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  • Title: Analysis of Critical and Redundant Vertices in Controlling Directed Complex Networks Using Feedback Vertex Sets.
    Author: Bao Y, Hayashida M, Liu P, Ishitsuka M, Nacher JC, Akutsu T.
    Journal: J Comput Biol; 2018 Oct; 25(10):1071-1090. PubMed ID: 30074414.
    Abstract:
    Controlling complex networks through a small number of controller vertices is of great importance in wide-ranging research fields. Recently, a new approach based on the minimum feedback vertex set (MFVS) has been proposed to find such vertices in directed networks in which the target states are restricted to steady states. However, multiple MFVS configurations may exist and thus the selection of vertices may depend on algorithms and input data representations. Our attempts to address this ambiguity led us to adopt an existing approach that classifies vertices into three categories. This approach has been successfully applied to maximum matching-based and minimum dominating set-based controllability analysis frameworks. In this article, we present an algorithm as well as its implementation to compute and evaluate the critical, intermittent, and redundant vertices under the MFVS-based framework, where these three categories include vertices belonging to all MFVSs, some (but not all) MFVSs, and none of the MFVSs, respectively. The results of computational experiments using artificially generated networks and real-world biological networks suggest that the proposed algorithm is useful for identifying these three kinds of vertices for relatively large-scale networks, and that the fraction of critical and intermittent vertices is considerably small. Moreover, an analysis of the signal pathways indicates that critical and intermittent MFVSs tend to be enriched by essential genes.
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