Ramsey numbers of Berge-hypergraphs and related structures

For a graph $G=(V,E)$, a hypergraph $\mathcal{H}$ is called a Berge-$G$, denoted by $BG$, if there exists a bijection $f: E(G) \to E(\mathcal{H})$ such that for every $e \in E(G)$, $e \subseteq f(e)$. Let the Ramsey number $R^r(BG,BG)$ be the smallest integer $n$ such that for any $2$-edge-coloring of a complete $r$-uniform hypergraph on $n$ vertices, there is a monochromatic Berge-$G$ subhypergraph. In this paper, we show that the 2-color Ramsey number of Berge cliques is linear. In particular, we show that $R^3(BK_s, BK_t) = s+t-3$ for $s,t \geq 4$ and $\max(s,t) \geq 5$ where $BK_n$ is a Berge-$K_n$ hypergraph. For higher uniformity, we show that $R^4(BK_t, BK_t) = t+1$ for $t\geq 6$ and $R^k(BK_t, BK_t)=t$ for $k \geq 5$ and $t$ sufficiently large. We also investigate the Ramsey number of trace hypergraphs, suspension hypergraphs and expansion hypergraphs.Comment: Updated to include suggestions of the refere

On Ramsey properties of classes with forbidden trees

Let F be a set of relational trees and let Forbh(F) be the class of all structures that admit no homomorphism from any tree in F; all this happens over a fixed finite relational signature $\sigma$. There is a natural way to expand Forbh(F) by unary relations to an amalgamation class. This expanded class, enhanced with a linear ordering, has the Ramsey property.Comment: Keywords: forbidden substructure; amalgamation; Ramsey class; partite method v2: changed definition of expanded class; v3: final versio

Unavoidable Multicoloured Families of Configurations

Balogh and Bollob\'as [{\em Combinatorica 25, 2005}] prove that for any $k$ there is a constant $f(k)$ such that any set system with at least $f(k)$ sets reduces to a $k$-star, an $k$-costar or an $k$-chain. They proved $f(k)<(2k)^{2^k}$. Here we improve it to $f(k)<2^{ck^2}$ for some constant $c>0$. This is a special case of the following result on the multi-coloured forbidden configurations at 2 colours. Let $r$ be given. Then there exists a constant $c_r$ so that a matrix with entries drawn from $\{0,1,...,r-1\}$ with at least $2^{c_rk^2}$ different columns will have a $k\times k$ submatrix that can have its rows and columns permuted so that in the resulting matrix will be either $I_k(a,b)$ or $T_k(a,b)$ (for some $a\ne b\in \{0,1,..., r-1\}$), where $I_k(a,b)$ is the $k\times k$ matrix with $a$'s on the diagonal and $b$'s else where, $T_k(a,b)$ the $k\times k$ matrix with $a$'s below the diagonal and $b$'s elsewhere. We also extend to considering the bound on the number of distinct columns, given that the number of rows is $m$, when avoiding a $t k\times k$ matrix obtained by taking any one of the $k \times k$ matrices above and repeating each column $t$ times. We use Ramsey Theory.Comment: 16 pages, add two application

Innocent strategies as presheaves and interactive equivalences for CCS

Seeking a general framework for reasoning about and comparing programming languages, we derive a new view of Milner's CCS. We construct a category E of plays, and a subcategory V of views. We argue that presheaves on V adequately represent innocent strategies, in the sense of game semantics. We then equip innocent strategies with a simple notion of interaction. This results in an interpretation of CCS. Based on this, we propose a notion of interactive equivalence for innocent strategies, which is close in spirit to Beffara's interpretation of testing equivalences in concurrency theory. In this framework we prove that the analogues of fair and must testing equivalences coincide, while they differ in the standard setting.Comment: In Proceedings ICE 2011, arXiv:1108.014

Analysis of Generative Chemistries

For the modelling of chemistry we use undirected, labelled graphs as explicit models of molecules and graph transformation rules for modelling generalised chemical reactions. This is used to define artificial chemistries on the level of individual bonds and atoms, where formal graph grammars implicitly represent large spaces of chemical compounds. We use a graph rewriting formalism, rooted in category theory, called the Double Pushout approach, which directly expresses the transition state of chemical reactions. Using concurrency theory for transformation rules, we define algorithms for the composition of rewrite rules in a chemically intuitive manner that enable automatic abstraction of the level of detail in chemical pathways. Based on this rule composition we define an algorithmic framework for generation of vast reaction networks for specific spaces of a given chemistry, while still maintaining the level of detail of the model down to the atomic level. The framework also allows for computation with graphs and graph grammars, which is utilised to model non-trivial chemical systems. The graph generation relies on graph isomorphism testing, and we review the general individualisation-refinement paradigm used in the state-of-the-art algorithms for graph canonicalisation, isomorphism testing, and automorphism discovery. We present a model for chemical pathways based on a generalisation of network flows from ordinary directed graphs to directed hypergraphs. The model allows for reasoning about the flow of individual molecules in general pathways, and the introduction of chemically motivated routing constraints. It further provides the foundation for defining specialised pathway motifs, which is illustrated by defining necessary topological constraints for both catalytic and autocatalytic pathways. We also prove that central types of pathway questions are NP-complete, even for restricted classes of reaction networks. The complete pathway model, including constraints for catalytic and autocatalytic pathways, is implemented using integer linear programming. This implementation is used in a tree search method to enumerate both optimal and near-optimal pathway solutions. The formal methods are applied to multiple chemical systems: the enzyme catalysed beta-lactamase reaction, variations of the glycolysis pathway, and the formose process. In each of these systems we use rule composition to abstract pathways and calculate traces for isotope labelled carbon atoms. The pathway model is used to automatically enumerate alternative non-oxidative glycolysis pathways, and enumerate thousands of candidates for autocatalytic pathways in the formose process