You're looking at the docs for v1, not v2: http://jung.sourceforge.net/doc/api/edu/uci/ics/jung/algorithms/filters/EdgePredicateFilter.html In v2, EdgePredicateFilter.transform() returns a Graph, plain and simple.
If you want to remove the nodes without edges after your edge predicate filter has finished, you can do that as a separate VertexPredicateFilter pass.