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Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…
In a bidirected graph an edge has a direction at each end, so bidirected graphs generalize directed graphs. We generalize the definitions of transitive closure and transitive reduction from directed graphs to bidirected graphs by…
Graphings serve as limit objects for bounded-degree graphs. We define the ``cycle matroid'' of a graphing as a submodular setfunction, with values in [0,1], which generalizes (up to normalization) the cycle matroid of finite graphs. We…
For a representation of a Lie algebra, one can construct a diagram of the representation, i. e. a directed graph with edges labeled by matrix elements of the representation. This article explains how to use these diagrams to describe normal…
In this paper, our goal is to characterize two graph classes based on the properties of minimal vertex (edge) separators. We first present a structural characterization of graphs in which every minimal vertex separator is a stable set. We…
A mixed graph is a graph with some directed edges and some undirected edges. We introduce the notion of mixed matroids as a generalization of mixed graphs. A mixed matroid can be viewed as an oriented matroid in which the signs over a fixed…
An important property of chordal graphs is that these graphs are characterized by existence of perfect elimination orderings on their vertex sets. In this paper, we generalize the notion of perfect elimination orderings to signed graphs,…
A graph is 1-planar if it can be drawn on a plane so that each edge is crossed by at most one other edge. In this paper, we first give a useful structural theorem for 1-planar graphs, and then apply it to the list edge and list total…
In fields ranging from business to systems biology, directed graphs with edges labeled by signs are used to model systems in a simple way: the nodes represent entities of some sort, and an edge indicates that one entity directly affects…
A graph is called dominating if its vertices can be labelled with integers in such a way that for every function f: omega-> omega the graph contains a ray whose sequence of labels eventually exceeds f. We obtain a characterization of these…
A signed graph is a graph where the edges are assigned labels of either "$+$" or "$-$". The sign of a cycle in the graph is the product of the signs of its edges. We equip each signed complete graph with a vector whose entries are the…
Pseudodiagrams are diagrams of knots where some information about which strand goes over/under at certain crossings may be missing. Pseudoknots are equivalence classes of pseudodiagrams, with equivalence defined by a class of…
Wiring diagrams usually serve as a tool in the study of arrangements of lines and pseudolines. In this paper we go in the opposite direction, using known properties of line arrangements to motivate certain equivalence relations and actions…
Graph embedding algorithms are used to efficiently represent (encode) a graph in a low-dimensional continuous vector space that preserves the most important properties of the graph. One aspect that is often overlooked is whether the graph…
We define the crossing graph of a given embedded graph (such as a road network) to be a graph with a vertex for each edge of the embedding, with two crossing graph vertices adjacent when the corresponding two edges of the embedding cross…
We give a new combinatorial explanation for well-known relations between determinants and traces of matrix powers. Such relations can be used to obtain polynomial-time and poly-logarithmic space algorithms for the determinant. Our new…
In a signed graph each edge has a sign, $+1$ or $-1$. We introduce in the present paper a new definition of connection in a signed graph by the existence of both positive and negative chains between vertices. We prove some results and…
A universal cycle is a compact listing of a class of combinatorial objects. In this paper, we prove the existence of universal cycles of classes of labeled graphs, including simple graphs, trees, graphs with m edges, graphs with loops,…
This paper develops a structural theory of unique shortest paths in real-weighted graphs. Our main goal is to characterize exactly which sets of node sequences, which we call path systems, can be realized as unique shortest paths in a graph…
The signature of a path is a sequence of tensors which allows to uniquely reconstruct the path. By employing the geometric theory of nonlinear systems of ordinary differential equations, we find necessary and sufficient algebraic conditions…