diff --git a/downloads-generation/models_class1_pan_refined/hyperparameters.yaml b/downloads-generation/models_class1_pan_refined/hyperparameters.yaml index 9dbb95757b5930a1fb7e346901efb1801cdaf83e..a1747f7ada068f5f37c10560b020e168e706222b 100644 --- a/downloads-generation/models_class1_pan_refined/hyperparameters.yaml +++ b/downloads-generation/models_class1_pan_refined/hyperparameters.yaml @@ -2,7 +2,7 @@ # Batch generation ######################### batch_generator_validation_split: 0.1 -batch_generator_batch_size: 10240 +batch_generator_batch_size: 1024 batch_generator_affinity_fraction: 0.5 max_epochs: 500 random_negative_rate: 1.0 diff --git a/mhcflurry/class1_presentation_neural_network.py b/mhcflurry/class1_presentation_neural_network.py index 58be681341adab8f42461b7920e535433e02a8f0..2e1156e619deaa4762a0a1146b12a157f5f50422 100644 --- a/mhcflurry/class1_presentation_neural_network.py +++ b/mhcflurry/class1_presentation_neural_network.py @@ -453,7 +453,7 @@ class Class1PresentationNeuralNetwork(object): allele_representations_hash = self.set_allele_representations( allele_representations) - loss_reduction = "none" + loss_reduction = "sum_over_batch_size" self.network.compile( loss=[ affinities_loss.get_keras_loss(reduction=loss_reduction), diff --git a/mhcflurry/downloads.yml b/mhcflurry/downloads.yml index 5de672d9b7e7d7fff85aac79fbca36ebd57c15ea..286121fd3e8a21953cf9fb495bd6a008d1807283 100644 --- a/mhcflurry/downloads.yml +++ b/mhcflurry/downloads.yml @@ -30,7 +30,7 @@ releases: default: false - name: models_class1_pan_refined - url: https://github.com/openvax/mhcflurry/releases/download/1.4.0/models_class1_pan_refined.20191211.tar.bz2 + url: https://github.com/openvax/mhcflurry/releases/download/1.4.0/models_class1_pan_refined.20191211b.tar.bz2 default: false - name: models_class1_pan_variants