Recent advances in technology have dramatically increased the availability of protein-protein interaction (PPI) data and stimulated the development of many methods for improving the systems level understanding the cell. However, those efforts have been significantly hindered by the high level of noise, sparseness and highly skewed degree distribution of PPI networks. Here, we present a novel algorithm to reduce the noise present in PPI networks. The key idea of our algorithm is that two proteins sharing some higher-order topological similarities, measured by a novel random walk-based procedure, are likely interacting with each other and may belong to the same protein complex.