Related papers: On the readability of overlap digraphs
In the final project paper we consider a graph parameter called readability. Motivation for readability comes from bioinformatics applications. Graphs arising in problems related to genome sequencing are of small readability, which…
We study a parameter of bipartite graphs called readability, introduced by Chikhi et al. (Discrete Applied Mathematics, 2016) and motivated by applications of overlap graphs in bioinformatics. The behavior of the parameter is poorly…
An overlap representation is an assignment of sets to the vertices of a graph in such a way that two vertices are adjacent if and only if the sets assigned to them overlap. The overlap number of a graph is the minimum number of elements…
Existing graph layout algorithms are usually not able to optimize all the aesthetic properties desired in a graph layout. To evaluate how well the desired visual features are reflected in a graph layout, many readability metrics have been…
Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intramolecular) model, called simple gene assembly, has been…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
We present a simple iterative strategy for measuring the connection strength between a pair of vertices in a graph. The method is attractive in that it has a linear complexity and can be easily parallelized. Based on an analysis of the…
Graphs on integer points of polytopes whose edges come from a set of allowed differences are studied. It is shown that any simple graph can be embedded in that way. The minimal dimension of such a representation is the fiber dimension of…
String diagrams are a powerful tool for reasoning about composite structures in symmetric monoidal categories. By representing string diagrams as graphs, equational reasoning can be done automatically by double-pushout rewriting. !-graphs…
We consider the task of drawing a graph on multiple horizontal layers, where each node is assigned a layer, and each edge connects nodes of different layers. Known algorithms determine the orders of nodes on each layer to minimize crossings…
Graphs, consisting of vertices and edges, are vital for representing complex relationships in fields like social networks, finance, and blockchain. Visualizing these graphs helps analysts identify structural patterns, with readability…
Given a set of finite words, the Overlap Graph (OG) is a complete weighted digraph where each word is a node and where the weight of an arc equals the length of the longest overlap of one word onto the other (Overlap is an asymmetric…
A graph is a mathematical object consisting of a set of vertices and a set of edges connecting vertices. Graphs can be drawn on paper in various ways, but until recently all published methods of drawing graphs have had undesirable…
Hypergraphs, a generalization of graphs, naturally represent groupwise relationships among multiple individuals or objects, which are common in many application areas, including web, bioinformatics, and social networks. The flexibility in…
The guessing number of a directed graph (digraph), equivalent to the entropy of that digraph, was introduced as a direct criterion on the solvability of a network coding instance. This paper makes two contributions on the guessing number.…
In this paper we consider aspects of geometric observability for hypergraphs, extending our earlier work from the uniform to the nonuniform case. Hypergraphs, a generalization of graphs, allow hyperedges to connect multiple nodes and…
Consider a graph G = G(k,d,s) with vertex set the set of all k-letter words over an alphabet of size d. An edge e = vw is in E iff v is distinct from w and the last(first) k-s letters of v are identical to the first(last) k-s letters of w.…
When drawing graphs whose edges and nodes contain text or graphics, such informa tion needs to be displayed without overlaps, either as part of the initial layout or as a post-processing step. The core problem in removing overlaps lies in…
We introduce the \emph{ID-index} of a finite simple connected graph. For a graph $G=(V,\ E)$ with diameter $d$, we let $f:V\longrightarrow \mathbb{R}$ assign \emph{ranks} to the vertices, then under $f$, each vertex $v$ gets a…
We characterise the structure of those graphs of a given order which maximise the number of connected induced subgraphs for seven different graph classes, each with other prescribed parameters like minimum degree, independence number,…