NeuralNetwork(object):
validation_output_indices=None,
steps_per_epoch=10,
epochs=1000,
+ min_epochs=0,
patience=10,
min_delta=0.0,
- verbose=1):
+ verbose=1,
+ progress_callback=None,
+ progress_preamble="",
+ progress_print_interval=5.0):
"""
Fit using a generator. Does not support many of the features of fit(),
such as random negative peptides.
@@ -569,31 +573,63 @@ class Class1NeuralNetwork(object):
verbose=verbose)
iterator = itertools.chain([first_chunk], iterator)
- def progress_update(epoch, logs):
- if verbose:
- print(
- "Cumulative training points:",
- mutable_generator_state['yielded_values'])
-
- fit_history = network.fit_generator(
- iterator,
- steps_per_epoch=steps_per_epoch,
- epochs=epochs,
- use_multiprocessing=False,
- workers=1,
- validation_data=(validation_x_dict, validation_y_dict),
- verbose=verbose,
- callbacks=[
- keras.callbacks.EarlyStopping(
- monitor="val_loss",
- patience=patience,
- min_delta=min_delta,
- verbose=verbose),
- keras.callbacks.LambdaCallback(on_epoch_end=progress_update),
- ]
- )
- for (key, value) in fit_history.history.items():
- fit_info[key].extend(value)
+ min_val_loss_iteration = None
+ min_val_loss = None
+ last_progress_print = 0
+ epoch = 1
+ while True:
+ epoch_start_time = time.time()
+ fit_history = network.fit_generator(
+ iterator,
+ steps_per_epoch=steps_per_epoch,
+ initial_epoch=epoch - 1,
+ epochs=epoch,
+ use_multiprocessing=False,
+ workers=1,
+ validation_data=(validation_x_dict, validation_y_dict),
+ verbose=verbose,
+ )
+ epoch_time = time.time() - epoch_start_time
+ for (key, value) in fit_history.history.items():
+ fit_info[key].extend(value)
+ val_loss = fit_info['val_loss'][-1]
+
+ if min_val_loss is None or val_loss < min_val_loss - min_delta:
+ min_val_loss = val_loss
+ min_val_loss_iteration = epoch
+
+ patience_epoch_threshold = min(
+ epochs, max(min_val_loss_iteration + patience, min_epochs))
+
+ progress_message = (
+ "epoch %3d / %3d [%0.2f sec.]: loss=%g val_loss=%g. Min val "
+ "loss (%g) at epoch %s. Cumulative training points: %d. "
+ "Earliest stop epoch: %d." % (
+ epoch,
+ epochs,
+ epoch_time,
+ fit_info['loss'][-1],
+ val_loss,
+ min_val_loss,
+ min_val_loss_iteration,
+ mutable_generator_state['yielded_values'],
+ patience_epoch_threshold,
+ )).strip()
+
+ # Print progress no more often than once every few seconds.
