From 4a2f6a182546dda094c0fc1977f7760bc072ecb0 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Wed, 18 Sep 2019 18:07:40 -0400
Subject: [PATCH] fix
---
.../GENERATE.WITH_HPC_CLUSTER.sh | 2 +-
.../models_class1_pan_unselected/GENERATE.sh | 2 +-
mhcflurry/select_pan_allele_models_command.py | 28 +++---------
mhcflurry/train_pan_allele_models_command.py | 14 +++---
test/test_train_pan_allele_models_command.py | 43 +++++++++++++------
5 files changed, 43 insertions(+), 46 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 d3d232f7..d8b70a64 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
@@ -61,7 +61,7 @@ do
--allele-sequences "$(mhcflurry-downloads path allele_sequences)/allele_sequences.csv" \
--pretrain-data "$(mhcflurry-downloads path random_peptide_predictions)/predictions.csv.bz2" \
--held-out-measurements-per-allele-fraction-and-max 0.25 100 \
- --ensemble-size 4 \
+ --num-folds 4 \
--hyperparameters hyperparameters.yaml \
--out-models-dir $(pwd)/models.${kind} \
--worker-log-dir "$SCRATCH_DIR/$DOWNLOAD_NAME" \
diff --git a/downloads-generation/models_class1_pan_unselected/GENERATE.sh b/downloads-generation/models_class1_pan_unselected/GENERATE.sh
index 51676bf0..c5799bb9 100755
--- a/downloads-generation/models_class1_pan_unselected/GENERATE.sh
+++ b/downloads-generation/models_class1_pan_unselected/GENERATE.sh
@@ -73,7 +73,7 @@ do
--allele-sequences "$(mhcflurry-downloads path allele_sequences)/allele_sequences.csv" \
--pretrain-data "$(mhcflurry-downloads path random_peptide_predictions)/predictions.csv.bz2" \
--held-out-measurements-per-allele-fraction-and-max 0.25 100 \
- --ensemble-size 4 \
+ --num-folds 4 \
--hyperparameters hyperparameters.yaml \
--out-models-dir models.${kind} \
--worker-log-dir "$SCRATCH_DIR/$DOWNLOAD_NAME" \
diff --git a/mhcflurry/select_pan_allele_models_command.py b/mhcflurry/select_pan_allele_models_command.py
index c931632b..b99657f4 100644
--- a/mhcflurry/select_pan_allele_models_command.py
+++ b/mhcflurry/select_pan_allele_models_command.py
@@ -51,11 +51,6 @@ parser.add_argument(
help=(
"Model selection data CSV. Expected columns: "
"allele, peptide, measurement_value"))
-parser.add_argument(
- "--folds",
- metavar="FILE.csv",
- required=False,
- help=(""))
parser.add_argument(
"--models-dir",
metavar="DIR",
@@ -161,19 +156,6 @@ def run(argv=sys.argv[1:]):
metadata_dfs = {}
- if args.folds:
- folds_df = pandas.read_csv(args.folds)
- matches = all([
- len(folds_df) == len(df),
- (folds_df.peptide == df.peptide).all(),
- (folds_df.allele == df.allele).all(),
- ])
- if not matches:
- raise ValueError("Training data and fold data do not match")
- fold_cols = [c for c in folds_df if c.startswith("fold_")]
- for col in fold_cols:
- df[col] = folds_df[col]
-
fold_cols = [c for c in df if c.startswith("fold_")]
num_folds = len(fold_cols)
if num_folds <= 1:
@@ -193,8 +175,6 @@ def run(argv=sys.argv[1:]):
df = df.loc[df.allele.isin(alleles)].dropna()
print("Subselected to supported alleles: %s" % str(df.shape))
- print("Selected %d alleles: %s" % (len(alleles), ' '.join(alleles)))
-
metadata_dfs["model_selection_data"] = df
df["mass_spec"] = df.measurement_source.str.contains(
@@ -248,13 +228,13 @@ def run(argv=sys.argv[1:]):
if serial_run:
# Serial run
print("Running in serial.")
- results = (do_model_select_task(item) for item in work_items)
+ results = (model_select(**item) for item in work_items)
elif args.cluster_parallelism:
# Run using separate processes HPC cluster.
print("Running on cluster.")
results = cluster_results_from_args(
args,
- work_function=do_model_select_task,
+ work_function=model_select,
work_items=work_items,
constant_data=GLOBAL_DATA,
result_serialization_method="pickle")
@@ -268,7 +248,9 @@ def run(argv=sys.argv[1:]):
# Parallel run
results = worker_pool.imap_unordered(
- do_model_select_task, work_items, chunksize=1)
+ do_model_select_task,
+ work_items,
+ chunksize=1)
models_by_fold = {}
summary_dfs = []
diff --git a/mhcflurry/train_pan_allele_models_command.py b/mhcflurry/train_pan_allele_models_command.py
index f20c9e3e..5947183e 100644
--- a/mhcflurry/train_pan_allele_models_command.py
+++ b/mhcflurry/train_pan_allele_models_command.py
@@ -84,11 +84,11 @@ parser.add_argument(
default=False,
help="Do not use affinity value inequalities even when present in data")
parser.add_argument(
- "--ensemble-size",
+ "--num-folds",
type=int,
+ default=4,
metavar="N",
- help="Ensemble size, i.e. how many models to retain the final predictor. "
- "In the current implementation, this is also the number of training folds.")
