Computational Feasibility of Increasing the Visibility of Vertices in Covert Networks

Disrupting terrorist and other covert networks requires identifying and capturing key leaders. Previous research by Martonosi et al. (2009) defines a load metric on vertices of a covert network representing the amount of communication in which a vertex is expected to participate. They suggest that the visibility of a target vertex can be increased by removing other, more accessible members of the network. This report evaluates the feasibility of efficiently calculating the optimal subset of vertices to remove. We begin by proving that the general problem of identifying the optimally load maximizing vertex set removal is NP-complete. We then consider the feasibility of more quickly computing the load maximizing single vertex removal by designing an efficient algorithm for recomputing Gomory- Hu trees. This leads to a result regarding the uniqueness of Gomory- Hu trees with implications towards the feasibility of one approach for Gomory- Hu tree reconstruction. Finally, we propose a warm start algorithm which performs this reconstruction, and analyze its runtime experimentally

Jane: a new tool for the cophylogeny reconstruction problem

<p>Abstract</p> <p>Background</p> <p>This paper describes the theory and implementation of a new software tool, called <it>Jane</it>, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new <it>Jane </it>tool described here provides functionality that complements existing tools.</p> <p>Results</p> <p>The <it>Jane </it>software tool uses a polynomial time dynamic programming algorithm in conjunction with a genetic algorithm to find very good, and often optimal, solutions even for relatively large pairs of trees. The tool allows the user to provide rich timing information on both the host and parasite trees. In addition the user can limit host switch distance and specify multiple host switch costs by specifying regions in the host tree and costs for host switches between pairs of regions. <it>Jane </it>also provides a graphical user interface that allows the user to interactively experiment with modifications to the solutions found by the program.</p> <p>Conclusions</p> <p><it>Jane </it>is shown to be a useful tool for cophylogenetic reconstruction. Its functionality complements existing tools and it is therefore likely to be of use to researchers in the areas of parasitology, molecular systematics, and biogeography.</p

The Cophylogeny Reconstruction Problem is NP-Complete

The cophylogeny reconstruction problem arises in the study of host-parasite relationships. Specif- ically, we are given a host tree H, a parasite tree P, and a function \u27 mapping the leaves (extant taxa) of P to the leaves of H. Four biologically plausible operations are considered: cospeciation, duplication, host switching, and loss (Figure 1). A host switch is permitted in conjunction with a duplication event but not with a cospeciation event [1]

Jane: A New Tool for the Cophylogeny Reconstruction Problem

Background This paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new Jane tool described here provides functionality that complements existing tools. Results The Jane software tool uses a polynomial time dynamic programming algorithm in conjunction with a genetic algorithm to find very good, and often optimal, solutions even for relatively large pairs of trees. The tool allows the user to provide rich timing information on both the host and parasite trees. In addition the user can limit host switch distance and specify multiple host switch costs by specifying regions in the host tree and costs for host switches between pairs of regions. Jane also provides a graphical user interface that allows the user to interactively experiment with modifications to the solutions found by the program. Conclusions Jane is shown to be a useful tool for cophylogenetic reconstruction. Its functionality complements existing tools and it is therefore likely to be of use to researchers in the areas of parasitology, molecular systematics, and biogeography

Computational Feasibility of Increasing the Visibility of Vertices in Covert Networks

Abstract Disrupting terrorist and other covert networks requires identifying and capturing key leaders. Previous research by We begin by proving that the general problem of identifying the optimally load maximizing vertex set removal is NP-complete. We then consider the feasibility of more quickly computing the load maximizing single vertex removal by designing an efficient algorithm for recomputing Gomory-Hu trees. This leads to a result regarding the uniqueness of GomoryHu trees with implications towards the feasibility of one approach for Gomory-Hu tree reconstruction. Finally, we propose a warm start algorithm which performs this reconstruction, and analyze its runtime experimentally