Related papers: Average-Tree Phylogenetic Diversity Parameterized …
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
The notion of treewidth plays an important role in theoretical and practical studies of graph problems. It has been recognized that, especially in practical environments, when computing the treewidth of a graph it is invaluable to first…
We introduce a new spatial data structure for high dimensional data called the \emph{approximate principal direction tree} (APD tree) that adapts to the intrinsic dimension of the data. Our algorithm ensures vector-quantization accuracy…
Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still be present at some future time, then this…
The Subgraph Isomorphism problem is of considerable importance in computer science. We examine the problem when the pattern graph H is of bounded treewidth, as occurs in a variety of applications. This problem has a well-known algorithm via…
Rooted triples, rooted binary phylogenetic trees on three leaves, are sufficient to encode rooted binary phylogenetic trees. That is, if $\mathcal T$ and $\mathcal T'$ are rooted binary phylogenetic $X$-trees that infers the same set of…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
An added edge to a graph is called an inset edge. Predicting k inset edges which minimize the average distance of a graph is known to be NP-Hard. When k = 1 the complexity of the problem is polynomial. In this paper, we further find the…
Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods…
Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…
A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…
In the study of rooted phylogenetic networks, analyzing the set of rooted phylogenetic trees that are embedded in such a network is a recurring task. From an algorithmic viewpoint, this analysis almost always requires an exhaustive search…
The maximum/minimum bisection problems are, given an edge-weighted graph, to find a bipartition of the vertex set into two sets whose sizes differ by at most one, such that the total weight of edges between the two sets is…
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…
Tree-width and path-width are widely successful concepts. Many NP-hard problems have efficient solutions when restricted to graphs of bounded tree-width. Many efficient algorithms are based on a tree decomposition. Sometimes the more…
The three-in-a-tree problem asks for an induced tree of the input graph containing three mandatory vertices. In 2006, Chudnovsky and Seymour [Combinatorica, 2010] presented the first polynomial time algorithm for this problem, which has…
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…
The planted densest subgraph detection problem refers to the task of testing whether in a given (random) graph there is a subgraph that is unusually dense. Specifically, we observe an undirected and unweighted graph on $n$ vertices. Under…
We consider algorithms for finding and counting small, fixed graphs in sparse host graphs. In the non-sparse setting, the parameters treedepth and treewidth play a crucial role in fast, constant-space and polynomial-space algorithms…