diff --git a/parakeet/utils/conf.py b/parakeet/utils/conf.py
index fdeee58..5c13264 100644
--- a/parakeet/utils/conf.py
+++ b/parakeet/utils/conf.py
@@ -25,6 +25,10 @@ class Config(attrdict.AttrDict):
 
     def merge_args(self, args):
         args_dict = vars(args)
+        # remove options that is not passed via CLI
+        for k, v in args_dict:
+            if v is None:
+                args_dict.pop(k)
         args_dict.pop("config") # exclude config file path
         nested_dict = flatdict.FlatDict(args_dict, delimiter=".").as_dict()
         self.update(nested_dict)