Update training data

openvax · Apr 27, 2020 · ef08dac · ef08dac
1 parent 755451f
commit ef08dac
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Showing 3 changed files with 110 additions and 3 deletions.
diff --git a/downloads-generation/data_curated/curate.py b/downloads-generation/data_curated/curate.py
@@ -56,7 +56,7 @@ def normalize_allele_name(s):
 
 QUALITATIVE_TO_AFFINITY_AND_INEQUALITY = {
     "Negative": (5000.0, ">"),
-    "Positive": (50.0, "<"),  # used for mass-spec hits
+    "Positive": (500.0, "<"),  # 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
@@ -36,7 +36,7 @@
     'peptide_amino_acid_encoding': 'BLOSUM62',
     'peptide_dense_layer_sizes': [],
     'random_negative_affinity_max': 50000.0,
-    'random_negative_affinity_min': 35000.0,
+    'random_negative_affinity_min': 20000.0,
     '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
@@ -8,7 +8,7 @@
 # by name, the downloads with "default=true" are downloaded.
 
 # This should usually be the latest release.
-current-release: 1.6.0
+current-release: 1.7.0
 
 # An integer indicating what models the current MHCflurry code base is compatible
 # with. Increment this integer when changes are made to MHCflurry that would break
@@ -17,6 +17,113 @@ current-compatibility-version: 2
 
 # Add new releases here as they are made.
 releases:
+    1.7.0:
+        compatibility-version: 2
+        downloads:
+            - name: models_class1_pan
+              url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/models_class1_pan.selected.20200204.tar.bz2
+              default: false
+
+            - name: models_class1_presentation
+              url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/models_class1_presentation.20200205.tar.bz2
+              default: true
+
+            - name: models_class1_processing
+              url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/models_class1_processing.selected.20200122.tar.bz2
+              default: false
+
+            - name: models_class1_pan_unselected
+              url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/models_class1_pan.20200104.tar.bz2
+              default: false
+
+            - name: models_class1_pan_variants
+              url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/models_class1_pan_variants.selected.20200307.tar.bz2
+              default: false
+
+            - name: models_class1_processing_variants
+              url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/models_class1_processing_variants.selected.20200124.tar.bz2
+              default: false
+
+            - name: data_evaluation
+              url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_evaluation.20200209.tar.bz2
+              default: false
+
+            - name: data_mass_spec_benchmark
+              part_urls:
+                - https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_mass_spec_benchmark.20200105.tar.bz2.part.aa
+                - https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_mass_spec_benchmark.20200105.tar.bz2.part.ab
+                - https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_mass_spec_benchmark.20200105.tar.bz2.part.ac
+                - https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_mass_spec_benchmark.20200105.tar.bz2.part.ad
+                - https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_mass_spec_benchmark.20200105.tar.bz2.part.ae
+                - https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_mass_spec_benchmark.20200105.tar.bz2.part.af
+                - https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_mass_spec_benchmark.20200105.tar.bz2.part.ag
+                - https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_mass_spec_benchmark.20200105.tar.bz2.part.ah
+                - https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_mass_spec_benchmark.20200105.tar.bz2.part.ai
+                - https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_mass_spec_benchmark.20200105.tar.bz2.part.aj
+                - https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_mass_spec_benchmark.20200105.tar.bz2.part.ak
+                - https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_mass_spec_benchmark.20200105.tar.bz2.part.al
+                - https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_mass_spec_benchmark.20200105.tar.bz2.part.am
+                - https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_mass_spec_benchmark.20200105.tar.bz2.part.an
+                - https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_mass_spec_benchmark.20200105.tar.bz2.part.ao
+              default: false
+
+            - name: data_mass_spec_annotated
+              url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/data_mass_spec_annotated.20191226.tar.bz2
+              default: false
+
+            - name: data_references
+              url: https://github.com/openvax/mhcflurry/releases/download/pre-1.4.0/data_references.20190927.tar.bz2
+              default: false
+
+            - name: data_iedb
+              url: https://github.com/openvax/mhcflurry/releases/download/pre-1.7.0/data_iedb.20200427.tar.bz2
+              default: false
+
+            - name: data_systemhcatlas
+              url: http://github.com/openvax/mhcflurry/releases/download/pan-dev1/data_systemhcatlas.20190506.tar.bz2
+              default: false
+
+            - name: allele_sequences
+              url: https://github.com/openvax/mhcflurry/releases/download/1.4.0/allele_sequences.20191231.tar.bz2
+              default: false
+
+            - name: random_peptide_predictions
+              url: http://github.com/openvax/mhcflurry/releases/download/pan-dev1/random_peptide_predictions.20190506.tar.bz2
+              default: false
+
+            - name: data_published
+              url: https://github.com/openvax/mhcflurry/releases/download/1.4.0/data_published.20191220.tar.bz2
+              default: false
+
+            - name: data_curated
+              url: https://github.com/openvax/mhcflurry/releases/download/pre-1.7.0/data_curated.20200427.tar.bz2
+              default: true
+
+            # Older downloads
+            - name: models_class1
+              url: http://github.com/openvax/mhcflurry/releases/download/pre-1.2/models_class1.20180225.tar.bz2
+              default: true
+
+            - name: models_class1_selected_no_mass_spec
+              url: http://github.com/openvax/mhcflurry/releases/download/pre-1.2/models_class1_selected_no_mass_spec.20180225.tar.bz2
+              default: false
+
+            - name: models_class1_unselected
+              url: http://github.com/openvax/mhcflurry/releases/download/pre-1.2/models_class1_unselected.20180221.tar.bz2
+              default: false
+
+            - name: models_class1_trained_with_mass_spec
+              url: http://github.com/openvax/mhcflurry/releases/download/pre-1.2.1/models_class1_trained_with_mass_spec.20180228.tar.bz2
+              default: false
+
+            - name: models_class1_unselected_with_mass_spec
+              url: http://github.com/openvax/mhcflurry/releases/download/pre-1.2.1/models_class1_unselected_with_mass_spec.20180227.tar.bz2
+              default: false
+
+            - name: models_class1_minimal
+              url: http://github.com/openvax/mhcflurry/releases/download/pre-1.2/models_class1_minimal.20180226.tar.bz2
+              default: false
+
     1.6.0:
         compatibility-version: 2
         downloads: