model select over fewer hyperparameters

downloads-generation/models_class1/generate_hyperparameters.py

@@ -64,8 +64,8 @@ base_hyperparameters = {
 
 grid = []
 for train_subset in ["all", "quantitative"]:
-    for minibatch_size in [128, 512]:
-        for dense_layer_size in [8, 16, 32, 64, 128]:
+    for minibatch_size in [32]:
+        for dense_layer_size in [8, 16, 32, 64]:
             for l1 in [0.0, 0.001]:
                 for num_lc in [0, 1, 2]:
                     for lc_kernel_size in [3, 5]:

downloads-generation/models_class1_unselected/GENERATE.sh

@@ -38,6 +38,7 @@ PROCESSORS=$(getconf _NPROCESSORS_ONLN)
 echo "Detected processors: $PROCESSORS"
 
 time mhcflurry-class1-train-allele-specific-models \
+    --allele HLA-A*02:01 HLA-A*01:01 HLA-A*03:01 HLA-A*11:01 HLA-A*24:02 HLA-B*07:02 HLA-B*15:01 \
     --data "$(mhcflurry-downloads path data_curated)/curated_training_data.no_mass_spec.csv.bz2" \
     --hyperparameters hyperparameters.yaml \
     --out-models-dir models \