Affinity measure is a key factor that determines the quality of the analysis of a complex network. Here, we introduce a type of statistics, activation forces, to weight the links of a complex network and thereby develop a desired affinity measure. We show that the approach is superior in facilitating the analysis through experiments on a large-scale word network and a protein-protein interaction (PPI) network consisting of ∼5,000 human proteins. The experiment on the word network verifies that the measured word affinities are highly consistent with human knowledge. Further, the experiment on the PPI network verifies the measure and presents a general method for the identification of functionally similar proteins based on PPIs. Most strikingly, we find an affinity network that compactly connects the cancer-associated proteins to each other, which may reveal novel information for cancer study; this includes likely protein interactions and key proteins in cancer-related signal transduction pathways.

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