Before revision:  AptRank naturally combines protein-protein associations and  function-function relationships into a two-layer network model , and takes full advantage of the hierarchical structure of the Gene Ontology, using directional diffusion without flattening the ontological hierarchy into a similarity kernel.
After revision:  AptRank naturally combines protein-protein associations and function-function relationships into a two-layer network model without flattening the ontological hierarchy into a similarity kernel.