Related papers: Unique perfect phylogeny is NP-hard
Geometric embedding of graphs in a point set in the plane is a well known problem. In this paper, the complexity of a variant of this problem, where the point set is bounded by a simple polygon, is considered. Given a point set in the plane…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
We investigate the tractability of a simple fusion of two fundamental structures on graphs, a spanning tree and a perfect matching. Specifically, we consider the following problem: given an edge-weighted graph, find a minimum-weight…
Recently, the minimum number of reticulation events that is required to simultaneously embed a collection P of rooted binary phylogenetic trees into a so-called temporal network has been characterized in terms of cherry-picking sequences.…
It has recently been shown that the NP-hard problem of calculating the minimum number of hybridization events that is needed to explain a set of rooted binary phylogenetic trees by means of a hybridization network is fixed-parameter…
Recently, Hajirasouliha and Raphael (WABI 2014) proposed a model for deconvoluting mixed tumor samples measured from a collection of high-throughput sequencing reads. This is related to understanding tumor evolution and critical cancer…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
We study the problem of decomposing (clustering) a tree with respect to costs attributed to pairs of nodes, so as to minimize the sum of costs for those pairs of nodes that are in the same component (cluster). For the general case and for…
The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view…
In a previous work, we gave a metric on the class of semibinary tree-sibling time consistent phylogenetic networks that is computable in polynomial time; in particular, the problem of deciding if two networks of this kind are isomorphic is…
In computational phylogenetics, the problem of constructing a supertree of a given set of rooted input trees can be formalized in different ways, to cope with contradictory information in the input. We consider the Minimum Flip Supertree…
We prove that it is NP-hard to decide whether two points in a polygonal domain with holes can be connected by a wire. This implies that finding any approximation to the shortest path for a long snake amidst polygonal obstacles is NP-hard.…
We consider the task of properly PAC learning decision trees with queries. Recent work of Koch, Strassle, and Tan showed that the strictest version of this task, where the hypothesis tree $T$ is required to be optimally small, is NP-hard.…
In the Maximize Phylogenetic Diversity problem, we are given a phylogenetic tree that represents the genetic proximity of species, and we are asked to select a subset of species of maximum phylogenetic diversity to be preserved through…
Given an order, a commutative ring whose additive group is free of finite rank, a natural computational question is whether a fixed univariate polynomial $f \in \mathbb{Z}[X]$ has a root in this ring. In this paper, we show that the…
In conservation biology, phylogenetic diversity (PD) provides a way to quantify the impact of the current rapid extinction of species on the evolutionary `Tree of Life'. This approach recognises that extinction not only removes species but…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
We prove that multilinear (tensor) analogues of many efficiently computable problems in numerical linear algebra are NP-hard. Our list here includes: determining the feasibility of a system of bilinear equations, deciding whether a 3-tensor…
The perfect phylogeny problem is a classic problem in computational biology, where we seek an unrooted phylogeny that is compatible with a set of qualitative characters. Such a tree exists precisely when an intersection graph associated…