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A new, fast algorithm for detecting protein coevolution using maximum compatible cliques
Algorithms for Molecular Biology, 2011 Background The MatrixMatchMaker algorithm was recently introduced to detect the similarity between phylogenetic trees and thus the coevolution between proteins. MMM finds the largest common submatrices between pairs of phylogenetic distance matrices, and
Rose Jonathan +3 more
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Deciding Clique-Width for Graphs of Bounded Tree-Width [PDF]
Journal of Graph Algorithms and Applications, 2001 Summary: We show that there exists a linear time algorithm for deciding whether a graph of bounded tree-width has clique-width \(k\) for some fixed integer \(k\).
Espelage, Wolfgang +2 more
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Asteroidal Quadruples in non Rooted Path Graphs
Discussiones Mathematicae Graph Theory, 2015 A directed path graph is the intersection graph of a family of directed subpaths of a directed tree. A rooted path graph is the intersection graph of a family of directed subpaths of a rooted tree. Rooted path graphs are directed path graphs.
Gutierrez Marisa +2 more
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1-Skeletons of the Spanning Tree Problems with Additional Constraints
Моделирование и анализ информационных систем, 2015 In this paper, we study polyhedral properties of two spanning tree problems with additional constraints. In the first problem, it is required to find a tree with a minimum sum of edge weights among all spanning trees with the number of leaves less than ...
V. A. Bondarenko +2 more
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Canonizing Graphs of Bounded Tree Width in Logspace [PDF]
, 2015 Graph canonization is the problem of computing a unique representative, a canon, from the isomorphism class of a given graph. This implies that two graphs are isomorphic exactly if their canons are equal.
Elberfeld, Michael, Schweitzer, Pascal
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Clique-sums, tree-decompositions and compactness
Discrete Mathematics, 1990 The results presented in this paper seem to be in the line with previous papers of Robertson and Seymour. Five definitions fix basic ideas related with tree decompositions, cliques, \(k\)-simplexes, \(k\)-complexes and chordal graphs as well as \(k\)-summability and other related subjects.
Kříž, Igor, Thomas, Robin
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BMC Bioinformatics, 2017 Background Disease progression models are important for understanding the critical steps during the development of diseases. The models are imbedded in a statistical framework to deal with random variations due to biology and the sampling process when ...
Katrin Hainke +3 more
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Modelling epidemics on d-cliqued graphs
Letters in Biomathematics, 2018 Since social interactions have been shown to lead to symmetric clusters, we propose here that symmetries play a key role in epidemic modelling. Mathematical models on d-ary tree graphs were recently shown to be particularly effective for modelling ...
Laura P. Schaposnik, Anlin Zhang
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IEEE Access, 2018 A network of modular protein complexes inside a cell coordinates many biological processes and is known as protein-protein interaction (PPI) network. APPI network can be modeled as a graph, in which edges represent interactions among proteins, and sub ...
Aisha Sikandar +7 more
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Independence of causal influence and clique tree propagation
International Journal of Approximate Reasoning, 1998 Appears in Proceedings of the Thirteenth Conference on Uncertainty in Artificial Intelligence (UAI1997)
Zhang, NL, Yan, L.
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