From 79a30a1db891baf538db1ca02e1216f1647ad5c9 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 29 Jan 2018 21:43:04 -0500
Subject: [PATCH] update models_class1_no_mass_spec
---
.../models_class1_no_mass_spec/GENERATE.sh | 5 +-
.../generate_hyperparameters.py | 1 +
.../hyperparameters.test.json | 37 --------------
.../hyperparameters.yaml | 50 -------------------
4 files changed, 3 insertions(+), 90 deletions(-)
create mode 120000 downloads-generation/models_class1_no_mass_spec/generate_hyperparameters.py
delete mode 100644 downloads-generation/models_class1_no_mass_spec/hyperparameters.test.json
delete mode 100644 downloads-generation/models_class1_no_mass_spec/hyperparameters.yaml
diff --git a/downloads-generation/models_class1_no_mass_spec/GENERATE.sh b/downloads-generation/models_class1_no_mass_spec/GENERATE.sh
index 42860af5..1aebe4fc 100755
--- a/downloads-generation/models_class1_no_mass_spec/GENERATE.sh
+++ b/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
diff --git a/downloads-generation/models_class1_no_mass_spec/generate_hyperparameters.py b/downloads-generation/models_class1_no_mass_spec/generate_hyperparameters.py
new file mode 120000
index 00000000..5f2599b4
--- /dev/null
+++ b/downloads-generation/models_class1_no_mass_spec/generate_hyperparameters.py
@@ -0,0 +1 @@
+../models_class1/generate_hyperparameters.py
\ No newline at end of file
diff --git a/downloads-generation/models_class1_no_mass_spec/hyperparameters.test.json b/downloads-generation/models_class1_no_mass_spec/hyperparameters.test.json
deleted file mode 100644
index 609fa583..00000000
--- a/downloads-generation/models_class1_no_mass_spec/hyperparameters.test.json
+++ /dev/null
@@ -1,37 +0,0 @@
-[
- {
- "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
- }
-]
diff --git a/downloads-generation/models_class1_no_mass_spec/hyperparameters.yaml b/downloads-generation/models_class1_no_mass_spec/hyperparameters.yaml
deleted file mode 100644
index 9c4a232b..00000000
--- a/downloads-generation/models_class1_no_mass_spec/hyperparameters.yaml
+++ /dev/null
@@ -1,50 +0,0 @@
-[{
-##########################################
-# 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,
-}]
--
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