Graph parameters and the speed of hereditary properties

In this thesis we study the speed of hereditary properties of graphs and how this defines some of the structure of the properties. We start by characterizing several graph parameters by means of minimal hereditary classes. We then give a global characterization of properties of low speed, before looking at properties with higher speeds starting at the Bell number. We then introduce a new parameter, clique-width, and show that there are an infinite amount of minimal hereditary properties with unbounded clique-width. We then look at the factorial layer in more detail and focus on P7-free bipartite graphs. Finally we discuss word-representable graphs

On functional module detection in metabolic networks

Functional modules of metabolic networks are essential for understanding the metabolism of an organism as a whole. With the vast amount of experimental data and the construction of complex and large-scale, often genome-wide, models, the computer-aided identification of functional modules becomes more and more important. Since steady states play a key role in biology, many methods have been developed in that context, for example, elementary flux modes, extreme pathways, transition invariants and place invariants. Metabolic networks can be studied also from the point of view of graph theory, and algorithms for graph decomposition have been applied for the identification of functional modules. A prominent and currently intensively discussed field of methods in graph theory addresses the Q-modularity. In this paper, we recall known concepts of module detection based on the steady-state assumption, focusing on transition-invariants (elementary modes) and their computation as minimal solutions of systems of Diophantine equations. We present the Fourier-Motzkin algorithm in detail. Afterwards, we introduce the Q-modularity as an example for a useful non-steady-state method and its application to metabolic networks. To illustrate and discuss the concepts of invariants and Q-modularity, we apply a part of the central carbon metabolism in potato tubers (Solanum tuberosum) as running example. The intention of the paper is to give a compact presentation of known steady-state concepts from a graph-theoretical viewpoint in the context of network decomposition and reduction and to introduce the application of Q-modularity to metabolic Petri net models

Minimal classes of graphs of unbounded clique-width defined by finitely many forbidden induced subgraphs

We discover new hereditary classes of graphs that are minimal (with respect to set inclusion) of unbounded clique-width. The new examples include split permutation graphs and bichain graphs. Each of these classes is characterised by a finite list of minimal forbidden induced subgraphs. These, therefore, disprove a conjecture due to Daligault, Rao and Thomasse from 2010 claiming that all such minimal classes must be defined by infinitely many forbidden induced subgraphs. In the same paper, Daligault, Rao and Thomasse make another conjecture that every hereditary class of unbounded clique-width must contain a labelled infinite antichain. We show that the two example classes we consider here satisfy this conjecture. Indeed, they each contain a canonical labelled infinite antichain, which leads us to propose a stronger conjecture: that every hereditary class of graphs that is minimal of unbounded clique-width contains a canonical labelled infinite antichain.Comment: 17 pages, 7 figure

Balanced supersaturation for some degenerate hypergraphs

A classical theorem of Simonovits from the 1980s asserts that every graph $G$ satisfying ${e(G) \gg v(G)^{1+1/k}}$ must contain $\gtrsim \left(\frac{e(G)}{v(G)}\right)^{2k}$ copies of $C_{2k}$. Recently, Morris and Saxton established a balanced version of Simonovits' theorem, showing that such $G$ has $\gtrsim \left(\frac{e(G)}{v(G)}\right)^{2k}$ copies of $C_{2k}$, which are `uniformly distributed' over the edges of $G$. Moreover, they used this result to obtain a sharp bound on the number of $C_{2k}$-free graphs via the container method. In this paper, we generalise Morris-Saxton's results for even cycles to $\Theta$-graphs. We also prove analogous results for complete $r$-partite $r$-graphs.Comment: Changed title, abstract and introduction were rewritte

An on-line competitive algorithm for coloring bipartite graphs without long induced paths

The existence of an on-line competitive algorithm for coloring bipartite graphs remains a tantalizing open problem. So far there are only partial positive results for bipartite graphs with certain small forbidden graphs as induced subgraphs. We propose a new on-line competitive coloring algorithm for $P_9$-free bipartite graphs

Complexity of C_k-Coloring in Hereditary Classes of Graphs

For a graph F, a graph G is F-free if it does not contain an induced subgraph isomorphic to F. For two graphs G and H, an H-coloring of G is a mapping f:V(G) -> V(H) such that for every edge uv in E(G) it holds that f(u)f(v)in E(H). We are interested in the complexity of the problem H-Coloring, which asks for the existence of an H-coloring of an input graph G. In particular, we consider H-Coloring of F-free graphs, where F is a fixed graph and H is an odd cycle of length at least 5. This problem is closely related to the well known open problem of determining the complexity of 3-Coloring of P_t-free graphs. We show that for every odd k >= 5 the C_k-Coloring problem, even in the precoloring-extension variant, can be solved in polynomial time in P_9-free graphs. On the other hand, we prove that the extension version of C_k-Coloring is NP-complete for F-free graphs whenever some component of F is not a subgraph of a subdivided claw