diff --git a/mhcflurry/class1_binding_predictor.py b/mhcflurry/class1_binding_predictor.py index 8efcadcd00d6f9e96b92de73a60d79ac2a9b1895..9b24b6d7d890ec8fb6813f393befe1a1c62d9d64 100644 --- a/mhcflurry/class1_binding_predictor.py +++ b/mhcflurry/class1_binding_predictor.py @@ -230,7 +230,7 @@ class Class1BindingPredictor(PredictorBase): X_random = np.random.randint( low=min_value, high=max_value + 1, - shape=(n_random_negative_samples, n_cols)).astype(X.dtype) + size=(n_random_negative_samples, n_cols)).astype(X.dtype) Y_random = np.zeros(n_random_negative_samples, dtype=float) weights_random = np.ones(n_random_negative_samples, dtype=float) X_with_negative = np.vstack([X, X_random]) @@ -330,7 +330,6 @@ class Class1BindingPredictor(PredictorBase): # only use synthetic data if it contributes at least 1/1000th of # sample weight if verbose: - real_data_percent = ( ((1.0 - pretrain_fraction_contribution) * 100) if use_pretrain_data @@ -364,7 +363,8 @@ class Class1BindingPredictor(PredictorBase): self._extend_with_negative_random_samples( X_curr_iter, Y_curr_iter, - weights_curr_iter) + weights_curr_iter, + n_random_negative_samples) self.model.fit( X_curr_iter,