16,745 research outputs found
A General Purpose Algorithm for Counting Simple Cycles and Simple Paths of Any Length
International audienceWe describe a general purpose algorithm for counting simple cycles and simple paths of any length on a (weighted di)graph on N vertices and M edges, achieving a time complexity of O N + M + ω + ∆ |S |. In this expression, |S | is the number of (weakly) connected induced subgraphs of G on at most vertices, ∆ is the maximum degree of any vertex and ω is the exponent of matrix multiplication. We compare the algorithm complexity both theoretically and experimentally with most of the existing algorithms for the same task. These comparisons show that the algorithm described here is the best general purpose algorithm for the class of graphs where (ω−1 ∆ −1 +1)|S | ≤ |Cycle |, with |Cycle | the total number of simple cycles of length at most , including backtracks and self-loops. On Erdős-Rényi random graphs, we find empirically that this happens when the edge probability is larger than circa 4/N. In addition, we show that some real-world networks also belong to this class. Finally, the algorithm permits the enumeration of simple cycles and simple paths on networks where vertices are labeled from an alphabet on n letters with a time complexity of O N + M + n ω + ∆ |S |. A Matlab implementation of the algorithm proposed here is available for download
Efficient Enumeration of Induced Subtrees in a K-Degenerate Graph
In this paper, we address the problem of enumerating all induced subtrees in
an input k-degenerate graph, where an induced subtree is an acyclic and
connected induced subgraph. A graph G = (V, E) is a k-degenerate graph if for
any its induced subgraph has a vertex whose degree is less than or equal to k,
and many real-world graphs have small degeneracies, or very close to small
degeneracies. Although, the studies are on subgraphs enumeration, such as
trees, paths, and matchings, but the problem addresses the subgraph
enumeration, such as enumeration of subgraphs that are trees. Their induced
subgraph versions have not been studied well. One of few example is for
chordless paths and cycles. Our motivation is to reduce the time complexity
close to O(1) for each solution. This type of optimal algorithms are proposed
many subgraph classes such as trees, and spanning trees. Induced subtrees are
fundamental object thus it should be studied deeply and there possibly exist
some efficient algorithms. Our algorithm utilizes nice properties of
k-degeneracy to state an effective amortized analysis. As a result, the time
complexity is reduced to O(k) time per induced subtree. The problem is solved
in constant time for each in planar graphs, as a corollary
Efficient Generation of Stable Planar Cages for Chemistry
In this paper we describe an algorithm which generates all colored planar
maps with a good minimum sparsity from simple motifs and rules to connect them.
An implementation of this algorithm is available and is used by chemists who
want to quickly generate all sound molecules they can obtain by mixing some
basic components.Comment: 17 pages, 7 figures. Accepted at the 14th International Symposium on
Experimental Algorithms (SEA 2015
On the Enumeration of Minimal Dominating Sets and Related Notions
A dominating set in a graph is a subset of its vertex set such that each
vertex is either in or has a neighbour in . In this paper, we are
interested in the enumeration of (inclusion-wise) minimal dominating sets in
graphs, called the Dom-Enum problem. It is well known that this problem can be
polynomially reduced to the Trans-Enum problem in hypergraphs, i.e., the
problem of enumerating all minimal transversals in a hypergraph. Firstly we
show that the Trans-Enum problem can be polynomially reduced to the Dom-Enum
problem. As a consequence there exists an output-polynomial time algorithm for
the Trans-Enum problem if and only if there exists one for the Dom-Enum
problem. Secondly, we study the Dom-Enum problem in some graph classes. We give
an output-polynomial time algorithm for the Dom-Enum problem in split graphs,
and introduce the completion of a graph to obtain an output-polynomial time
algorithm for the Dom-Enum problem in -free chordal graphs, a proper
superclass of split graphs. Finally, we investigate the complexity of the
enumeration of (inclusion-wise) minimal connected dominating sets and minimal
total dominating sets of graphs. We show that there exists an output-polynomial
time algorithm for the Dom-Enum problem (or equivalently Trans-Enum problem) if
and only if there exists one for the following enumeration problems: minimal
total dominating sets, minimal total dominating sets in split graphs, minimal
connected dominating sets in split graphs, minimal dominating sets in
co-bipartite graphs.Comment: 15 pages, 3 figures, In revisio
Combinatorial algorithm for counting small induced graphs and orbits
Graphlet analysis is an approach to network analysis that is particularly
popular in bioinformatics. We show how to set up a system of linear equations
that relate the orbit counts and can be used in an algorithm that is
significantly faster than the existing approaches based on direct enumeration
of graphlets. The algorithm requires existence of a vertex with certain
properties; we show that such vertex exists for graphlets of arbitrary size,
except for complete graphs and , which are treated separately. Empirical
analysis of running time agrees with the theoretical results
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