diff --git a/src/sdk/pynni/nni/bohb_advisor/config_generator.py b/src/sdk/pynni/nni/bohb_advisor/config_generator.py
index 5bd039844f..c6a13c6b35 100644
--- a/src/sdk/pynni/nni/bohb_advisor/config_generator.py
+++ b/src/sdk/pynni/nni/bohb_advisor/config_generator.py
@@ -236,7 +236,7 @@ def get_config(self, budget):
         return sample
 
     def impute_conditional_data(self, array):
-        return_array = np.empty_like(array)
+        return_array = np.zeros(array.shape)
         for i in range(array.shape[0]):
             datum = np.copy(array[i])
             nan_indices = np.argwhere(np.isnan(datum)).flatten()