Related papers: Treewidth of display graphs: bounds, brambles and …
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
Graphs with bounded treewidth and bounded maximum degree are known to have tree-partitions of bounded width. What can be said if the bounded treewidth assumption is strengthened to bounded pathwidth? We prove that every graph with bounded…
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…
Let $H=(V,F)$ be a simple hypergraph without loops. $H$ is called linear if $|f\cap g|\le 1$ for any $f,g\in F$ with $f\not=g$. The $2$-section of $H$, denoted by $[H]_2$, is a graph with $V([H]_2)=V$ and for any $ u,v\in V([H]_2)$, $uv\in…
Bounded infinite graphs are defined on the basis of natural physical requirements. When specialized to trees this definition leads to a natural conjecture that the average connectivity dimension of bounded trees cannot exceed two. We verify…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…
We continue the study of $(\mathrm{tw},\omega)$-bounded graph classes, that is, hereditary graph classes in which the treewidth can only be large due to the presence of a large clique, with the goal of understanding the extent to which this…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
Rooted acyclic graphs appear naturally when the phylogenetic relationship of a set $X$ of taxa involves not only speciations but also recombination, horizontal transfer, or hybridization, that cannot be captured by trees. A variety of…
Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…
We identify a sufficient condition, treewidth-pliability, that gives a polynomial-time algorithm for an arbitrarily good approximation of the optimal value in a large class of Max-2-CSPs parameterised by the class of allowed constraint…
Parameterized algorithms are a way to solve hard problems more efficiently, given that a specific parameter of the input is small. In this paper, we apply this idea to the field of answer set programming (ASP). To this end, we propose two…
Treewidth is a useful tool in designing graph algorithms. Although many NP-hard graph problems can be solved in linear time when the input graphs have small treewidth, there are problems which remain hard on graphs of bounded treewidth. In…
In this paper we extend the theory of bidimensionality to two families of graphs that do not exclude fixed minors: map graphs and power graphs. In both cases we prove a polynomial relation between the treewidth of a graph in the family and…
Consider a drawing of a graph $G$ in the plane such that crossing edges are coloured differently. The minimum number of colours, taken over all drawings of $G$, is the classical graph parameter "thickness". By restricting the edges to be…
Phylogenetic networks are used to study evolutionary relationships between species in biology. Such networks are often categorized into classes by their topological features, which stem from both biological and computational motivations. We…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
This work presents novel algorithms for learning Bayesian network structures with bounded treewidth. Both exact and approximate methods are developed. The exact method combines mixed-integer linear programming formulations for structure…