From 7f1e6c99ca3a113ee66af575079bcec0fba25036 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Thu, 27 Jul 2017 12:17:02 -0400
Subject: [PATCH] Script and experiment updates
* Add more experiments to models_class1_experiments
* Add `--quantitative-only` flag to training script
* Add `--no-throw` flag to prediction script
---
.../models_class1_experiments1/GENERATE.sh | 13 +++++++++-
.../hyperparameters-0local.json | 2 +-
.../hyperparameters-0local_noL1.json | 26 +++++++++++++++++++
.../hyperparameters-standard.json | 1 +
.../train_allele_specific_models_command.py | 11 ++++++++
mhcflurry/predict_command.py | 8 +++++-
6 files changed, 58 insertions(+), 3 deletions(-)
create mode 100644 downloads-generation/models_class1_experiments1/hyperparameters-0local_noL1.json
create mode 120000 downloads-generation/models_class1_experiments1/hyperparameters-standard.json
diff --git a/downloads-generation/models_class1_experiments1/GENERATE.sh b/downloads-generation/models_class1_experiments1/GENERATE.sh
index b92b2701..989fb5ce 100755
--- a/downloads-generation/models_class1_experiments1/GENERATE.sh
+++ b/downloads-generation/models_class1_experiments1/GENERATE.sh
@@ -23,7 +23,18 @@ git status
cd $SCRATCH_DIR/$DOWNLOAD_NAME
-for mod in 0local 1local dense16 dense64 noL1
+# Standard architecture on quantitative only
+cp $SCRIPT_DIR/hyperparameters-standard.json .
+mkdir models-standard-quantitative
+time mhcflurry-class1-train-allele-specific-models \
+ --data "$(mhcflurry-downloads path data_curated)/curated_training_data.csv.bz2" \
+ --only-quantitative \
+ --hyperparameters hyperparameters-standard.json \
+ --out-models-dir models-standard-quantitative \
+ --min-measurements-per-allele 100
+
+# Model variations on qualitative + quantitative
+for mod in 0local_noL1 0local 1local dense16 dense64 noL1
do
cp $SCRIPT_DIR/hyperparameters-${mod}.json .
mkdir models-${mod}
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-0local.json b/downloads-generation/models_class1_experiments1/hyperparameters-0local.json
index 82f5a361..b39d5b60 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-0local.json
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-0local.json
@@ -23,4 +23,4 @@
"dense_layer_l1_regularization": 0.001,
"dropout_probability": 0.0
}
-]
\ No newline at end of file
+]
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-0local_noL1.json b/downloads-generation/models_class1_experiments1/hyperparameters-0local_noL1.json
new file mode 100644
index 00000000..82f5a361
--- /dev/null
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-0local_noL1.json
@@ -0,0 +1,26 @@
+[
+ {
+ "n_models": 8,
+ "max_epochs": 500,
+ "patience": 10,
+ "early_stopping": true,
+ "validation_split": 0.2,
+
+ "random_negative_rate": 0.0,
+ "random_negative_constant": 25,
+
+ "use_embedding": false,
+ "kmer_size": 15,
+ "batch_normalization": false,
+ "locally_connected_layers": [],
+ "activation": "relu",
+ "output_activation": "sigmoid",
+ "layer_sizes": [
+ 32
+ ],
+ "random_negative_affinity_min": 20000.0,
+ "random_negative_affinity_max": 50000.0,
+ "dense_layer_l1_regularization": 0.001,
+ "dropout_probability": 0.0
+ }
+]
\ No newline at end of file
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-standard.json b/downloads-generation/models_class1_experiments1/hyperparameters-standard.json
new file mode 120000
index 00000000..8d78d631
--- /dev/null
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-standard.json
@@ -0,0 +1 @@
+../models_class1/hyperparameters.json
\ No newline at end of file
diff --git a/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py b/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py
index 212e8918..6e03489d 100644
--- a/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py
+++ b/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py
@@ -43,6 +43,11 @@ parser.add_argument(
metavar="N",
default=50,
help="Train models for alleles with >=N measurements.")
+parser.add_argument(
+ "--only-quantitative",
+ action="store_true",
+ default=False,
+ help="Use only quantitative training data")
parser.add_argument(
"--verbosity",
type=int,
@@ -67,6 +72,12 @@ def run(argv=sys.argv[1:]):
]
print("Subselected to 8-15mers: %s" % (str(df.shape)))
+ if args.only_quantitative:
+ df = df.loc[
+ df.measurement_type == "quantitative"
+ ]
+ print("Subselected to quantitative: %s" % (str(df.shape)))
+
allele_counts = df.allele.value_counts()
if args.allele:
diff --git a/mhcflurry/predict_command.py b/mhcflurry/predict_command.py
index 40cb7130..f3a4a201 100644
--- a/mhcflurry/predict_command.py
+++ b/mhcflurry/predict_command.py
@@ -105,6 +105,11 @@ input_mod_args.add_argument(
metavar="NAME",
default="peptide",
help="Input column name for peptides. Default: '%(default)s'")
+input_mod_args.add_argument(
+ "--no-throw",
+ action="store_true",
+ default=False,
+ help="Return NaNs for unsupported alleles or peptides instead of raising")
output_args = parser.add_argument_group(title="Optional output modifiers")
@@ -200,7 +205,8 @@ def run(argv=sys.argv[1:]):
predictions = predictor.predict_to_dataframe(
peptides=df[args.peptide_column].values,
alleles=df[args.allele_column].values,
- include_individual_model_predictions=args.include_individual_model_predictions)
+ include_individual_model_predictions=args.include_individual_model_predictions,
+ throw=not args.no_throw)
for col in predictions.columns:
if col not in ("allele", "peptide"):
--
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