diff --git a/mhcflurry/class1_neural_network.py b/mhcflurry/class1_neural_network.py index d75f66b71ddb3f330b4a1d3db76770d8a4014c3e..86a0cdf5a11766e02116e7c27ee9020a6b9fdfb3 100644 --- a/mhcflurry/class1_neural_network.py +++ b/mhcflurry/class1_neural_network.py @@ -1368,6 +1368,7 @@ class Class1NeuralNetwork(object): m is the length of the vectors used to represent amino acids """ from keras.models import clone_model + import keras.backend as K reshaped = allele_representations.reshape( (allele_representations.shape[0], -1)) original_model = self.network() diff --git a/test/test_class1_neural_network.py b/test/test_class1_neural_network.py index 0566b6a610ce108c6bd68f2fb2e4672530ede772..8baaded0a02d88d43d6e77ad7551a687adc3528f 100644 --- a/test/test_class1_neural_network.py +++ b/test/test_class1_neural_network.py @@ -90,7 +90,7 @@ def test_inequalities(): hyperparameters = dict( peptide_amino_acid_encoding="one-hot", activation="tanh", - layer_sizes=[16], + layer_sizes=[64], max_epochs=200, minibatch_size=32, random_negative_rate=0.0, @@ -108,7 +108,7 @@ def test_inequalities(): loss="custom:mse_with_inequalities_and_multiple_outputs") df = pandas.DataFrame() - df["peptide"] = random_peptides(1000, length=9) + df["peptide"] = random_peptides(100, length=9) # First half are binders df["binder"] = df.index < len(df) / 2 diff --git a/test/test_released_predictors_well_correlated.py b/test/test_released_predictors_well_correlated.py index a6034b3ed8935d359f9203c15a29e2719dfa5c23..395a6e80b54c699c664d5b5ddbb9ff5990743648 100644 --- a/test/test_released_predictors_well_correlated.py +++ b/test/test_released_predictors_well_correlated.py @@ -23,7 +23,7 @@ PREDICTORS = { get_path("models_class1_pan", "models.with_mass_spec")) } -PREDICTORS["pan-allele"].optimize() +# PREDICTORS["pan-allele"].optimize() def test_correlation(