From 3136d2f1ff5b760e1a244ba7c9eff8876c19f2d7 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 3 Jan 2020 13:32:35 -0500
Subject: [PATCH] update data_curated
---
downloads-generation/data_curated/curate.py | 2 +-
.../models_class1_pan/generate_hyperparameters.py | 2 +-
mhcflurry/downloads.yml | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/downloads-generation/data_curated/curate.py b/downloads-generation/data_curated/curate.py
index 9c56c2f7..12e5a9ac 100755
--- a/downloads-generation/data_curated/curate.py
+++ b/downloads-generation/data_curated/curate.py
@@ -56,7 +56,7 @@ parser.add_argument(
QUALITATIVE_TO_AFFINITY_AND_INEQUALITY = {
"Negative": (5000.0, ">"),
- "Positive": (500.0, "<"), # used for mass-spec hits
+ "Positive": (50.0, "<"), # used for mass-spec hits
"Positive-High": (100.0, "<"),
"Positive-Intermediate": (1000.0, "<"),
"Positive-Low": (5000.0, "<"),
diff --git a/downloads-generation/models_class1_pan/generate_hyperparameters.py b/downloads-generation/models_class1_pan/generate_hyperparameters.py
index ecd47386..d24b253d 100644
--- a/downloads-generation/models_class1_pan/generate_hyperparameters.py
+++ b/downloads-generation/models_class1_pan/generate_hyperparameters.py
@@ -36,7 +36,7 @@ base_hyperparameters = {
'peptide_amino_acid_encoding': 'BLOSUM62',
'peptide_dense_layer_sizes': [],
'random_negative_affinity_max': 50000.0,
- 'random_negative_affinity_min': 20000.0,
+ 'random_negative_affinity_min': 35000.0,
'random_negative_constant': 1,
'random_negative_distribution_smoothing': 0.0,
'random_negative_match_distribution': True,
diff --git a/mhcflurry/downloads.yml b/mhcflurry/downloads.yml
index ed2514a9..bc8accf0 100644
--- a/mhcflurry/downloads.yml
+++ b/mhcflurry/downloads.yml
@@ -83,7 +83,7 @@ releases:
default: false
- name: data_curated
- url: https://github.com/openvax/mhcflurry/releases/download/1.4.0/data_curated.20200101.tar.bz2
+ url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_curated.20200103.tar.bz2
default: true
# Older downloads
--
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