Alignments of biomolecular contact maps

Alignments of discrete objects can be constructed in a very general setting as super-objects from which the constituent objects are recovered by means of projections. Here, we focus on contact maps, i.e. undirected graphs with an ordered set of vertices. These serve as natural discretizations of RNA and protein structures. In the general case, the alignment problem for vertex-ordered graphs is NP-complete. In the special case of RNA secondary structures, i.e. crossing-free matchings, however, the alignments have a recursive structure. The alignment problem then can be solved by a variant of the Sankoff algorithm in polynomial time. Moreover, the tree or forest alignments of RNA secondary structure can be understood as the alignments of ordered edge sets.

Ramsey Numbers of Ordered Graphs

An ordered graph is a pair $\mathcal{G}=(G,\prec)$ where $G$ is a graph and $\prec$ is a total ordering of its vertices. The ordered Ramsey number $\overline{R}(\mathcal{G})$ is the minimum number $N$ such that every ordered complete graph with $N$ vertices and with edges colored by two colors contains a monochromatic copy of $\mathcal{G}$. In contrast with the case of unordered graphs, we show that there are arbitrarily large ordered matchings $\mathcal{M}_n$ on $n$ vertices for which $\overline{R}(\mathcal{M}_n)$ is superpolynomial in $n$. This implies that ordered Ramsey numbers of the same graph can grow superpolynomially in the size of the graph in one ordering and remain linear in another ordering. We also prove that the ordered Ramsey number $\overline{R}(\mathcal{G})$ is polynomial in the number of vertices of $\mathcal{G}$ if the bandwidth of $\mathcal{G}$ is constant or if $\mathcal{G}$ is an ordered graph of constant degeneracy and constant interval chromatic number. The first result gives a positive answer to a question of Conlon, Fox, Lee, and Sudakov. For a few special classes of ordered paths, stars or matchings, we give asymptotically tight bounds on their ordered Ramsey numbers. For so-called monotone cycles we compute their ordered Ramsey numbers exactly. This result implies exact formulas for geometric Ramsey numbers of cycles introduced by Károlyi, Pach, Tóth, and Valtr.

A dual Ramsey theorem for finite ordered oriented graphs

In contrast to the abundance of “direct” Ramsey results for classes of finite structures (such as finite ordered graphs, finite ordered metric spaces and finite posets with a linear extension), in only a handful of cases we have a meaningful dual Ramsey result. In this paper we prove a dual Ramsey theorem for finite ordered oriented graphs. Instead of embeddings, which are crucial for “direct” Ramsey results, we consider a special class of surjective homomorphisms between finite ordered oriented graphs. Since the setting we are interested in involves both structures and morphisms, all our results are spelled out using the reinterpretation of the (dual) Ramsey property in the language of category theory.

Off-Diagonal Ordered Ramsey Numbers of Matchings

For ordered graphs $G$ and $H$, the ordered Ramsey number $r_<(G,H)$ is the smallest $n$ such that every red/blue edge coloring of the complete ordered graph on vertices $\{1,\dots,n\}$ contains either a blue copy of $G$ or a red copy of $H$, where the embedding must preserve the relative order of vertices. One number of interest, first studied by Conlon, Fox, Lee, and Sudakov, is the off-diagonal ordered Ramsey number $r_<(M, K_3)$, where $M$ is an ordered matching on $n$ vertices. In particular, Conlon et al. asked what asymptotic bounds (in $n$) can be obtained for $\max r_<(M, K_3)$, where the maximum is over all ordered matchings $M$ on $n$ vertices. The best-known upper bound is $O(n^2/\log n)$, whereas the best-known lower bound is $\Omega((n/\log n)^{4/3})$, and Conlon et al. hypothesize that there is some fixed $\epsilon > 0$ such that $r_<(M, K_3) = O(n^{2-\epsilon})$ for every ordered matching $M$. We resolve two special cases of this conjecture. We show that the off-diagonal ordered Ramsey numbers for ordered matchings in which edges do not cross are nearly linear. We also prove a truly sub-quadratic upper bound for random ordered matchings with interval chromatic number $2$.