Related papers: Parameterized Algorithms for Diversity of Networks…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
We consider the parameterized complexity of the problem of tracking shortest s-t paths in graphs, motivated by applications in security and wireless networks. Given an undirected and unweighted graph with a source s and a destination t,…
A phylogenetic network is a graph-theoretical tool that is used by biologists to represent the evolutionary history of a collection of species. One potential way of constructing such networks is via a distance-based approach, where one is…
Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks, to distinguish different networks, and to see when one…
We consider the well-studied problem of finding a spanning tree with minimum average distance between vertex pairs (called a MAD tree). This is a classic network design problem which is known to be NP-hard. While approximation algorithms…
The Edge Multicut problem is a classical cut problem where given an undirected graph $G$, a set of pairs of vertices $\mathcal{P}$, and a budget $k$, the goal is to determine if there is a set $S$ of at most $k$ edges such that for each…
We consider a the minimum k-way cut problem for unweighted graphs with a size bound s on the number of cut edges allowed. Thus we seek to remove as few edges as possible so as to split a graph into k components, or report that this requires…
Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the…
In this work, we study the $d$-Hitting Set and Feedback Vertex Set problems through the paradigm of finding diverse collections of $r$ solutions of size at most $k$ each, which has recently been introduced to the field of parameterized…
The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture.…
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…
Let G = (V, E) be a directed and weighted graph with vertex set V of size n and edge set E of size m, such that each edge (u, v) \in E has a real-valued weight w(u, c). An arborescence in G is a subgraph T = (V, E') such that for a vertex u…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
We introduce a general method for obtaining fixed-parameter algorithms for problems about finding paths in undirected graphs, where the length of the path could be unbounded in the parameter. The first application of our method is as…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
We present an axiomatic framework for analyzing the algorithmic properties of decision trees. This framework supports the classification of decision tree problems through structural and ancestral constraints within a rigorous mathematical…
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…
The Secluded Path problem models a situation where a sensitive information has to be transmitted between a pair of nodes along a path in a network. The measure of the quality of a selected path is its exposure, which is the total weight of…