Related papers: The Structure of 2-Colored Best Match Graphs
One of the most important concepts in biological network analysis is that of network motifs, which are patterns of interconnections that occur in a given network at a frequency higher than expected in a random network. In this work we are…
A $k$-colouring (not necessarily proper) of vertices of a graph is called {\it acyclic}, if for every pair of distinct colours $i$ and $j$ the subgraph induced by the edges whose endpoints have colours $i$ and $j$ is acyclic. In the paper…
We introduce two novel evolutionary formulations of the problem of coloring the nodes of a graph. The first formulation is based on the relationship that exists between a graph's chromatic number and its acyclic orientations. It views such…
Three well-studied types of subgraph-restricted matchings are induced matchings, uniquely restricted matchings, and acyclic matchings. While it is hard to determine the maximum size of a matching of each of these types, whether some given…
We characterize the compatibility of a collection of unrooted phylogenetic trees as a question of determining whether a graph derived from these trees --- the display graph --- has a specific kind of triangulation, which we call legal. Our…
We adapt the classical 3-decomposition of any 2-connected graph to the case of simple graphs (no loops or multiple edges). By analogy with the block-cutpoint tree of a connected graph, we deduce from this decomposition a bicolored tree…
Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics and can be approximated with the help of similarity measures between gene sequences, albeit not without errors. The corresponding…
Mixed graphs can be seen as digraphs with arcs and edges (or digons, that is, two opposite arcs). In this paper, we consider the case where such graphs are bipartite and in which the undirected and directed degrees are one. The best graphs,…
In this paper, we present a foundation study for proper colouring of edge-set graphs. The authors consider that a detailed study of the colouring of edge-set graphs corresponding to the family of paths is best suitable for such foundation…
We recall several known results about minimally 2-connected graphs, and show that they all follow from a decomposition theorem. Starting from an analogy with critically 2-connected graphs, we give structural characterizations of the classes…
A graph is called 1-planar if it can be drawn on the plane so that each edge is crossed by at most one other edge. In this paper, we establish a local property of 1-planar graphs which describes the structure in the neighborhood of small…
Subgraph matching is a fundamental building block for graph-based applications and is challenging due to its high-order combinatorial nature. Existing studies usually tackle it by combinatorial optimization or learning-based methods.…
Tree representations of (sets of) symmetric binary relations, or equivalently edge-colored undirected graphs, are of central interest, e.g.\ in phylogenomics. In this context symbolic ultrametrics play a crucial role. Symbolic ultrametrics…
We study a version of online edge coloring, where the goal is to color as many edges as possible using only a given number, $k$, of available colors. All of our results are with regard to competitive analysis. Previous attempts to identify…
We study two parameters that arise from the dichromatic number and the vertex-arboricity in the same way that the achromatic number comes from the chromatic number. The adichromatic number of a digraph is the largest number of colors its…
A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the…
We show that the edges of any graph $G$ containing two edge-disjoint spanning trees can be blue/red coloured so that the blue and red graphs are connected and the blue and red degrees at each vertex differ by at most four. This improves a…
2-quasi best match graphs (2-qBMGs) are directed graphs that capture a notion of close relatedness in phylogenetics. Here, we investigate the undirected underlying graph of a 2-qBMG (un-2qBMG) and show that they contain neither a path $P_l$…
Following the recent paper which initiated the study of colour isomorphism problems for complete graphs, we obtain upper bounds for $f_2(n,H)$ for a family of graphs $H$ obtained as the $K_0$-th rooted power of a balanced rooted tree for…
Maximal planar graph refers to the planar graph with the most edges, which means no more edges can be added so that the resulting graph is still planar. The Four-Color Conjecture says that every planar graph without loops is 4-colorable.…