Related papers: Treewidth distance on phylogenetic trees
The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small world property of real…
The constraint complexity of a graphical realization of a linear code is the maximum dimension of the local constraint codes in the realization. The treewidth of a linear code is the least constraint complexity of any of its cycle-free…
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…
We present a method for learning treewidth-bounded Bayesian networks from data sets containing thousands of variables. Bounding the treewidth of a Bayesian greatly reduces the complexity of inferences. Yet, being a global property of the…
We present a constraint model for the problem of producing a tree decomposition of a graph. The inputs to the model are a simple graph G, the number of nodes in the desired tree decomposition and the maximum cardinality of each node in that…
Cliquewidth is a dense analogue of treewidth. It can be deduced from recent results by Hickingbotham [arXiv:2501.10840] and Nguyen, Scott, and Seymour [arXiv:2501.09839] that graphs of bounded cliquewidth are quasi-isometric to graphs of…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
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…
In this paper, we characterise graphs that are quasi-isometric to graphs with bounded treewidth. Specifically, we prove that a graph is quasi-isometric to a graph with bounded treewidth if and only if it has a tree-decomposition where each…
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…
In the first paper of the Graph Minors series [JCTB '83], Robertson and Seymour proved the Forest Minor theorem: the $H$-minor-free graphs have bounded pathwidth if and only if $H$ is a forest. In recent years, considerable effort has been…
Treewidth is a measure of how tree-like a graph is. It has many important algorithmic applications because many NP-hard problems on general graphs become tractable when restricted to graphs of bounded treewidth. Algorithms for problems on…
For a fixed finite collection of graphs ${\cal F}$, the ${\cal F}$-M-DELETION problem asks, given an $n$-vertex input graph $G,$ for the minimum number of vertices that intersect all minor models in $G$ of the graphs in ${\cal F}$. by…
The notion of directed treewidth was introduced by Johnson, Robertson, Seymour and Thomas [Journal of Combinatorial Theory, Series B, Vol 82, 2001] as a first step towards an algorithmic metatheory for digraphs. They showed that some…
Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…
We apply a recent duality theorem for tangles in abstract separation systems to derive tangle-type duality theorems for width-parameters in graphs and matroids. We further derive a duality theorem for the existence of clusters in large data…
A graph class is monotone if it is closed under taking subgraphs. It is known that a monotone class defined by finitely many obstructions has bounded treewidth if and only if one of the obstructions is a so-called tripod, that is, a…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…