From 28041d1c2b11a1fb86462219803868f96c142f88 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 1 Dec 2017 16:59:56 -0500
Subject: [PATCH] Switch back to dense=16
---
downloads-generation/models_class1/hyperparameters.yaml | 2 +-
downloads-generation/models_class1_experiments1/GENERATE.sh | 2 +-
.../models_class1_experiments1/hyperparameters-0local.yaml | 2 +-
.../models_class1_experiments1/hyperparameters-0local_noL1.yaml | 2 +-
.../models_class1_experiments1/hyperparameters-2local.yaml | 2 +-
...yperparameters-dense16.yaml => hyperparameters-dense32.yaml} | 2 +-
...hyperparameters-dense64.yaml => hyperparameters-dense8.yaml} | 2 +-
.../models_class1_experiments1/hyperparameters-embedding.yaml | 2 +-
.../models_class1_experiments1/hyperparameters-noL1.yaml | 2 +-
.../models_class1_experiments1/hyperparameters-onehot.yaml | 2 +-
.../models_class1_experiments1/hyperparameters-widelocal.yaml | 2 +-
11 files changed, 11 insertions(+), 11 deletions(-)
rename downloads-generation/models_class1_experiments1/{hyperparameters-dense16.yaml => hyperparameters-dense32.yaml} (99%)
rename downloads-generation/models_class1_experiments1/{hyperparameters-dense64.yaml => hyperparameters-dense8.yaml} (99%)
diff --git a/downloads-generation/models_class1/hyperparameters.yaml b/downloads-generation/models_class1/hyperparameters.yaml
index fd23856c..9d38ad1a 100644
--- a/downloads-generation/models_class1/hyperparameters.yaml
+++ b/downloads-generation/models_class1/hyperparameters.yaml
@@ -42,7 +42,7 @@
],
"activation": "relu",
"output_activation": "sigmoid",
-"layer_sizes": [32],
+"layer_sizes": [16],
"dense_layer_l1_regularization": 0.001,
"batch_normalization": false,
"dropout_probability": 0.0,
diff --git a/downloads-generation/models_class1_experiments1/GENERATE.sh b/downloads-generation/models_class1_experiments1/GENERATE.sh
index adc6ecda..6edd4348 100755
--- a/downloads-generation/models_class1_experiments1/GENERATE.sh
+++ b/downloads-generation/models_class1_experiments1/GENERATE.sh
@@ -40,7 +40,7 @@ time mhcflurry-class1-train-allele-specific-models \
--allele $ALLELES 2>&1 | tee -a LOG.standard.txt &
# Model variations on qualitative + quantitative
-for mod in 0local_noL1 0local 2local widelocal dense16 dense64 noL1 onehot embedding
+for mod in 0local_noL1 0local 2local widelocal dense8 dense32 noL1 onehot embedding
do
cp $SCRIPT_DIR/hyperparameters-${mod}.yaml .
mkdir models-${mod}
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-0local.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-0local.yaml
index 08f1525c..e39d96d6 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-0local.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-0local.yaml
@@ -37,7 +37,7 @@
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
- 32
+ 16
],
"dense_layer_l1_regularization": 0.001,
"batch_normalization": false,
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-0local_noL1.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-0local_noL1.yaml
index 88871342..abe4d296 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-0local_noL1.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-0local_noL1.yaml
@@ -37,7 +37,7 @@
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
- 32
+ 16
],
"dense_layer_l1_regularization": 0.0,
"batch_normalization": false,
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-2local.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-2local.yaml
index a06ab8f7..4ce0eea2 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-2local.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-2local.yaml
@@ -47,7 +47,7 @@
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
- 32
+ 16
],
"dense_layer_l1_regularization": 0.001,
"batch_normalization": false,
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-dense16.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-dense32.yaml
similarity index 99%
rename from downloads-generation/models_class1_experiments1/hyperparameters-dense16.yaml
rename to downloads-generation/models_class1_experiments1/hyperparameters-dense32.yaml
index a714d2ad..ef6b334a 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-dense16.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-dense32.yaml
@@ -42,7 +42,7 @@
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
- 16
+ 32
],
"dense_layer_l1_regularization": 0.001,
"batch_normalization": false,
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-dense64.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-dense8.yaml
similarity index 99%
rename from downloads-generation/models_class1_experiments1/hyperparameters-dense64.yaml
rename to downloads-generation/models_class1_experiments1/hyperparameters-dense8.yaml
index 77ed95e1..b16983a8 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-dense64.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-dense8.yaml
@@ -42,7 +42,7 @@
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
- 64
+ 8
],
"dense_layer_l1_regularization": 0.001,
"batch_normalization": false,
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-embedding.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-embedding.yaml
index 1598f3a1..ea30d9eb 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-embedding.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-embedding.yaml
@@ -43,7 +43,7 @@
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
- 32
+ 16
],
"dense_layer_l1_regularization": 0.001,
"batch_normalization": false,
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-noL1.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-noL1.yaml
index cb910a2e..25c1942b 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-noL1.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-noL1.yaml
@@ -42,7 +42,7 @@
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
- 32
+ 16
],
"dense_layer_l1_regularization": 0.0,
"batch_normalization": false,
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-onehot.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-onehot.yaml
index dad568de..d6c83f93 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-onehot.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-onehot.yaml
@@ -42,7 +42,7 @@
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
- 32
+ 16
],
"dense_layer_l1_regularization": 0.001,
"batch_normalization": false,
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-widelocal.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-widelocal.yaml
index c2a39f14..6123c79f 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-widelocal.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-widelocal.yaml
@@ -43,7 +43,7 @@
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
- 32
+ 16
],
"dense_layer_l1_regularization": 0.001,
"batch_normalization": false,
--
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