update models_class1_no_mass_spec

downloads-generation/models_class1_no_mass_spec/GENERATE.sh

@@ -29,7 +29,7 @@ cd $SCRATCH_DIR/$DOWNLOAD_NAME
 
 mkdir models
 
-cp $SCRIPT_DIR/hyperparameters.yaml .
+python $SCRIPT_DIR/generate_hyperparameters.py > hyperparameters.yaml
 
 time mhcflurry-class1-train-allele-specific-models \
     --data "$(mhcflurry-downloads path data_curated)/curated_training_data.no_mass_spec.csv.bz2" \
@@ -37,8 +37,7 @@ time mhcflurry-class1-train-allele-specific-models \
     --out-models-dir models \
     --percent-rank-calibration-num-peptides-per-length 1000000 \
     --min-measurements-per-allele 75 \
-    --ignore-inequalities
-
+    --num-jobs 32 8
 
 cp $SCRIPT_ABSOLUTE_PATH .
 bzip2 LOG.txt

downloads-generation/models_class1_no_mass_spec/generate_hyperparameters.py

+../models_class1/generate_hyperparameters.py
\ No newline at end of file

downloads-generation/models_class1_no_mass_spec/hyperparameters.test.json

-[
-    {
-        "n_models": 8,
-        "max_epochs": 2,
-        "patience": 10,
-        "early_stopping": true,
-        "validation_split": 0.2,
-
-        "random_negative_rate": 0.0,
-        "random_negative_constant": 25,
-
-        "use_embedding": false,
-        "kmer_size": 15,
-        "batch_normalization": false,
-        "locally_connected_layers": [
-            {
-                "filters": 8,
-                "activation": "tanh",
-                "kernel_size": 3
-            },
-            {
-                "filters": 8,
-                "activation": "tanh",
-                "kernel_size": 3
-            }
-        ],
-        "activation": "relu",
-        "output_activation": "sigmoid",
-        "layer_sizes": [
-            32
-        ],
-        "random_negative_affinity_min": 20000.0,
-        "random_negative_affinity_max": 50000.0,
-        "dense_layer_l1_regularization": 0.001,
-        "dropout_probability": 0.0
-    }
-]

downloads-generation/models_class1_no_mass_spec/hyperparameters.yaml

-[{
-##########################################
-# ENSEMBLE SIZE
-##########################################
-"n_models": 8,
-
-##########################################
-# OPTIMIZATION
-##########################################
-"max_epochs": 500,
-"patience": 20,
-"early_stopping": true,
-"validation_split": 0.1,
-"minibatch_size": 128,
-"loss": "custom:mse_with_inequalities",
-
-##########################################
-# RANDOM NEGATIVE PEPTIDES
-##########################################
-"random_negative_rate": 0.2,
-"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
-"embedding_output_dim": 8,  # only used if using embedding
-"kmer_size": 15,
-
-##########################################
-# NEURAL NETWORK ARCHITECTURE
-##########################################
-"locally_connected_layers": [
-    {
-        "filters": 8,
-        "activation": "tanh",
-        "kernel_size": 3
-    }
-],
-"activation": "relu",
-"output_activation": "sigmoid",
-"layer_sizes": [16],
-"dense_layer_l1_regularization": 0.001,
-"batch_normalization": false,
-"dropout_probability": 0.0,
-}]