+ if progress_print_interval is not None and (
+ time.time() - last_progress_print > progress_print_interval):
+ print(progress_preamble, progress_message)
+ last_progress_print = time.time()
+
+ if progress_callback:
+ progress_callback()
+
+ if epoch >= patience_epoch_threshold:
+ if progress_print_interval is not None:
+ print(progress_preamble, "STOPPING", progress_message)
+ break
+ epoch += 1
fit_info["time"] = time.time() - start
fit_info["num_points"] = mutable_generator_state["yielded_values"]
@@ -828,7 +864,6 @@ class Class1NeuralNetwork(object):
y_dict_with_random_negatives['output'],
**encode_y_kwargs)
- val_losses = []
min_val_loss_iteration = None
min_val_loss = None
@@ -929,7 +964,6 @@ class Class1NeuralNetwork(object):
if self.hyperparameters['validation_split']:
val_loss = fit_info['val_loss'][-1]
- val_losses.append(val_loss)
if min_val_loss is None or (
val_loss < min_val_loss - self.hyperparameters['min_delta']):
@@ -944,11 +978,13 @@ class Class1NeuralNetwork(object):
if progress_print_interval is not None:
print((progress_preamble + " " +
"Stopping at epoch %3d / %3d: loss=%g. "
- "Min val loss (%s) at epoch %s" % (
+ "Min val loss (%g) at epoch %s" % (
i,
self.hyperparameters['max_epochs'],
fit_info['loss'][-1],
- str(min_val_loss),
+ (
+ min_val_loss if min_val_loss is not None
+ else numpy.nan),
min_val_loss_iteration)).strip())
break
diff --git a/mhcflurry/train_pan_allele_models_command.py b/mhcflurry/train_pan_allele_models_command.py
index ca5a5a75..78c29da6 100644
--- a/mhcflurry/train_pan_allele_models_command.py
+++ b/mhcflurry/train_pan_allele_models_command.py
@@ -195,19 +195,20 @@ def pretrain_data_iterator(
numpy.tile(usable_alleles, peptides_per_chunk),
borrow_from=master_allele_encoding)
- synthetic_iter = pandas.read_csv(
- filename, index_col=0, chunksize=peptides_per_chunk)
- for (k, df) in enumerate(synthetic_iter):
- if len(df) != peptides_per_chunk:
- continue
+ while True:
+ synthetic_iter = pandas.read_csv(
+ filename, index_col=0, chunksize=peptides_per_chunk)
+ for (k, df) in enumerate(synthetic_iter):
+ if len(df) != peptides_per_chunk:
+ continue
- df = df[usable_alleles]
- encodable_peptides = EncodableSequences(
- numpy.repeat(
- df.index.values,
- len(usable_alleles)))
+ df = df[usable_alleles]
+ encodable_peptides = EncodableSequences(
+ numpy.repeat(
+ df.index.values,
+ len(usable_alleles)))
- yield (allele_encoding, encodable_peptides, df.stack().values)
+ yield (allele_encoding, encodable_peptides, df.stack().values)
def run(argv=sys.argv[1:]):
@@ -493,8 +494,8 @@ def train_model(
pretrain_min_delta = get_train_param("pretrain_min_delta", 0.0)
pretrain_steps_per_epoch = get_train_param(
"pretrain_steps_per_epoch", 10)
- pretrain_max_epochs = get_train_param(
- "pretrain_max_epochs", 1000)
+ pretrain_max_epochs = get_train_param("pretrain_max_epochs", 1000)
+ pretrain_min_epochs = get_train_param("pretrain_min_epochs", 0)
pretrain_peptides_per_step = get_train_param(
"pretrain_peptides_per_step", 1024)
max_val_loss = get_train_param("pretrain_max_val_loss", None)
@@ -527,7 +528,10 @@ def train_model(
min_delta=pretrain_min_delta,
steps_per_epoch=pretrain_steps_per_epoch,
epochs=pretrain_max_epochs,
+ min_epochs=pretrain_min_epochs,
verbose=verbose,
+ progress_preamble=progress_preamble + "PRETRAIN",
+ progress_print_interval=progress_print_interval,
)
model.fit_info[-1].setdefault(
"training_info", {})["pretrain_attempt"] = attempt
diff --git a/test/expensive_test_pretrain_optimizable.py b/test/expensive_test_pretrain_optimizable.py
index 027a88bb..99f9497e 100644
--- a/test/expensive_test_pretrain_optimizable.py
+++ b/test/expensive_test_pretrain_optimizable.py
@@ -51,8 +51,9 @@ HYPERPARAMTERS = {
'random_negative_match_distribution': True, 'random_negative_rate': 0.2,
'train_data': {'pretrain': True,
'pretrain_max_epochs': 30,
- 'pretrain_patience': 5,
- 'pretrain_peptides_per_step': 32,
+ 'pretrain_min_epochs': 5,
+ 'pretrain_patience': 3,
+ 'pretrain_peptides_per_step': 8,
'pretrain_steps_per_epoch': 256},
'validation_split': 0.1,
'data_dependent_initialization_method': "lsuv",
--
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