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RNA molecules are known to form complex secondary structures including pseudoknots. A systematic framework for the enumeration, classification and prediction of secondary structures is critical to determine the biological significance of…

Biomolecules · Quantitative Biology 2025-12-24 Rayan Ibrahim , Allison H. Moore

An obstacle representation of a graph is a mapping of the vertices onto points in the plane and a set of connected regions of the plane (called obstacles) such that the straight-line segment connecting the points corresponding to two…

A transitive graph is 2-dimensional if it can be represented as the intersection of two linear orders. Such representations make answering of reachability queries trivial, and allow many problems that are NP-hard on arbitrary graphs to be…

Discrete Mathematics · Computer Science 2019-04-09 Henning Koehler

Some graphs admit drawings in the Euclidean k-space in such a (natu- ral) way, that edges are represented as line segments of unit length. Such drawings will be called k dimensional unit distance representations. When two non-adjacent…

Combinatorics · Mathematics 2010-01-07 Jan Kratochvil , Boris Horvat , Tomaz Pisanski

The most elusive problem around the class of circular-arc graphs is identifying all minimal graphs that are not in this class. The main obstacle is the lack of a systematic way of enumerating these minimal graphs. McConnell [FOCS 2001]…

Combinatorics · Mathematics 2025-03-18 Yixin Cao , Jan Derbisz , Tomasz Krawczyk

In this paper we consider the concept of preintersection numbers of a graph. These numbers are determined by the spectrum of the adjacency matrix of the graph, and generalize the intersection numbers of a distance-regular graph. By using…

Combinatorics · Mathematics 2016-04-20 A. Abiad , E. R. van Dam , M. A. Fiol

Oriented closed curves on an orientable surface with boundary are described up to continuous deformation by reduced cyclic words in the generators of the fundamental group and their inverses. By self-intersection number one means the…

Geometric Topology · Mathematics 2011-08-03 Moira Chas , Steven P. Lalley

Given a non empty set $S$ of vertices of a graph, the partiality of a vertex with respect to $S$ is the difference between maximum and minimum of the distances of the vertex to the vertices of $S$. The vertices with minimum partiality…

Discrete Mathematics · Computer Science 2013-04-25 R. Ram Kumar , Kannan Balakrishnan , Prasanth G. Narasimha-Shenoi

Spectral graph bisections are a popular heuristic aimed at approximating the solution of the NP-complete graph bisection problem. This technique, however, does not always provide a robust tool for graph partitioning. Using a special class…

Numerical Analysis · Mathematics 2015-12-22 John C. Urschel , Ludmil T. Zikatanov

The intersection graph of a family of sets $\{S_{1},S_{2},\ldots,S_{n}\}$ is a graph whose vertex set is $\{S_{1},S_{2},\ldots,S_{n}\}$ and two distinct vertices are adjacent if the intersection of the corresponding sets is non-empty.…

Combinatorics · Mathematics 2025-07-23 Vinny Susan Prebhath , Sudev Naduvath

An asteroidal triple is a stable set of three vertices such that each pair is connected by a path avoiding the neighborhood of the third vertex. Asteroidal triples play a central role in a classical characterization of interval graphs by…

Discrete Mathematics · Computer Science 2008-12-30 Kathie Cameron , Chinh Hoàng , Benjamin Lévêque

We consider the problem of estimating graph limits, known as graphons, from observations of sequences of sparse finite graphs. In this paper we show a simple method that can shed light on a subset of sparse graphs. The method involves…

Machine Learning · Statistics 2025-07-08 Sevvandi Kandanaarachchi , Cheng Soon Ong

These lecture notes are on automorphism groups of Cayley graphs and their applications to optimal fault-tolerance of some interconnection networks. We first give an introduction to automorphisms of graphs and an introduction to Cayley…

Combinatorics · Mathematics 2017-04-04 Ashwin Ganesan

A \emph{locally irregular graph} is a graph whose adjacent vertices have distinct degrees. We say that a graph $G$ can be decomposed into $k$ locally irregular subgraphs if its edge set may be partitioned into $k$ subsets each of which…

Combinatorics · Mathematics 2017-03-02 Jakub Przybyło

In the 1970s, Erdos asked whether the chromatic number of intersection graphs of line segments in the plane is bounded by a function of their clique number. We show the answer is no. Specifically, for each positive integer $k$, we construct…

We consider the size of the smallest set of vertices required to intersect every longest path in a chordal graph. Such sets are known as longest path transversals. We show that if $\omega(G)$ is the clique number of a chordal graph $G$,…

Combinatorics · Mathematics 2020-12-15 Daniel J. Harvey , Michael S. Payne

A graph class $\mathcal{G}$ admits product structure if there exists a constant $k$ such that every $G \in \mathcal{G}$ is a subgraph of $H \boxtimes P$ for a path $P$ and some graph $H$ of treewidth $k$. Famously, the class of planar…

Combinatorics · Mathematics 2024-09-04 Laura Merker , Lena Scherzer , Samuel Schneider , Torsten Ueckerdt

We investigate string graphs through the lens of graph product structure theory, which describes complicated graphs as subgraphs of strong products of simpler building blocks. A graph $G$ is called a string graph if its vertices can be…

Combinatorics · Mathematics 2025-11-20 Nikolai Karol

A commonly used paradigm for representing graphs is to use a vector that contains normalized frequencies of occurrence of certain motifs or sub-graphs. This vector representation can be used in a variety of applications, such as, for…

Machine Learning · Computer Science 2014-03-05 Pinar Yanardag , S. V. N. Vishwanathan

A graph $G$ is said to be the intersection of graphs $G_1,G_2,\ldots,G_k$ if $V(G)=V(G_1)=V(G_2)=\cdots=V(G_k)$ and $E(G)=E(G_1)\cap E(G_2)\cap\cdots\cap E(G_k)$. For a graph $G$, $\mathrm{dim}_{COG}(G)$ (resp. $\mathrm{dim}_{TH}(G)$)…

Discrete Mathematics · Computer Science 2020-01-06 Daphna Chacko , Mathew C. Francis