+ help="Number of training folds.")
parser.add_argument(
"--num-replicates",
type=int,
@@ -296,7 +296,7 @@ def initialize_training(args):
"data",
"out_models_dir",
"hyperparameters",
- "ensemble_size",
+ "num_folds",
]
for arg in required_arguments:
if getattr(args, arg) is None:
@@ -338,7 +338,7 @@ def initialize_training(args):
folds_df = assign_folds(
df=df,
- num_folds=args.ensemble_size,
+ num_folds=args.num_folds,
held_out_fraction=held_out_fraction,
held_out_max=held_out_max)
@@ -387,14 +387,14 @@ def initialize_training(args):
if not args.pretrain_data:
raise ValueError("--pretrain-data is required")
- for fold in range(args.ensemble_size):
+ for fold in range(args.num_folds):
for replicate in range(args.num_replicates):
work_dict = {
'work_item_name': str(uuid.uuid4()),
'architecture_num': h,
'num_architectures': len(hyperparameters_lst),
'fold_num': fold,
- 'num_folds': args.ensemble_size,
+ 'num_folds': args.num_folds,
'replicate_num': replicate,
'num_replicates': args.num_replicates,
'hyperparameters': hyperparameters,
diff --git a/test/test_train_pan_allele_models_command.py b/test/test_train_pan_allele_models_command.py
index 53c5bb25..c214ec56 100644
--- a/test/test_train_pan_allele_models_command.py
+++ b/test/test_train_pan_allele_models_command.py
@@ -2,6 +2,11 @@
Tests for training and predicting using Class1 pan-allele models.
"""
+import logging
+logging.getLogger('tensorflow').disabled = True
+logging.getLogger('matplotlib').disabled = True
+
+
import json
import os
import shutil
@@ -36,7 +41,7 @@ HYPERPARAMETERS_LIST = [
'learning_rate': None,
'locally_connected_layers': [],
'loss': 'custom:mse_with_inequalities',
- 'max_epochs': 5,
+ 'max_epochs': 0, # never selected
'minibatch_size': 256,
'optimizer': 'rmsprop',
'output_activation': 'sigmoid',
@@ -100,7 +105,7 @@ HYPERPARAMETERS_LIST = [
},
'validation_split': 0.1,
},
-][1:]
+]
def run_and_check(n_jobs=0, delete=True, additional_args=[]):
@@ -114,37 +119,47 @@ def run_and_check(n_jobs=0, delete=True, additional_args=[]):
get_path("data_curated", "curated_training_data.no_mass_spec.csv.bz2"))
selected_data_df = data_df.loc[data_df.allele.str.startswith("HLA-A")]
selected_data_df.to_csv(
- os.path.join(models_dir, "train_data.csv"), index=False)
+ os.path.join(models_dir, "_train_data.csv"), index=False)
args = [
"mhcflurry-class1-train-pan-allele-models",
- "--data", os.path.join(models_dir, "train_data.csv"),
+ "--data", os.path.join(models_dir, "_train_data.csv"),
"--allele-sequences", get_path("allele_sequences", "allele_sequences.csv"),
"--hyperparameters", hyperparameters_filename,
"--out-models-dir", models_dir,
"--num-jobs", str(n_jobs),
- "--ensemble-size", "2",
+ "--num-folds", "2",
"--verbosity", "1",
- # "--pretrain-data", get_path(
- # "random_peptide_predictions", "predictions.csv.bz2"),
] + additional_args
print("Running with args: %s" % args)
subprocess.check_call(args)
- result = Class1AffinityPredictor.load(models_dir)
- predictions = result.predict(
- peptides=["SLYNTVATL"],
+ # Run model selection
+ models_dir_selected = tempfile.mkdtemp(
+ prefix="mhcflurry-test-models-selected")
+ args = [
+ "mhcflurry-class1-select-pan-allele-models",
+ "--data", os.path.join(models_dir, "train_data.csv.bz2"),
+ "--models-dir", models_dir,
+ "--out-models-dir", models_dir_selected,
+ "--max-models", "1",
+ "--num-jobs", str(n_jobs),
+ ] + additional_args
+ print("Running with args: %s" % args)
+ subprocess.check_call(args)
+
+ result = Class1AffinityPredictor.load(
+ models_dir_selected, optimization_level=0)
+ assert_equal(len(result.neural_networks), 2)
+ predictions = result.predict(peptides=["SLYNTVATL"],
alleles=["HLA-A*02:01"])
assert_equal(predictions.shape, (1,))
assert_array_less(predictions, 1000)
- df = result.predict_to_dataframe(
- peptides=["SLYNTVATL"],
- alleles=["HLA-A*02:01"])
- print(df)
if delete:
print("Deleting: %s" % models_dir)
shutil.rmtree(models_dir)
+ shutil.rmtree(models_dir_selected)
if os.environ.get("KERAS_BACKEND") != "theano":
--
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