From d65f774059bc3388db6afda3e5db868a62799e89 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Thu, 30 Nov 2017 10:10:35 -0500
Subject: [PATCH] Switch back to dense layer size 32 from 16
---
.../models_class1/hyperparameters.yaml | 4 +-
.../models_class1_experiments1/GENERATE.sh | 2 +-
.../hyperparameters-0local.yaml | 2 +-
.../hyperparameters-0local_noL1.yaml | 2 +-
.../hyperparameters-2local.yaml | 2 +-
...nse8.yaml => hyperparameters-dense16.yaml} | 2 +-
.../hyperparameters-dense32.yaml | 50 -------------------
.../hyperparameters-embedding.yaml | 2 +-
.../hyperparameters-noL1.yaml | 2 +-
.../hyperparameters-onehot.yaml | 2 +-
.../hyperparameters-widelocal.yaml | 2 +-
11 files changed, 10 insertions(+), 62 deletions(-)
rename downloads-generation/models_class1_experiments1/{hyperparameters-dense8.yaml => hyperparameters-dense16.yaml} (99%)
delete mode 100644 downloads-generation/models_class1_experiments1/hyperparameters-dense32.yaml
diff --git a/downloads-generation/models_class1/hyperparameters.yaml b/downloads-generation/models_class1/hyperparameters.yaml
index 964cc7e5..fd23856c 100644
--- a/downloads-generation/models_class1/hyperparameters.yaml
+++ b/downloads-generation/models_class1/hyperparameters.yaml
@@ -42,9 +42,7 @@
],
"activation": "relu",
"output_activation": "sigmoid",
-"layer_sizes": [
- 16
-],
+"layer_sizes": [32],
"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 da0354ea..adc6ecda 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 dense8 dense32 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}
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-0local.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-0local.yaml
index 25e4410c..08f1525c 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": [
- 16
+ 32
],
"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 abe4d296..88871342 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": [
- 16
+ 32
],
"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 61319daa..a06ab8f7 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": [
- 16
+ 32
],
"dense_layer_l1_regularization": 0.001,
"batch_normalization": false,
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-dense8.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-dense16.yaml
similarity index 99%
rename from downloads-generation/models_class1_experiments1/hyperparameters-dense8.yaml
rename to downloads-generation/models_class1_experiments1/hyperparameters-dense16.yaml
index 1c2d48d3..a714d2ad 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-dense8.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-dense16.yaml
@@ -42,7 +42,7 @@
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
- 8
+ 16
],
"dense_layer_l1_regularization": 0.001,
"batch_normalization": false,
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-dense32.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-dense32.yaml
deleted file mode 100644
index a1dd1af4..00000000
--- a/downloads-generation/models_class1_experiments1/hyperparameters-dense32.yaml
+++ /dev/null
@@ -1,50 +0,0 @@
-[{
-##########################################
-# ENSEMBLE SIZE
-##########################################
-"n_models": 8,
-
-##########################################
-# OPTIMIZATION
-##########################################
-"max_epochs": 500,
-"patience": 10,
-"early_stopping": true,
-"validation_split": 0.2,
-"minibatch_size": 128,
-
-##########################################
-# 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
-"kmer_size": 15,
-
-##########################################
-# NEURAL NETWORK ARCHITECTURE
-##########################################
-"locally_connected_layers": [
- {
- "filters": 8,
- "activation": "tanh",
- "kernel_size": 3
- }
-],
-"activation": "relu",
-"output_activation": "sigmoid",
-"layer_sizes": [
- 32
-],
-"dense_layer_l1_regularization": 0.001,
-"batch_normalization": false,
-"dropout_probability": 0.0,
-}]
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-embedding.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-embedding.yaml
index 0bfed0e1..1598f3a1 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": [
- 16
+ 32
],
"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 4d3f9ced..cb910a2e 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": [
- 16
+ 32
],
"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 a8c14b14..dad568de 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": [
- 16
+ 32
],
"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 a927bdd5..c2a39f14 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": [
- 16
+ 32
],
"dense_layer_l1_regularization": 0.001,
"batch_normalization": false,
--
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