diff --git a/mhcflurry/class1_affinity_prediction/class1_neural_network.py b/mhcflurry/class1_affinity_prediction/class1_neural_network.py index df8e767c46060fbef92a77cecb2b4d3847972529..a6d93d2eb6c5dcf7dededc521a1299da59a29df2 100644 --- a/mhcflurry/class1_affinity_prediction/class1_neural_network.py +++ b/mhcflurry/class1_affinity_prediction/class1_neural_network.py @@ -73,13 +73,12 @@ class Class1NeuralNetwork(object): self.hyperparameters = self.hyperparameter_defaults.with_defaults( hyperparameters) self.network = None - self.fit_history = None + self.loss_history = None self.fit_seconds = None def __getstate__(self): result = dict(self.__dict__) del result['network'] - result['fit_history'] = None result['network_json'] = self.network.to_json() result['network_weights'] = self.get_weights() return result @@ -204,7 +203,7 @@ class Class1NeuralNetwork(object): min_val_loss_iteration = None min_val_loss = None - self.fit_history = collections.defaultdict(list) + self.loss_history = collections.defaultdict(list) start = time.time() for i in range(self.hyperparameters['max_epochs']): random_negative_peptides_list = [] @@ -243,17 +242,17 @@ class Class1NeuralNetwork(object): sample_weight=sample_weights) for (key, value) in fit_history.history.items(): - self.fit_history[key].extend(value) + self.loss_history[key].extend(value) logging.info( "Epoch %3d / %3d: loss=%g. Min val loss at epoch %s" % ( i, self.hyperparameters['max_epochs'], - self.fit_history['loss'][-1], + self.loss_history['loss'][-1], min_val_loss_iteration)) if self.hyperparameters['validation_split']: - val_loss = fit_history.history['val_loss'][-1] + val_loss = self.loss_history['val_loss'][-1] val_losses.append(val_loss) if min_val_loss is None or val_loss <= min_val_loss: diff --git a/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py b/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py index 4b4201915e8700b6fe633f94db3d2b711edd0d5c..e3d7f71543a0b8731eda2e10af275a3d1a6d2d50 100644 --- a/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py +++ b/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py @@ -16,6 +16,7 @@ import mhcnames from .class1_neural_network import Class1NeuralNetwork from ..common import configure_logging + def normalize_allele_name(s): try: return mhcnames.normalize_allele_name(s)