diff --git a/gigl/common/utils/proto_utils.py b/gigl/common/utils/proto_utils.py
index 56b78b312..e61258756 100644
--- a/gigl/common/utils/proto_utils.py
+++ b/gigl/common/utils/proto_utils.py
@@ -1,5 +1,5 @@
 from tempfile import NamedTemporaryFile
-from typing import Optional, Type, TypeVar
+from typing import Optional, Type, TypeVar, cast
 
 import yaml
 from google.protobuf import message
@@ -28,7 +28,12 @@ def read_proto_from_yaml(self, uri: Uri, proto_cls: Type[T]) -> T:
             omega_conf_obj = OmegaConf.create(raw_data)
         tfh.close()
         obj_dict = OmegaConf.to_object(omega_conf_obj)
-        proto = ParseDict(js_dict=obj_dict, message=proto_cls())
+        if not isinstance(obj_dict, dict):
+            raise TypeError(
+                f"ProtoUtils.read_proto_from_yaml expected a mapping at the YAML root for "
+                f"{uri}, got {type(obj_dict).__name__}."
+            )
+        proto = ParseDict(js_dict=cast(dict, obj_dict), message=proto_cls())
         return proto
 
     def read_proto_from_binary(self, uri: Uri, proto_cls: Type[T]) -> T:
diff --git a/gigl/experimental/knowledge_graph_embedding/lib/config/__init__.py b/gigl/experimental/knowledge_graph_embedding/lib/config/__init__.py
index 094f1375b..9caf7fe38 100644
--- a/gigl/experimental/knowledge_graph_embedding/lib/config/__init__.py
+++ b/gigl/experimental/knowledge_graph_embedding/lib/config/__init__.py
@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from dataclasses import dataclass, field
-from typing import cast
+from typing import Any, cast
 
 import torch
 from google.protobuf.json_format import ParseDict
@@ -70,8 +70,15 @@ def from_omegaconf(config: DictConfig) -> HeterogeneousGraphSparseEmbeddingConfi
         assert graph_metadata is not None, "Graph metadata is required in the config."
 
         graph_metadata_dict = OmegaConf.to_container(graph_metadata, resolve=True)
+        if not isinstance(graph_metadata_dict, dict):
+            raise TypeError(
+                f"HeterogeneousGraphSparseEmbeddingConfig.from_omegaconf expected "
+                f"dataset.metadata to resolve to a mapping, got "
+                f"{type(graph_metadata_dict).__name__}."
+            )
         pb = ParseDict(
-            js_dict=graph_metadata_dict, message=graph_schema_pb2.GraphMetadata()
+            js_dict=cast(dict[str, Any], graph_metadata_dict),
+            message=graph_schema_pb2.GraphMetadata(),
         )
         graph_metadata = GraphMetadataPbWrapper(graph_metadata_pb=pb)
 
diff --git a/tests/unit/common/utils/proto_utils_test.py b/tests/unit/common/utils/proto_utils_test.py
index 1e8dd54a9..793e0e7a6 100644
--- a/tests/unit/common/utils/proto_utils_test.py
+++ b/tests/unit/common/utils/proto_utils_test.py
@@ -68,6 +68,20 @@ def test_can_read_gbml_config_from_yaml(self):
             f"{expected_positive_label_date_range_start}:{expected_positive_label_date_range_end}",
         )
 
+    def test_read_proto_from_yaml_raises_typeerror_when_root_is_not_a_mapping(self):
+        list_yaml = "- a\n- b\n- c\n"
+        tmp_file = NamedTemporaryFile(delete=False)
+        tmp_file.write(list_yaml.encode())
+        tmp_file.close()
+        try:
+            with self.assertRaises(TypeError):
+                self.proto_utils.read_proto_from_yaml(
+                    uri=LocalUri(tmp_file.name),
+                    proto_cls=gbml_config_pb2.GbmlConfig,
+                )
+        finally:
+            os.remove(tmp_file.name)
+
 
 if __name__ == "__main__":
     absltest.main()