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Tim O'Donnell authoredTim O'Donnell authored
select_allele_specific_models_command.py 24.24 KiB
"""
Model select class1 single allele models.
"""
import argparse
import os
import signal
import sys
import time
import traceback
import random
from pprint import pprint
import numpy
import pandas
from scipy.stats import kendalltau, percentileofscore
from mhcnames import normalize_allele_name
import tqdm # progress bar
tqdm.monitor_interval = 0 # see https://github.com/tqdm/tqdm/issues/481
from .class1_affinity_predictor import Class1AffinityPredictor
from .encodable_sequences import EncodableSequences
from .common import configure_logging, random_peptides
from .parallelism import worker_pool_with_gpu_assignments_from_args, add_worker_pool_args
from .regression_target import from_ic50
# To avoid pickling large matrices to send to child processes when running in
# parallel, we use this global variable as a place to store data. Data that is
# stored here before creating the thread pool will be inherited to the child
# processes upon fork() call, allowing us to share large data with the workers
# via shared memory.
GLOBAL_DATA = {}
parser = argparse.ArgumentParser(usage=__doc__)
parser.add_argument(
"--data",
metavar="FILE.csv",
required=False,
help=(
"Model selection data CSV. Expected columns: "
"allele, peptide, measurement_value"))
parser.add_argument(
"--exclude-data",
metavar="FILE.csv",
required=False,
help=(
"Data to EXCLUDE from model selection. Useful to specify the original "
"training data used"))
parser.add_argument(
"--models-dir",
metavar="DIR",
required=True,
help="Directory to read models")
parser.add_argument(
"--out-models-dir",
metavar="DIR",
required=True,
help="Directory to write selected models")
parser.add_argument(
"--out-unselected-predictions",
metavar="FILE.csv",
help="Write predictions for validation data using unselected predictor to "
"FILE.csv")
parser.add_argument(
"--unselected-accuracy-scorer",
metavar="SCORER",
default="combined:mass-spec,mse")
parser.add_argument(
"--unselected-accuracy-scorer-num-samples",
type=int,
default=1000)
parser.add_argument(
"--unselected-accuracy-percentile-threshold",
type=float,
metavar="X",
default=95)
parser.add_argument(
"--allele",
default=None,
nargs="+",
help="Alleles to select models for. If not specified, all alleles with "
"enough measurements will be used.")
parser.add_argument(
"--combined-min-models",
type=int,
default=8,
metavar="N",
help="Min number of models to select per allele when using combined selector")
parser.add_argument(
"--combined-max-models",
type=int,
default=1000,
metavar="N",
help="Max number of models to select per allele when using combined selector")
parser.add_argument(
"--mass-spec-min-measurements",
type=int,
metavar="N",
default=1,
help="Min number of measurements required for an allele to use mass-spec model "
"selection")
parser.add_argument(
"--mass-spec-min-models",
type=int,
default=8,
metavar="N",
help="Min number of models to select per allele when using mass-spec selector")
parser.add_argument(
"--mass-spec-max-models",
type=int,
default=1000,
metavar="N",
help="Max number of models to select per allele when using mass-spec selector")
parser.add_argument(
"--mse-min-measurements",
type=int,
metavar="N",
default=1,
help="Min number of measurements required for an allele to use MSE model "
"selection")
parser.add_argument(
"--mse-min-models",
type=int,
default=8,
metavar="N",
help="Min number of models to select per allele when using MSE selector")
parser.add_argument(
"--mse-max-models",
type=int,
default=1000,
metavar="N",
help="Max number of models to select per allele when using MSE selector")
parser.add_argument(
"--scoring",
nargs="+",
default=["mse", "consensus"],
help="Scoring procedures to use in order")
parser.add_argument(
"--consensus-min-models",
type=int,
default=8,
metavar="N",
help="Min number of models to select per allele when using consensus selector")
parser.add_argument(
"--consensus-max-models",
type=int,
default=1000,
metavar="N",
help="Max number of models to select per allele when using consensus selector")
parser.add_argument(
"--consensus-num-peptides-per-length",
type=int,
default=10000,
help="Num peptides per length to use for consensus scoring")
parser.add_argument(
"--mass-spec-regex",
metavar="REGEX",
default="mass[- ]spec",
help="Regular expression for mass-spec data. Runs on measurement_source col."
