Improvement of biological networks reconstructed from high-throughput expression data is an important challenge in systems biology. Link prediction is a problem of interest in many application domains that can be used for this purpose. In this paper after a short review of several biological networks, we present the latest definition of the link prediction problem and review it from several viewpoints. With a comprehensive search in the literature using PubMed, Science Direct and Google Scholar databases, and carefully reviewing the related papers having the ‘link prediction’ plus at least one of the biological network terms in their title, abstract or keywords, we classify the results based on the graph type and major link prediction outlooks. Finally, we analyse the preformed researches to find new insights about potential uses in addition to understanding the current state, and propose several hints and directions for future works.
