Prime Graphs and Exponential Composition of Species

In this paper, we enumerate prime graphs with respect to the Cartesian multiplication of graphs. We use the unique factorization of a connected graph into the product of prime graphs given by Sabidussi to find explicit formulas for labeled and unlabeled prime graphs. In the case of species, we construct the exponential composition of species based on the arithmetic product of species of Maia and M\'endez and the quotient species, and express the species of connected graphs as the exponential composition of the species of prime graphs.Comment: 30 pages, 7 figures, 1 tabl

Automatic enumeration of regular objects

We describe a framework for systematic enumeration of families combinatorial structures which possess a certain regularity. More precisely, we describe how to obtain the differential equations satisfied by their generating series. These differential equations are then used to determine the initial counting sequence and for asymptotic analysis. The key tool is the scalar product for symmetric functions and that this operation preserves D-finiteness.Comment: Corrected for readability; To appear in the Journal of Integer Sequence

Metastability and anomalous fixation in evolutionary games on scale-free networks

We study the influence of complex graphs on the metastability and fixation properties of a set of evolutionary processes. In the framework of evolutionary game theory, where the fitness and selection are frequency-dependent and vary with the population composition, we analyze the dynamics of snowdrift games (characterized by a metastable coexistence state) on scale-free networks. Using an effective diffusion theory in the weak selection limit, we demonstrate how the scale-free structure affects the system's metastable state and leads to anomalous fixation. In particular, we analytically and numerically show that the probability and mean time of fixation are characterized by stretched exponential behaviors with exponents depending on the network's degree distribution.Comment: 5 pages, 4 figures, to appear in Physical Review Letter

Some results on more flexible versions of Graph Motif

The problems studied in this paper originate from Graph Motif, a problem introduced in 2006 in the context of biological networks. Informally speaking, it consists in deciding if a multiset of colors occurs in a connected subgraph of a vertex-colored graph. Due to the high rate of noise in the biological data, more flexible definitions of the problem have been outlined. We present in this paper two inapproximability results for two different optimization variants of Graph Motif: one where the size of the solution is maximized, the other when the number of substitutions of colors to obtain the motif from the solution is minimized. We also study a decision version of Graph Motif where the connectivity constraint is replaced by the well known notion of graph modularity. While the problem remains NP-complete, it allows algorithms in FPT for biologically relevant parameterizations

{\Gamma}-species, quotients, and graph enumeration

The theory of {\Gamma}-species is developed to allow species-theoretic study of quotient structures in a categorically rigorous fashion. This new approach is then applied to two graph-enumeration problems which were previously unsolved in the unlabeled case-bipartite blocks and general k-trees.Comment: 84 pages, 10 figures, dissertatio

Statistics on Graphs, Exponential Formula and Combinatorial Physics

The concern of this paper is a famous combinatorial formula known under the name "exponential formula". It occurs quite naturally in many contexts (physics, mathematics, computer science). Roughly speaking, it expresses that the exponential generating function of a whole structure is equal to the exponential of those of connected substructures. Keeping this descriptive statement as a guideline, we develop a general framework to handle many different situations in which the exponential formula can be applied

Arithmetical Semirings

We study the number of connected graphs with $n$ vertices that cannot be written as the cartesian product of two graphs with fewer vertices. We give an upper bound which implies that for large $n$ almost all graphs are both connected and cartesian prime. For graphs with an even number of vertices, a full asymptotic expansion is obtained. Our method, inspired by Knopfmacher's theory of arithmetical semigroups, is based on reduction to Wright's asymptotic expansion for the number of connected graphs with $n$ vertices.Comment: 18 pages, enhanced exposition, minor correction