Switch back to dense layer size 32 from 16

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,

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}

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,

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,

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,

downloads-generation/models_class1_experiments1/hyperparameters-dense8.yaml → 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,

downloads-generation/models_class1_experiments1/hyperparameters-dense32.yaml

-[{
-##########################################
-# 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,
-}]

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,

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,

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,

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,