"Default: %(default)s.")
parser.add_argument(
"--verbosity",
type=int,
help="Keras verbosity. Default: %(default)s",
default=0)
add_worker_pool_args(parser)
def run(argv=sys.argv[1:]):
global GLOBAL_DATA
# On sigusr1 print stack trace
print("To show stack trace, run:\nkill -s USR1 %d" % os.getpid())
signal.signal(signal.SIGUSR1, lambda sig, frame: traceback.print_stack())
args = parser.parse_args(argv)
args.out_models_dir = os.path.abspath(args.out_models_dir)
configure_logging(verbose=args.verbosity > 1)
input_predictor = Class1AffinityPredictor.load(args.models_dir)
print("Loaded: %s" % input_predictor)
if args.allele:
alleles = [normalize_allele_name(a) for a in args.allele]
else:
alleles = input_predictor.supported_alleles
metadata_dfs = {}
if args.data:
df = pandas.read_csv(args.data)
print("Loaded data: %s" % (str(df.shape)))
df = df.ix[
(df.peptide.str.len() >= 8) & (df.peptide.str.len() <= 15)
]
print("Subselected to 8-15mers: %s" % (str(df.shape)))
# Allele names in data are assumed to be already normalized.
df = df.loc[df.allele.isin(alleles)].dropna()
print("Selected %d alleles: %s" % (len(alleles), ' '.join(alleles)))
if args.exclude_data:
exclude_df = pandas.read_csv(args.exclude_data)
metadata_dfs["model_selection_exclude"] = exclude_df
print("Loaded exclude data: %s" % (str(df.shape)))
df["_key"] = df.allele + "__" + df.peptide
exclude_df["_key"] = exclude_df.allele + "__" + exclude_df.peptide
df["_excluded"] = df._key.isin(exclude_df._key.unique())
print("Excluding measurements per allele (counts): ")
print(df.groupby("allele")._excluded.sum())
print("Excluding measurements per allele (fractions): ")
print(df.groupby("allele")._excluded.mean())
df = df.loc[~df._excluded]
del df["_excluded"]
del df["_key"]
print("Reduced data to: %s" % (str(df.shape)))
metadata_dfs["model_selection_data"] = df
df["mass_spec"] = df.measurement_source.str.contains(
args.mass_spec_regex)
else:
df = None
if args.out_unselected_predictions:
df["unselected_prediction"] = input_predictor.predict(
alleles=df.allele.values,
peptides=df.peptide.values)
df.to_csv(args.out_unselected_predictions)
print("Wrote: %s" % args.out_unselected_predictions)
selectors = {}
selector_to_model_selection_kwargs = {}
def make_selector(scoring):
if scoring in selectors:
return selectors[scoring]
start = time.time()
if scoring.startswith("combined:"):
model_selection_kwargs = {
'min_models': args.combined_min_models,
'max_models': args.combined_max_models,
}
component_selectors = []
for component_selector in scoring.split(":", 1)[1].split(","):
component_selectors.append(
make_selector(
component_selector)[0])
selector = CombinedModelSelector(component_selectors)
elif scoring == "mse":
model_selection_kwargs = {
'min_models': args.mse_min_models,
'max_models': args.mse_max_models,
}
min_measurements = args.mse_min_measurements
selector = MSEModelSelector(
df=df.loc[~df.mass_spec],
predictor=input_predictor,
min_measurements=min_measurements)
elif scoring == "mass-spec":
mass_spec_df = df.loc[df.mass_spec]
model_selection_kwargs = {
'min_models': args.mass_spec_min_models,
'max_models': args.mass_spec_max_models,
}
min_measurements = args.mass_spec_min_measurements
selector = MassSpecModelSelector(
df=mass_spec_df,
predictor=input_predictor,
min_measurements=min_measurements)
elif scoring == "consensus":
model_selection_kwargs = {
'min_models': args.consensus_min_models,
'max_models': args.consensus_max_models,
}
selector = ConsensusModelSelector(
predictor=input_predictor,
num_peptides_per_length=args.consensus_num_peptides_per_length)
else:
