Related papers: Treewidth distance on phylogenetic trees
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
We address the problem of building and maintaining distributed spanning trees in highly dynamic networks, in which topological events can occur at any time and any rate, and no stable periods can be assumed. In these harsh environments, we…
Merge trees are a type of graph-based topological summary that tracks the evolution of connected components in the sublevel sets of scalar functions. They enjoy widespread applications in data analysis and scientific visualization. In this…
We describe a polynomial-time algorithm which, given a graph $G$ with treewidth $t$, approximates the pathwidth of $G$ to within a ratio of $O(t\sqrt{\log t})$. This is the first algorithm to achieve an $f(t)$-approximation for some…
The Subtree Isomorphism problem asks whether a given tree is contained in another given tree. The problem is of fundamental importance and has been studied since the 1960s. For some variants, e.g., ordered trees, near-linear time algorithms…
The notion of treewidth plays an important role in theoretical and practical studies of graph problems. It has been recognized that, especially in practical environments, when computing the treewidth of a graph it is invaluable to first…
A breakthrough result of Cygan et al. (FOCS 2011) showed that connectivity problems parameterized by treewidth can be solved much faster than the previously best known time $\mathcal{O}^*(2^{\mathcal{O}(tw \log(tw))})$. Using their inspired…
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…
Merge trees are a common topological descriptor for data with a hierarchical component, such as terrains and scalar fields. The interleaving distance, in turn, is a common distance for comparing merge trees. However, the interleaving…
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…
When does a graph admit a tree-decomposition in which every bag has small diameter? For finite graphs, this is a property of interest in algorithmic graph theory, where it is called having bounded ``tree-length''. We will show that this is…
Reticulate evolution gives rise to complex phylogenetic networks, making their interpretation challenging. A typical approach is to extract trees within such networks. Since Francis and Steel's seminal paper, "Which Phylogenetic Networks…
Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…
We present a concept called the branch-depth of a connectivity function, that generalizes the tree-depth of graphs. Then we prove two theorems showing that this concept aligns closely with the notions of tree-depth and shrub-depth of graphs…
Brambles were introduced as the dual notion to treewidth, one of the most central concepts of the graph minor theory of Robertson and Seymour. Recently, Grohe and Marx showed that there are graphs G, in which every bramble of order larger…
Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that…
In this paper, we give a constructive proof of the fact that the treewidth of a graph is at most its divisorial gonality. The proof gives a polynomial time algorithm to construct a tree decomposition of width at most $k$, when an effective…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
We introduce the problem of finding a spanning tree along with a partition of the tree edges into fewest number of feasible sets, where constraints on the edges define feasibility. The motivation comes from wireless networking, where we…
In this paper, we study Reiter's propositional default logic when the treewidth of a certain graph representation (semi-primal graph) of the input theory is bounded. We establish a dynamic programming algorithm on tree decompositions that…