Switch from 32 hidden layer size to 16 in standard models

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,

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,

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,

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,

downloads-generation/models_class1_experiments1/hyperparameters-dense16.yaml → 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,

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,

downloads-generation/models_class1_experiments1/hyperparameters-dense8.yaml

+[{
+##########################################
+# 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,
+}]

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,

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,

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,

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,