scholarly journals Exact Algorithms for Intervalizing Colored Graphs

2011 ◽  
pp. 45-56 ◽  
Author(s):  
Hans L. Bodlaender ◽  
Johan M. M. van Rooij
Keyword(s):  
Exact Algorithms ◽  
Colored Graphs

Efficient Computation of Representative Families with Applications in Parameterized and Exact Algorithms

2016 ◽  
Vol 63 (4) ◽  
pp. 1-60 ◽  
Author(s):  
Fedor V. Fomin ◽  
Daniel Lokshtanov ◽  
Fahad Panolan ◽  
Saket Saurabh
Keyword(s):  
Exact Algorithms ◽  
Efficient Computation

scholarly journals Indirect identification of horizontal gene transfer

2021 ◽  
Vol 83 (1) ◽  
Author(s):  
David Schaller ◽  
Manuel Lafond ◽  
Peter F. Stadler ◽  
Nicolas Wieseke ◽  
Marc Hellmuth
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Polynomial Time ◽  
Divergence Time ◽  
Recognition Algorithm ◽  
Vertex Coloring ◽  
Implicit Methods ◽  
Colored Graphs ◽  
Wide Range ◽  
Complete Multipartite

AbstractSeveral implicit methods to infer horizontal gene transfer (HGT) focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of a graph, the later-divergence-time (LDT) graph, whose vertices correspond to genes colored by their species. We investigate these graphs in the setting of relaxed scenarios, i.e., evolutionary scenarios that encompass all commonly used variants of duplication-transfer-loss scenarios in the literature. We characterize LDT graphs as a subclass of properly vertex-colored cographs, and provide a polynomial-time recognition algorithm as well as an algorithm to construct a relaxed scenario that explains a given LDT. An edge in an LDT graph implies that the two corresponding genes are separated by at least one HGT event. The converse is not true, however. We show that the complete xenology relation is described by an rs-Fitch graph, i.e., a complete multipartite graph satisfying constraints on the vertex coloring. This class of vertex-colored graphs is also recognizable in polynomial time. We finally address the question “how much information about all HGT events is contained in LDT graphs” with the help of simulations of evolutionary scenarios with a wide range of duplication, loss, and HGT events. In particular, we show that a simple greedy graph editing scheme can be used to efficiently detect HGT events that are implicitly contained in LDT graphs.

scholarly journals Path homology theory of edge-colored graphs

2021 ◽  
Vol 19 (1) ◽  
pp. 706-723
Author(s):  
Yuri V. Muranov ◽  
Anna Szczepkowska
Keyword(s):  
Spectral Sequence ◽  
Edge Coloring ◽  
Homology Theory ◽  
Homotopy Category ◽  
Homology Groups ◽  
Colored Graphs ◽  
Natural Filtration ◽  
Definition Of ◽  
Exact Sequences

Abstract In this paper, we introduce the category and the homotopy category of edge-colored digraphs and construct the functorial homology theory on the foundation of the path homology theory provided by Grigoryan, Muranov, and Shing-Tung Yau. We give the construction of the path homology theory for edge-colored graphs that follows immediately from the consideration of natural functor from the category of graphs to the subcategory of symmetrical digraphs. We describe the natural filtration of path homology groups of any digraph equipped with edge coloring, provide the definition of the corresponding spectral sequence, and obtain commutative diagrams and braids of exact sequences.

Efficient Directed Densest Subgraph Discovery

2021 ◽  
Vol 50 (1) ◽  
pp. 33-40
Author(s):  
Chenhao Ma ◽  
Yixiang Fang ◽  
Reynold Cheng ◽  
Laks V.S. Lakshmanan ◽  
Wenjie Zhang ◽  
...  
Keyword(s):  
Approximation Algorithms ◽  
State Of The Art ◽  
Exact Algorithms ◽  
Large Datasets ◽  
Dense Subgraph ◽  
Extensive Evaluation ◽  
Wide Range ◽  
Edge Graph ◽  
Community Mining ◽  
Densest Subgraph

Given a directed graph G, the directed densest subgraph (DDS) problem refers to the finding of a subgraph from G, whose density is the highest among all the subgraphs of G. The DDS problem is fundamental to a wide range of applications, such as fraud detection, community mining, and graph compression. However, existing DDS solutions suffer from efficiency and scalability problems: on a threethousand- edge graph, it takes three days for one of the best exact algorithms to complete. In this paper, we develop an efficient and scalable DDS solution. We introduce the notion of [x, y]-core, which is a dense subgraph for G, and show that the densest subgraph can be accurately located through the [x, y]-core with theoretical guarantees. Based on the [x, y]-core, we develop both exact and approximation algorithms. We have performed an extensive evaluation of our approaches on eight real large datasets. The results show that our proposed solutions are up to six orders of magnitude faster than the state-of-the-art.

scholarly journals The Action of the Weyl Group on the $$E_8$$ Root System

2021 ◽  
Author(s):  
Rosa Winter ◽  
Ronald van Luijk
Keyword(s):  
Automorphism Group ◽  
Weyl Group ◽  
Root System ◽  
Sufficient Conditions ◽  
Maximal Clique ◽  
Necessary And Sufficient Conditions ◽  
Inner Product ◽  
Colored Graphs ◽  
Necessary And Sufficient ◽  
Root Polytope

AbstractLet $$\varGamma $$ Γ be the graph on the roots of the $$E_8$$ E 8 root system, where any two distinct vertices e and f are connected by an edge with color equal to the inner product of e and f. For any set c of colors, let $$\varGamma _c$$ Γ c be the subgraph of $$\varGamma $$ Γ consisting of all the 240 vertices, and all the edges whose color lies in c. We consider cliques, i.e., complete subgraphs, of $$\varGamma $$ Γ that are either monochromatic, or of size at most 3, or a maximal clique in $$\varGamma _c$$ Γ c for some color set c, or whose vertices are the vertices of a face of the $$E_8$$ E 8 root polytope. We prove that, apart from two exceptions, two such cliques are conjugate under the automorphism group of $$\varGamma $$ Γ if and only if they are isomorphic as colored graphs. Moreover, for an isomorphism f from one such clique K to another, we give necessary and sufficient conditions for f to extend to an automorphism of $$\varGamma $$ Γ , in terms of the restrictions of f to certain special subgraphs of K of size at most 7.

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