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Commit 1c37ad3a authored by Tim O'Donnell's avatar Tim O'Donnell
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change models_class1_experiments1 to run each experiment in separate scripts

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downloads-generation/data_curated/GENERATE.sh
+ 1
− 1
View file @ 1c37ad3a
......@@ -4,7 +4,7 @@ set -e
set -x
DOWNLOAD_NAME=data_curated
SCRATCH_DIR=/tmp/mhcflurry-downloads-generation
SCRATCH_DIR=${TMPDIR-/tmp}/mhcflurry-downloads-generation
SCRIPT_ABSOLUTE_PATH="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/$(basename "${BASH_SOURCE[0]}")"
SCRIPT_DIR=$(dirname "$SCRIPT_ABSOLUTE_PATH")
export PYTHONUNBUFFERED=1
......
downloads-generation/data_iedb/GENERATE.sh
+ 1
− 1
View file @ 1c37ad3a
......@@ -4,7 +4,7 @@ set -e
set -x
DOWNLOAD_NAME=data_iedb
SCRATCH_DIR=/tmp/mhcflurry-downloads-generation
SCRATCH_DIR=${TMPDIR-/tmp}/mhcflurry-downloads-generation
SCRIPT_ABSOLUTE_PATH="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/$(basename "${BASH_SOURCE[0]}")"
mkdir -p "$SCRATCH_DIR"
......
downloads-generation/data_kim2014/GENERATE.sh
+ 1
− 1
View file @ 1c37ad3a
......@@ -4,7 +4,7 @@ set -e
set -x
DOWNLOAD_NAME=data_kim2014
SCRATCH_DIR=/tmp/mhcflurry-downloads-generation
SCRATCH_DIR=${TMPDIR-/tmp}/mhcflurry-downloads-generation
SCRIPT_ABSOLUTE_PATH="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/$(basename "${BASH_SOURCE[0]}")"
mkdir -p "$SCRATCH_DIR"
......
downloads-generation/models_class1/GENERATE.sh
+ 1
− 1
View file @ 1c37ad3a
......@@ -4,7 +4,7 @@ set -e
set -x
DOWNLOAD_NAME=models_class1
SCRATCH_DIR=/tmp/mhcflurry-downloads-generation
SCRATCH_DIR=${TMPDIR-/tmp}/mhcflurry-downloads-generation
SCRIPT_ABSOLUTE_PATH="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/$(basename "${BASH_SOURCE[0]}")"
SCRIPT_DIR=$(dirname "$SCRIPT_ABSOLUTE_PATH")
......
downloads-generation/models_class1_experiments1/GENERATE.sh
+ 10
− 9
View file @ 1c37ad3a
......@@ -23,15 +23,16 @@ git status
cd $SCRATCH_DIR/$DOWNLOAD_NAME
mkdir models
cp $SCRIPT_DIR/hyperparameters.json .
time mhcflurry-class1-train-allele-specific-models \
--data "$(mhcflurry-downloads path data_curated)/curated_training_data.csv.bz2" \
--hyperparameters hyperparameters.json \
--out-models-dir models \
--min-measurements-per-allele 100
for mod in 0local 1local dense16 dense64 noL1
do
cp $SCRIPT_DIR/hyperparameters-${mod}.json .
mkdir models-${mod}
time mhcflurry-class1-train-allele-specific-models \
--data "$(mhcflurry-downloads path data_curated)/curated_training_data.csv.bz2" \
--hyperparameters hyperparameters-${mod}.json \
--out-models-dir models-${mod} \
--min-measurements-per-allele 100
done
cp $SCRIPT_ABSOLUTE_PATH .
bzip2 LOG.txt
......
downloads-generation/models_class1_experiments1/hyperparameters-0local.json 0 → 100644
+ 26
− 0
View file @ 1c37ad3a
[
{
"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
downloads-generation/models_class1_experiments1/hyperparameters-1local.json 0 → 100644
+ 32
− 0
View file @ 1c37ad3a
[
{
"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": [
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
}
],
"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
downloads-generation/models_class1_experiments1/hyperparameters-dense16.json 0 → 100644
+ 37
− 0
View file @ 1c37ad3a
[
{
"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": [
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
},
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
}
],
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
16
],
"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
downloads-generation/models_class1_experiments1/hyperparameters-dense64.json 0 → 100644
+ 37
− 0
View file @ 1c37ad3a
[
{
"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": [
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
},
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
}
],
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
64
],
"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
downloads-generation/models_class1_experiments1/hyperparameters-noL1.json 0 → 100644
+ 37
− 0
View file @ 1c37ad3a
[
{
"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": [
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
},
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
}
],
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
32
],
"random_negative_affinity_min": 20000.0,
"random_negative_affinity_max": 50000.0,
"dense_layer_l1_regularization": 0.0,
"dropout_probability": 0.0
}
]
downloads-generation/models_class1_experiments1/hyperparameters.json deleted 100644 → 0
+ 0
− 194
View file @ d154bcbd
[
{
"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": [
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
},
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
}
],
"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
},
{
"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": [
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
}
],
"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
},
{
"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
},
{
"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": [
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
},
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
}
],
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
32
],
"random_negative_affinity_min": 20000.0,
"random_negative_affinity_max": 50000.0,
"dense_layer_l1_regularization": 0.0,
"dropout_probability": 0.0
},
{
"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": [
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
},
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
}
],
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
64
],
"random_negative_affinity_min": 20000.0,
"random_negative_affinity_max": 50000.0,
"dense_layer_l1_regularization": 0.001,
"dropout_probability": 0.0
},
{
"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": [
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
},
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
}
],
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
16
],
"random_negative_affinity_min": 20000.0,
"random_negative_affinity_max": 50000.0,
"dense_layer_l1_regularization": 0.001,
"dropout_probability": 0.0
}
]
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