Related papers: Kernelizations for the hybridization number proble…
We present a polynomial time algorithm that for any graph G and integer k >= 0, either finds a spanning tree with at least k internal vertices, or outputs a new graph G' on at most 3k vertices and an integer k' such that G has a spanning…
A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…
This paper focuses on kernelization algorithms for the fundamental Knapsack problem. A kernelization algorithm (or kernel) is a polynomial-time reduction from a problem onto itself, where the output size is bounded by a function of some…
Recently there has been considerable interest in the problem of finding a phylogenetic network with a minimum number of reticulation vertices which displays a given set of phylogenetic trees, that is, a network with minimum hybrid number.…
The most efficient algorithms for finding maximum independent sets in both theory and practice use reduction rules to obtain a much smaller problem instance called a kernel. The kernel can then be solved quickly using exact or heuristic…
For a fixed graph $H$, the $H$-Coloring problem asks whether a given graph admits an edge-preserving function from its vertex set to that of $H$. A seminal theorem of Hell and Ne\v{s}et\v{r}il asserts that the $H$-Coloring problem is…
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…
Phylogenetic trees and networks are graphs used to model evolutionary relationships, with trees representing strictly branching histories and networks allowing for events in which lineages merge, called reticulation events. While the…
We study a general class of problems called F-deletion problems. In an F-deletion problem, we are asked whether a subset of at most $k$ vertices can be deleted from a graph $G$ such that the resulting graph does not contain as a minor any…
Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set $\mathcal{T}$ of binary binets or…
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…
A new method for hierarchical clustering is presented. It combines treelets, a particular multiscale decomposition of data, with a projection on a reproducing kernel Hilbert space. The proposed approach, called kernel treelets (KT),…
We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages…
Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…
A normal (phylogenetic) network with $k$ reticulations displays $2^k$ phylogenetic trees. In this paper, we establish an analogous result for tree-child (phylogenetic) networks with no underlying $3$-cycles. In particular, we show that a…
We show that the problem of computing the hybridization number of two rooted binary phylogenetic trees on the same set of taxa X has a constant factor polynomial-time approximation if and only if the problem of computing a minimum-size…
The notion of Turing kernelization investigates whether a polynomial-time algorithm can solve an NP-hard problem, when it is aided by an oracle that can be queried for the answers to bounded-size subproblems. One of the main open problems…
Makespan minimization (on parallel identical or unrelated machines) is arguably the most natural and studied scheduling problem. A common approach in practical algorithm design is to reduce the size of a given instance by a fast…
The NP-complete $k$-Path problem asks whether a given undirected graph has a (simple) path of length at least $k$. We prove that $k$-Path has polynomial-size Turing kernels when restricted to planar graphs, graphs of bounded degree,…
For a given set $\mathcal{L}$ of species and a set $\mathcal{T}$ of triplets on $\mathcal{L}$, one wants to construct a phylogenetic network which is consistent with $\mathcal{T}$, i.e which represents all triplets of $\mathcal{T}$. The…