Related papers: The First Known Problem That Is FPT with Respect t…
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…
To measure the tree-likeness of a directed acyclic graph (DAG), a new width parameter that considers the directions of the arcs was recently introduced: scanwidth. We present the first algorithm that efficiently computes the exact scanwidth…
For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be…
Over the past decade, we witness an increasing amount of interest in the design of exact exponential-time and parameterized algorithms for problems in Graph Drawing. Unfortunately, we still lack knowledge of general methods to develop such…
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…
The recently introduced graph parameter tree-cut width plays a similar role with respect to immersions as the graph parameter treewidth plays with respect to minors. In this paper, we provide the first algorithmic applications of tree-cut…
We investigate parameterized algorithms for computing the average-tree phylogenetic diversity (APD) in rooted phylogenetic networks, studying the problem under different structural parameters that capture the deviation of a network from a…
We present the first fixed-parameter tractable (FPT) algorithms for exact computation of generalized hypertree width (ghw) and fractional hypertree width (fhw). Our algorithms are parameterized by the target width, the rank, and the maximum…
In the NP-hard Optimizing PD with Dependencies (PDD) problem, the input consists of a phylogenetic tree $T$ over a set of taxa $X$, a food-web that describes the prey-predator relationships in $X$, and integers $k$ and $D$. The task is to…
Decompositional parameters such as treewidth are commonly used to obtain fixed-parameter algorithms for NP-hard graph problems. For problems that are W[1]-hard parameterized by treewidth, a natural alternative would be to use a suitable…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
There are many classical problems in P whose time complexities have not been improved over the past decades. Recent studies of "Hardness in P" have revealed that, for several of such problems, the current fastest algorithm is the best…
Finding a few solutions for a given problem that are diverse, as opposed to finding a single best solution to solve the problem, has recently become a notable topic in theoretical computer science. Recently, Baste, Fellows, Jaffke,…
Branchwidth determines how graphs, and more generally, arbitrary connectivity (basically symmetric and submodular) functions could be decomposed into a tree-like structure by specific cuts. We develop a general framework for designing…
We show that some natural problems that are XNLP-hard (which implies W[t]-hardness for all t) when parameterized by pathwidth or treewidth, become FPT when parameterized by stable gonality, a novel graph parameter based on optimal maps from…
As proteins with similar structures often have similar functions, analysis of protein structures can help predict protein functions and is thus important. We consider the problem of protein structure classification, which computationally…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
Phylogenetic networks are directed acyclic graphs that depict the genomic evolution of related taxa. Reticulation nodes in such networks (nodes with more than one parent) represent reticulate evolutionary events, such as recombination,…
A set S of vertices of a graph is a defensive alliance if, for each element of S, the majority of its neighbors is in S. The problem of finding a defensive alliance of minimum size in a given graph is NP-hard and there are polynomial-time…
Grid graphs, and, more generally, $k\times r$ grid graphs, form one of the most basic classes of geometric graphs. Over the past few decades, a large body of works studied the (in)tractability of various computational problems on grid…