From b72fa21424d4e78665c1f8970c9e9b5066780e1b Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 12 Feb 2018 16:15:14 -0500
Subject: [PATCH] model select over fewer hyperparameters
---
.../models_class1/generate_hyperparameters.py | 4 ++--
downloads-generation/models_class1_unselected/GENERATE.sh | 1 +
2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/downloads-generation/models_class1/generate_hyperparameters.py b/downloads-generation/models_class1/generate_hyperparameters.py
index 579e88da..65491eaf 100644
--- a/downloads-generation/models_class1/generate_hyperparameters.py
+++ b/downloads-generation/models_class1/generate_hyperparameters.py
@@ -64,8 +64,8 @@ base_hyperparameters = {
grid = []
for train_subset in ["all", "quantitative"]:
- for minibatch_size in [128, 512]:
- for dense_layer_size in [8, 16, 32, 64, 128]:
+ for minibatch_size in [32]:
+ for dense_layer_size in [8, 16, 32, 64]:
for l1 in [0.0, 0.001]:
for num_lc in [0, 1, 2]:
for lc_kernel_size in [3, 5]:
diff --git a/downloads-generation/models_class1_unselected/GENERATE.sh b/downloads-generation/models_class1_unselected/GENERATE.sh
index a3cdb5c0..f9f3545c 100755
--- a/downloads-generation/models_class1_unselected/GENERATE.sh
+++ b/downloads-generation/models_class1_unselected/GENERATE.sh
@@ -38,6 +38,7 @@ PROCESSORS=$(getconf _NPROCESSORS_ONLN)
echo "Detected processors: $PROCESSORS"
time mhcflurry-class1-train-allele-specific-models \
+ --allele HLA-A*02:01 HLA-A*01:01 HLA-A*03:01 HLA-A*11:01 HLA-A*24:02 HLA-B*07:02 HLA-B*15:01 \
--data "$(mhcflurry-downloads path data_curated)/curated_training_data.no_mass_spec.csv.bz2" \
--hyperparameters hyperparameters.yaml \
--out-models-dir models \
--
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