raise ValueError("Unsupported scoring method: %s" % scoring)
print("Instantiated model selector %s in %0.2f sec." % (
scoring, time.time() - start))
return (selector, model_selection_kwargs)
for scoring in args.scoring:
(selector, model_selection_kwargs) = make_selector(scoring)
selectors[scoring] = selector
selector_to_model_selection_kwargs[scoring] = model_selection_kwargs
unselected_accuracy_scorer = None
if args.unselected_accuracy_scorer:
unselected_accuracy_scorer = make_selector(args.unselected_accuracy_scorer)[0]
print("Using unselected accuracy scorer: %s" % unselected_accuracy_scorer)
GLOBAL_DATA["unselected_accuracy_scorer"] = unselected_accuracy_scorer
print("Selectors for alleles:")
allele_to_selector = {}
allele_to_model_selection_kwargs = {}
for allele in alleles:
selector = None
for possible_selector in args.scoring:
if selectors[possible_selector].usable_for_allele(allele=allele):
selector = selectors[possible_selector]
print("%20s %s" % (allele, selector.plan_summary(allele)))
break
if selector is None:
raise ValueError("No selectors usable for allele: %s" % allele)
allele_to_selector[allele] = selector
allele_to_model_selection_kwargs[allele] = (
selector_to_model_selection_kwargs[possible_selector])
GLOBAL_DATA["args"] = args
GLOBAL_DATA["input_predictor"] = input_predictor
GLOBAL_DATA["unselected_accuracy_scorer"] = unselected_accuracy_scorer
GLOBAL_DATA["allele_to_selector"] = allele_to_selector
GLOBAL_DATA["allele_to_model_selection_kwargs"] = allele_to_model_selection_kwargs
if not os.path.exists(args.out_models_dir):
print("Attempting to create directory: %s" % args.out_models_dir)
os.mkdir(args.out_models_dir)
print("Done.")
result_predictor = Class1AffinityPredictor(metadata_dataframes=metadata_dfs)
worker_pool = worker_pool_with_gpu_assignments_from_args(args)
start = time.time()
if worker_pool is None:
# Serial run
print("Running in serial.")
results = (
model_select(allele) for allele in alleles)
else:
# Parallel run
random.shuffle(alleles)
results = worker_pool.imap_unordered(
model_select,
alleles,
chunksize=1)
unselected_summary = []
model_selection_dfs = []
for result in tqdm.tqdm(results, total=len(alleles)):
pprint(result)
summary_dict = dict(result)
summary_dict["retained"] = result["selected"] is not None
del summary_dict["selected"]
unselected_summary.append(summary_dict)
if result['selected'] is not None:
model_selection_dfs.append(
result['selected'].metadata_dataframes['model_selection'])
result_predictor.merge_in_place([result['selected']])
if model_selection_dfs:
model_selection_df = pandas.concat(
model_selection_dfs, ignore_index=True)
model_selection_df["selector"] = model_selection_df.allele.map(
allele_to_selector)
result_predictor.metadata_dataframes["model_selection"] = (
model_selection_df)
result_predictor.metadata_dataframes["unselected_summary"] = (
pandas.DataFrame(unselected_summary))
print("Done model selecting for %d alleles." % len(alleles))
result_predictor.save(args.out_models_dir)
model_selection_time = time.time() - start
if worker_pool:
worker_pool.close()
worker_pool.join()
print("Model selection time %0.2f min." % (model_selection_time / 60.0))
print("Predictor written to: %s" % args.out_models_dir)
class ScrambledPredictor(object):
def __init__(self, predictor):
self.predictor = predictor
self._predictions = {}
self._allele = None
def predict(self, peptides, allele):
if peptides not in self._predictions:
self._predictions[peptides] = pandas.Series(
self.predictor.predict(peptides=peptides, allele=allele))
self._allele = allele
assert allele == self._allele
