From e112e7bce61f09ec4388303228923a046ac372f2 Mon Sep 17 00:00:00 2001
From: Alex Rubinsteyn <alex.rubinsteyn@gmail.com>
Date: Fri, 23 Oct 2015 12:05:35 -0400
Subject: [PATCH] json serialization for models
---
mhcflurry/mhc1_binding_predictor.py | 12 ++++---
.../train-class1-allele-specific-models.py | 34 +++++++++++++++----
2 files changed, 34 insertions(+), 12 deletions(-)
diff --git a/mhcflurry/mhc1_binding_predictor.py b/mhcflurry/mhc1_binding_predictor.py
index bd41aa45..3c5ce32c 100644
--- a/mhcflurry/mhc1_binding_predictor.py
+++ b/mhcflurry/mhc1_binding_predictor.py
@@ -23,10 +23,11 @@ from __future__ import (
from os import listdir
from os.path import exists, join
from itertools import groupby
+import json
import numpy as np
import pandas as pd
-from keras.models import model_from_json
+from keras.models import model_from_config
from .class1_allele_specific_hyperparameters import MAX_IC50
from .data_helpers import index_encoding, normalize_allele_name
@@ -47,7 +48,7 @@ class Mhc1BindingPredictor(object):
raise ValueError(
"No MHC prediction models found in %s" % (model_directory,))
original_allele_name = allele
- self.allele = normalize_allele_name(allele)
+ allele = self.allele = normalize_allele_name(allele)
if self.allele not in _allele_model_cache:
json_filename = self.allele + ".json"
json_path = join(model_directory, json_filename)
@@ -62,10 +63,11 @@ class Mhc1BindingPredictor(object):
raise ValueError("Missing model weights for allele %s" % (
original_allele_name,))
- with open(hdf_path, "r") as f:
- self.model = model_from_json(f.read())
-
+ with open(json_path, "r") as f:
+ json_string = json.load(f)
+ self.model = model_from_config(json_string)
self.model.load_weights(hdf_path)
+
_allele_model_cache[self.allele] = self.model
else:
self.model = _allele_model_cache[self.allele]
diff --git a/scripts/train-class1-allele-specific-models.py b/scripts/train-class1-allele-specific-models.py
index a10e68b1..de9519d7 100755
--- a/scripts/train-class1-allele-specific-models.py
+++ b/scripts/train-class1-allele-specific-models.py
@@ -38,7 +38,7 @@ from __future__ import (
unicode_literals
)
from shutil import rmtree
-from os import makedirs
+from os import makedirs, remove
from os.path import exists, join
import argparse
@@ -81,7 +81,8 @@ parser.add_argument(
default=CSV_PATH,
help="CSV file with 'mhc', 'peptide', 'peptide_length', 'meas' columns")
-parser.add_argument("--min-samples-per-allele",
+parser.add_argument(
+ "--min-samples-per-allele",
default=5,
help="Don't train predictors for alleles with fewer samples than this",
type=int)
@@ -124,19 +125,38 @@ if __name__ == "__main__":
continue
n_allele = len(allele_data.Y)
print("%s: total count = %d" % (allele_name, n_allele))
- filename = allele_name + ".hdf"
- path = join(args.output_dir, filename)
- if exists(path) and not args.overwrite:
+
+ json_filename = allele_name + ".json"
+ json_path = join(args.output_dir, json_filename)
+
+ hdf_filename = allele_name + ".hdf"
+ hdf_path = join(args.output_dir, hdf_filename)
+
+ if exists(json_path) and exists(hdf_path) and not args.overwrite:
print("-- already exists, skipping")
continue
+
if n_allele < args.min_samples_per_allele:
print("-- too few data points, skipping")
continue
+
+ if exists(json_path):
+ print("-- removing old model description %s" % json_path)
+ remove(json_path)
+ if exists(hdf_path):
+ print("-- removing old weights file %s" % hdf_path)
+ remove(hdf_path)
+
model.set_weights(old_weights)
model.fit(
allele_data.X,
allele_data.Y,
nb_epoch=N_EPOCHS,
show_accuracy=True)
- print("Saving model for %s to %s" % (allele_name, path))
- model.save_weights(path)
+ print("Saving model description for %s to %s" % (
+ allele_name, json_path))
+ with open(json_path, "w") as f:
+ f.write(model.to_json())
+ print("Saving model weights for %s to %s" % (
+ allele_name, hdf_path))
+ model.save_weights(hdf_path)
--
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