From f052583da7e01ffef805e32c2100e52a4d6f7380 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Wed, 21 Sep 2016 18:13:58 -0400
Subject: [PATCH] Update models_class1_allele_specific_single_kim2014_only to
use hyperparameters roughly the same as preprint
---
.../GENERATE.sh | 2 +-
.../imputer.json | 4 ++--
.../models.py | 6 +++---
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/downloads-generation/models_class1_allele_specific_single_kim2014_only/GENERATE.sh b/downloads-generation/models_class1_allele_specific_single_kim2014_only/GENERATE.sh
index 3d7eb354..80c7e46a 100644
--- a/downloads-generation/models_class1_allele_specific_single_kim2014_only/GENERATE.sh
+++ b/downloads-generation/models_class1_allele_specific_single_kim2014_only/GENERATE.sh
@@ -40,7 +40,7 @@ time mhcflurry-class1-allele-specific-cv-and-train \
--imputer-description imputer.json \
--train-data "$(mhcflurry-downloads path data_kim2014)/bdata.2009.mhci.public.1.txt" \
--test-data "$(mhcflurry-downloads path data_kim2014)/bdata.2013.mhci.public.blind.1.txt" \
- --min-samples-per-allele 70 \
+ --min-samples-per-allele 50 \
--out-cv-results cv.csv \
--out-production-results production.csv \
--out-models models \
diff --git a/downloads-generation/models_class1_allele_specific_single_kim2014_only/imputer.json b/downloads-generation/models_class1_allele_specific_single_kim2014_only/imputer.json
index f7614316..c17f86cc 100644
--- a/downloads-generation/models_class1_allele_specific_single_kim2014_only/imputer.json
+++ b/downloads-generation/models_class1_allele_specific_single_kim2014_only/imputer.json
@@ -3,6 +3,6 @@
"n_burn_in": 5,
"n_imputations": 50,
"n_nearest_columns": 25,
- "min_observations_per_peptide": 5,
- "min_observations_per_allele": 100
+ "min_observations_per_peptide": 2,
+ "min_observations_per_allele": 2
}
diff --git a/downloads-generation/models_class1_allele_specific_single_kim2014_only/models.py b/downloads-generation/models_class1_allele_specific_single_kim2014_only/models.py
index 6375cd45..6e20239c 100644
--- a/downloads-generation/models_class1_allele_specific_single_kim2014_only/models.py
+++ b/downloads-generation/models_class1_allele_specific_single_kim2014_only/models.py
@@ -3,13 +3,13 @@ from mhcflurry.class1_allele_specific.train import HYPERPARAMETER_DEFAULTS
import json
models = HYPERPARAMETER_DEFAULTS.models_grid(
- #impute=[False, True],
- impute=[False],
+ impute=[False, True],
activation=["tanh"],
layer_sizes=[[12], [64], [128]],
embedding_output_dim=[8, 32, 64],
dropout_probability=[0, .1, .25],
- # fraction_negative=[0, .1, .2],
+ pretrain_decay=["1 / (1+epoch)**2"],
+ fraction_negative=[0, .1, .2],
n_training_epochs=[250])
sys.stderr.write("Models: %d\n" % len(models))
--
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