From 700535fa58a6854280f15f75fdf0df8f49764bf6 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sat, 25 Nov 2017 14:34:59 -0500
Subject: [PATCH] add widelocal variant
---
.../models_class1_experiments1/GENERATE.sh | 11 ++--
.../hyperparameters-widelocal.yaml | 50 +++++++++++++++++++
2 files changed, 57 insertions(+), 4 deletions(-)
create mode 100644 downloads-generation/models_class1_experiments1/hyperparameters-widelocal.yaml
diff --git a/downloads-generation/models_class1_experiments1/GENERATE.sh b/downloads-generation/models_class1_experiments1/GENERATE.sh
index 3afe151f..ae40082a 100755
--- a/downloads-generation/models_class1_experiments1/GENERATE.sh
+++ b/downloads-generation/models_class1_experiments1/GENERATE.sh
@@ -34,10 +34,10 @@ time mhcflurry-class1-train-allele-specific-models \
--hyperparameters hyperparameters-standard.yaml \
--out-models-dir models-standard-quantitative \
--percent-rank-calibration-num-peptides-per-length 0 \
- --alleles $ALLELES &
+ --allele $ALLELES 2>&1 | tee -a LOG.standard.txt &
# Model variations on qualitative + quantitative
-for mod in 0local_noL1 0local 2local dense16 dense64 noL1 onehot embedding
+for mod in 0local_noL1 0local 2local widelocal dense16 dense64 noL1 onehot embedding
do
cp $SCRIPT_DIR/hyperparameters-${mod}.yaml .
mkdir models-${mod}
@@ -46,12 +46,15 @@ do
--hyperparameters hyperparameters-${mod}.yaml \
--out-models-dir models-${mod} \
--percent-rank-calibration-num-peptides-per-length 0 \
- --alleles $ALLELES &
+ --allele $ALLELES 2>&1 | tee -a LOG.${mod}.txt &
done
wait
cp $SCRIPT_ABSOLUTE_PATH .
-bzip2 LOG.txt
+for i in $(ls *.txt)
+do
+ bzip2 $i
+done
tar -cjf "../${DOWNLOAD_NAME}.tar.bz2" *
echo "Created archive: $SCRATCH_DIR/$DOWNLOAD_NAME.tar.bz2"
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-widelocal.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-widelocal.yaml
new file mode 100644
index 00000000..cfde02c2
--- /dev/null
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-widelocal.yaml
@@ -0,0 +1,50 @@
+[{
+##########################################
+# ENSEMBLE SIZE
+##########################################
+"n_models": 8,
+
+##########################################
+# OPTIMIZATION
+##########################################
+"max_epochs": 500,
+"patience": 10,
+"early_stopping": true,
+"validation_split": 0.2,
+
+##########################################
+# RANDOM NEGATIVE PEPTIDES
+##########################################
+"random_negative_rate": 0.0,
+"random_negative_constant": 25,
+"random_negative_affinity_min": 20000.0,
+"random_negative_affinity_max": 50000.0,
+
+##########################################
+# PEPTIDE REPRESENTATION
+##########################################
+# One of "one-hot", "embedding", or "BLOSUM62".
+"peptide_amino_acid_encoding": "BLOSUM62",
+"use_embedding": false, # maintained for backward compatability
+"embedding_output_dim": 8, # only used if using embedding
+"kmer_size": 15,
+
+##########################################
+# NEURAL NETWORK ARCHITECTURE
+##########################################
+"locally_connected_layers": [
+ {
+ "filters": 8,
+ "activation": "tanh",
+ "kernel_size": 5
+ }
+],
+"activation": "relu",
+"output_activation": "sigmoid",
+"layer_sizes": [
+ 32
+],
+"dense_layer_l1_regularization": 0.001,
+"batch_normalization": false,
+"dropout_probability": 0.0,
+}]
--
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