From ee242d392a1a60494becbd8c23a71076ccf3fdfb Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sun, 26 Nov 2017 10:58:12 -0500
Subject: [PATCH] Switch from 32 hidden layer size to 16 in standard models
---
.../models_class1/hyperparameters.yaml | 2 +-
.../hyperparameters-0local.yaml | 2 +-
.../hyperparameters-0local_noL1.yaml | 2 +-
.../hyperparameters-2local.yaml | 2 +-
...se16.yaml => hyperparameters-dense32.yaml} | 2 +-
.../hyperparameters-dense64.yaml | 2 +-
.../hyperparameters-dense8.yaml | 49 +++++++++++++++++++
.../hyperparameters-embedding.yaml | 2 +-
.../hyperparameters-noL1.yaml | 2 +-
.../hyperparameters-onehot.yaml | 2 +-
.../hyperparameters-widelocal.yaml | 2 +-
11 files changed, 59 insertions(+), 10 deletions(-)
rename downloads-generation/models_class1_experiments1/{hyperparameters-dense16.yaml => hyperparameters-dense32.yaml} (99%)
create mode 100644 downloads-generation/models_class1_experiments1/hyperparameters-dense8.yaml
diff --git a/downloads-generation/models_class1/hyperparameters.yaml b/downloads-generation/models_class1/hyperparameters.yaml
index 7984d882..c6c2c2b6 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
+ 16
],
"dense_layer_l1_regularization": 0.001,
"batch_normalization": false,
diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-0local.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-0local.yaml
index bab32157..f36ec334 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-0local.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-0local.yaml
@@ -36,7 +36,7 @@
"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 62d50637..b7b5fe7a 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-0local_noL1.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-0local_noL1.yaml
@@ -36,7 +36,7 @@
"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 12835560..7f7427c6 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-2local.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-2local.yaml
@@ -46,7 +46,7 @@
"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 b7e4ee44..97fe80ed 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-dense16.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-dense32.yaml
@@ -41,7 +41,7 @@
"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-dense64.yaml
index c63c399d..33fcfd30 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-dense64.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-dense64.yaml
@@ -41,7 +41,7 @@
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
- 64
+ 64
],
"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-dense8.yaml
new file mode 100644
index 00000000..d6933e19
--- /dev/null
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-dense8.yaml
@@ -0,0 +1,49 @@
+[{
+##########################################
+# 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
+"kmer_size": 15,
+
+##########################################
+# NEURAL NETWORK ARCHITECTURE
+##########################################
+"locally_connected_layers": [
+ {
+ "filters": 8,
+ "activation": "tanh",
+ "kernel_size": 3
+ }
+],
+"activation": "relu",
+"output_activation": "sigmoid",
+"layer_sizes": [
+ 8
+],
+"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 40062bd5..a4c8d0b1 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-embedding.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-embedding.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-noL1.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-noL1.yaml
index 5b046c9a..4b02779d 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-noL1.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-noL1.yaml
@@ -41,7 +41,7 @@
"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 1742093d..aade715e 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-onehot.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-onehot.yaml
@@ -41,7 +41,7 @@
"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 cfde02c2..62c4707c 100644
--- a/downloads-generation/models_class1_experiments1/hyperparameters-widelocal.yaml
+++ b/downloads-generation/models_class1_experiments1/hyperparameters-widelocal.yaml
@@ -42,7 +42,7 @@
"activation": "relu",
"output_activation": "sigmoid",
"layer_sizes": [
- 32
+ 16
],
"dense_layer_l1_regularization": 0.001,
"batch_normalization": false,
--
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