diff --git a/torch_geometric/data/large_graph_indexer.py b/torch_geometric/data/large_graph_indexer.py
index ae131e829896..6f1ab3f245f0 100644
--- a/torch_geometric/data/large_graph_indexer.py
+++ b/torch_geometric/data/large_graph_indexer.py
@@ -195,8 +195,8 @@ def apply_transform(
             edges.append(edge_idx)
             # if edge_idx not in edges:
             #     edges.append(edge_idx)
-        nodes = ordered_dict(nodes)
-        edges = ordered_dict(edges)
+        nodes = ordered_set(nodes)
+        edges = ordered_set(edges)
         return cls(list(nodes), list(edges))
 
     @classmethod