return self._predictions[peptides].sample(frac=1.0).values
def model_select(allele):
global GLOBAL_DATA
unselected_accuracy_scorer = GLOBAL_DATA["unselected_accuracy_scorer"]
selector = GLOBAL_DATA["allele_to_selector"][allele]
model_selection_kwargs = GLOBAL_DATA[
"allele_to_model_selection_kwargs"
][allele]
predictor = GLOBAL_DATA["input_predictor"]
args = GLOBAL_DATA["args"]
unselected_accuracy_scorer_samples = GLOBAL_DATA["args"].unselected_accuracy_scorer_num_samples
result_dict = {
"allele": allele
}
unselected_score = None
unselected_score_percentile = None
unselected_score_scrambled_mean = None
if unselected_accuracy_scorer:
unselected_score_function = (
unselected_accuracy_scorer.score_function(allele))
unselected_score = unselected_score_function(predictor)
scrambled_predictor = ScrambledPredictor(predictor)
scrambled_scores = numpy.array([
unselected_score_function(scrambled_predictor)
for _ in range(unselected_accuracy_scorer_samples)
])
unselected_score_scrambled_mean = scrambled_scores.mean()
unselected_score_percentile = percentileofscore(
scrambled_scores, unselected_score)
print(
"Unselected score and percentile",
allele,
unselected_score,
unselected_score_percentile)
selected = None
threshold = args.unselected_accuracy_percentile_threshold
if unselected_score_percentile is None or unselected_score_percentile >= threshold:
selected = predictor.model_select(
score_function=selector.score_function(allele=allele),
alleles=[allele],
**model_selection_kwargs)
result_dict["unselected_score_plan"] = (
unselected_accuracy_scorer.plan_summary(allele)
if unselected_accuracy_scorer else None)
result_dict["selector_score_plan"] = selector.plan_summary(allele)
result_dict["unselected_accuracy_score_percentile"] = unselected_score_percentile
result_dict["unselected_score"] = unselected_score
result_dict["unselected_score_scrambled_mean"] = unselected_score_scrambled_mean
result_dict["selected"] = selected
result_dict["num_models"] = len(selected.neural_networks) if selected else None
return result_dict
def cache_encoding(predictor, peptides):
# Encode the peptides for each neural network, so the encoding
# becomes cached.
for network in predictor.neural_networks:
network.peptides_to_network_input(peptides)
class ScoreFunction(object):
def __init__(self, function, summary=None):
self.function = function
self.summary = summary if summary else "(n/a)"
def __call__(self, *args, **kwargs):
return self.function(*args, **kwargs)
class CombinedModelSelector(object):
def __init__(self, model_selectors, weights=None):
if weights is None:
weights = numpy.ones(shape=(len(model_selectors),))
self.model_selectors = model_selectors
self.selector_to_weight = dict(zip(self.model_selectors, weights))
def usable_for_allele(self, allele):
return any(
selector.usable_for_allele(allele)
for selector in self.model_selectors)
def plan_summary(self, allele):
return self.score_function(allele, dry_run=True).summary
def score_function(self, allele, dry_run=False):
selector_to_max_weighted_score = {}
for selector in self.model_selectors:
weight = self.selector_to_weight[selector]
if selector.usable_for_allele(allele):
max_weighted_score = selector.max_absolute_value(allele) * weight
else:
max_weighted_score = 0
selector_to_max_weighted_score[selector] = max_weighted_score
max_total_score = sum(selector_to_max_weighted_score.values())
# Use only selectors that can contribute >1% to the total score
selectors_to_use = [
selector
for selector in self.model_selectors
if selector_to_max_weighted_score[selector] > max_total_score / 100.
