Related papers: Unique perfect phylogeny is NP-hard
Pedigree graphs, or family trees, are typically constructed by an expensive process of examining genealogical records to determine which pairs of individuals are parent and child. New methods to automate this process take as input genetic…
We investigate the complexity of the reachability problem for (deep) neural networks: does it compute valid output given some valid input? It was recently claimed that the problem is NP-complete for general neural networks and…
Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…
Let $X$ be a finite set, $\mathcal N$ be a reticulation-visible network on $X$, and $\mathcal T$ be a rooted binary phylogenetic tree. We show that there is a polynomial-time algorithm for deciding whether or not $\mathcal N$ displays…
We consider the problem of finding a 1-planar drawing for a general graph, where a 1-planar drawing is a drawing in which each edge participates in at most one crossing. Since this problem is known to be NP-hard we investigate the…
We present approximation algorithms for the following NP-hard optimization problems related to bottleneck spanning trees in metric spaces. 1. The disjoint bottleneck spanning tree problem: Given $n$ pairs of points in a metric space, find…
In this paper we study the long-standing open question regarding the computational complexity of one of the core problems in supply chains management, the periodic joint replenishment problem. This problem has received a lot of attention…
We consider the following problem: Given a finite set of straight line segments in the plane, determine the positions of a minimal number of points on the segments, from which guards can see all segments. This problem can be interpreted as…
The complexity of the maximum common connected subgraph problem in partial $k$-trees is still not fully understood. Polynomial-time solutions are known for degree-bounded outerplanar graphs, a subclass of the partial $2$-trees. On the other…
We show that the following problems are NP-complete. 1. Can the vertex set of a graph be partitioned into two sets such that each set induces a perfect graph? 2. Is the difference between the chromatic number and clique number at most $1$…
For a fixed property (graph class) ${\Pi}$, given a graph G and an integer k, the ${\Pi}$-deletion problem consists in deciding if we can turn $G$ into a graph with the property ${\Pi}$ by deleting at most $k$ edges. The ${\Pi}$-deletion…
We prove that deciding whether the edge set of a graph can be partitionned into two spanning trees with orientation constraints is NP-complete. If P $\neq$ NP then this disproves a conjecture of Recski.
An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…
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…
A matching is a set of edges in a graph with no common endpoint. A matching M is called acyclic if the induced subgraph on the endpoints of the edges in M is acyclic. Given a graph G and an integer k, Acyclic Matching Problem seeks for an…
A treedepth decomposition of an undirected graph $G$ is a rooted forest $F$ on the vertex set of $G$ such that every edge $uv\in E(G)$ is in ancestor-descendant relationship in $F$. Given a weight function $w\colon V(G)\rightarrow…
In the Generalized Noah's Ark Problem, one is given a phylogenetic tree on a set of species X and a set of conservation projects for each species. Each project comes with a cost and raises the survival probability of the corresponding…
We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet is not consistent with the true…
This paper discusses the complexity of graph pebbling, dealing with both traditional pebbling and the recently introduced game of cover pebbling. Determining whether a configuration is solvable according to either the traditional definition…
In graph realization problems one is given a degree sequence and the task is to decide whether there is a graph whose vertex degrees match to the given sequence. This realization problem is known to be polynomial-time solvable when the…