diff --git a/src/edu/stanford/nlp/pipeline/ProtobufAnnotationSerializer.java b/src/edu/stanford/nlp/pipeline/ProtobufAnnotationSerializer.java
index 700a41ac84..eca5aaa23a 100644
--- a/src/edu/stanford/nlp/pipeline/ProtobufAnnotationSerializer.java
+++ b/src/edu/stanford/nlp/pipeline/ProtobufAnnotationSerializer.java
@@ -2390,7 +2390,6 @@ private static SemanticGraph fromProto(CoreNLPProtos.DependencyGraph proto, List
       max = in.getIndex() > max ? in.getIndex() : max;
     }
     // map from index, emptyIndex, copy -> IndexedWord
-    // TODO: still need to add the empty index to the proto, then use it here to build the graph
     ThreeDimensionalMap<Integer, Integer, Integer, IndexedWord> nodes = new ThreeDimensionalMap<>();
     // map from index, emptyIndex -> CoreLabel
     TwoDimensionalMap<Integer, Integer, CoreLabel> originalLabels = TwoDimensionalMap.hashMap();
@@ -2416,8 +2415,7 @@ private static SemanticGraph fromProto(CoreNLPProtos.DependencyGraph proto, List
       if (document.isPresent()) {
         token = document.get().get(SentencesAnnotation.class).get(in.getSentenceIndex()).get(TokensAnnotation.class).get(in.getIndex() - 1); // token index starts at 1!
       } else {
-        // TODO: index based on emptyIndex as well
-        token = originalLabels.get(in.getIndex(), 0);
+        token = originalLabels.get(in.getIndex(), in.getEmptyIndex());
         if (token == null) {
           throw new NullPointerException("Could not find the token for index " + in.getIndex());
         }
@@ -2449,12 +2447,11 @@ private static SemanticGraph fromProto(CoreNLPProtos.DependencyGraph proto, List
 
     // add all edges to the actual graph
     for(CoreNLPProtos.DependencyGraph.Edge ie: proto.getEdgeList()){
-      // TODO: source and target should index on emptyIndex as well
-      IndexedWord source = nodes.get(ie.getSource(), 0, ie.getSourceCopy());
+      IndexedWord source = nodes.get(ie.getSource(), ie.getSourceEmpty(), ie.getSourceCopy());
       if (source == null) {
         throw new AssertionError("Source of a dependency was null!  Edge: " + ie);
       }
-      IndexedWord target = nodes.get(ie.getTarget(), 0, ie.getTargetCopy());
+      IndexedWord target = nodes.get(ie.getTarget(), ie.getTargetEmpty(), ie.getTargetCopy());
       if (target == null) {
         throw new AssertionError("Target of a dependency was null!  Edge: " + ie);
       }