]
summary = ", ".join([
"%s(|%.3f|)" % (
selector.plan_summary(allele),
selector_to_max_weighted_score[selector])
for selector in selectors_to_use
])
if dry_run:
score = None
else:
score_functions_and_weights = [
(selector.score_function(allele=allele),
self.selector_to_weight[selector])
for selector in selectors_to_use
]
def score(predictor):
scores = numpy.array([
score_function(predictor) * weight
for (score_function, weight) in score_functions_and_weights
])
return scores.sum()
return ScoreFunction(score, summary=summary)
class ConsensusModelSelector(object):
def __init__(
self,
predictor,
num_peptides_per_length=10000,
multiply_score_by_value=10.0):
(min_length, max_length) = predictor.supported_peptide_lengths
peptides = []
for length in range(min_length, max_length + 1):
peptides.extend(
random_peptides(num_peptides_per_length, length=length))
self.peptides = EncodableSequences.create(peptides)
self.predictor = predictor
self.multiply_score_by_value = multiply_score_by_value
cache_encoding(self.predictor, self.peptides)
def usable_for_allele(self, allele):
return True
def max_absolute_value(self, allele):
return self.multiply_score_by_value
def plan_summary(self, allele):
return "consensus (%d points)" % len(self.peptides)
def score_function(self, allele):
full_ensemble_predictions = self.predictor.predict(
allele=allele,
peptides=self.peptides)
def score(predictor):
predictions = predictor.predict(
allele=allele,
peptides=self.peptides,
)
return (
kendalltau(predictions, full_ensemble_predictions).correlation *
self.multiply_score_by_value)
return ScoreFunction(
score, summary=self.plan_summary(allele))
class MSEModelSelector(object):
def __init__(
self,
df,
predictor,
min_measurements=1,
multiply_score_by_data_size=True):
self.df = df
self.predictor = predictor
self.min_measurements = min_measurements
self.multiply_score_by_data_size = multiply_score_by_data_size
def usable_for_allele(self, allele):
return (self.df.allele == allele).sum() >= self.min_measurements
def max_absolute_value(self, allele):
if self.multiply_score_by_data_size:
return (self.df.allele == allele).sum()
else:
return 1.0
def plan_summary(self, allele):
return self.score_function(allele).summary
def score_function(self, allele):
sub_df = self.df.loc[self.df.allele == allele]
peptides = EncodableSequences.create(sub_df.peptide.values)
def score(predictor):
predictions = predictor.predict(
allele=allele,
peptides=peptides,
)
deviations = from_ic50(predictions) - from_ic50(
sub_df.measurement_value)
if 'measurement_inequality' in sub_df.columns:
# Must reverse meaning of inequality since we are working with
# transformed 0-1 values, which are anti-correlated with the ic50s.
# The measurement_inequality column is given in terms of ic50s.
deviations.loc[
(
(sub_df.measurement_inequality == "<") & (deviations > 0)) |
((sub_df.measurement_inequality == ">") & (deviations < 0))
] = 0.0
return (1 - (deviations ** 2).mean()) * (
len(sub_df) if self.multiply_score_by_data_size else 1)
summary = "mse (%d points)" % (len(sub_df))
return ScoreFunction(score, summary=summary)
class MassSpecModelSelector(object):
def __init__(
self,
df,
predictor,
decoys_per_length=0,
min_measurements=100,
multiply_score_by_data_size=True):
# Index is peptide, columns are alleles
hit_matrix = df.groupby(
["peptide", "allele"]).measurement_value.count().unstack().fillna(
0).astype(bool)
if decoys_per_length:
(min_length, max_length) = predictor.supported_peptide_lengths
decoys = []
for length in range(min_length, max_length + 1):
decoys.extend(
random_peptides(decoys_per_length, length=length))
decoy_matrix = pandas.DataFrame(
index=decoys, columns=hit_matrix.columns, dtype=bool)
decoy_matrix[:] = False
full_matrix = pandas.concat([hit_matrix, decoy_matrix])
else:
full_matrix = hit_matrix
if len(full_matrix) > 0:
full_matrix = full_matrix.sample(frac=1.0).astype(float)
self.df = full_matrix
self.predictor = predictor
self.min_measurements = min_measurements
self.multiply_score_by_data_size = multiply_score_by_data_size
self.peptides = EncodableSequences.create(full_matrix.index.values)
cache_encoding(self.predictor, self.peptides)
@staticmethod
def ppv(y_true, predictions):
df = pandas.DataFrame({"prediction": predictions, "y_true": y_true})
return df.sort_values("prediction", ascending=True)[
: int(y_true.sum())
].y_true.mean()
def usable_for_allele(self, allele):
return allele in self.df.columns and (
self.df[allele].sum() >= self.min_measurements)
def max_absolute_value(self, allele):
if self.multiply_score_by_data_size:
return self.df[allele].sum()
else:
return 1.0
def plan_summary(self, allele):
return self.score_function(allele).summary
def score_function(self, allele):
total_hits = self.df[allele].sum()
total_decoys = (self.df[allele] == 0).sum()
multiplier = total_hits if self.multiply_score_by_data_size else 1
def score(predictor):
predictions = predictor.predict(
allele=allele,
peptides=self.peptides,
)
return self.ppv(self.df[allele], predictions) * multiplier
summary = "mass-spec (%d hits / %d decoys)" % (total_hits, total_decoys)
return ScoreFunction(score, summary=summary)
if __name__ == '__main__':
run()