Related papers: Kernelizations for the hybridization number proble…
Network Phylogenetic Diversity (Network-PD) is a measure for the diversity of a set of species based on a rooted phylogenetic network (with branch lengths and inheritance probabilities on the reticulation edges) describing the evolution of…
Given a dense triplet set $\mathcal{T}$, there arise two interesting questions: Does there exists any phylogenetic network consistent with $\mathcal{T}$? And if so, can we find an effective algorithm to construct one? For cases of networks…
In a parameterized problem, every instance I comes with a positive integer k. The problem is said to admit a polynomial kernel if, in polynomial time, one can reduce the size of the instance I to a polynomial in k, while preserving the…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
There are existing standard solvers for tackling discrete optimization problems. However, in practice, it is uncommon to apply them directly to the large input space typical of this class of problems. Rather, the input is preprocessed to…
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…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
Kernelization is a theoretical formalization of efficient preprocessing for NP-hard problems. Empirically, preprocessing is highly successful in practice, for example in state-of-the-art ILP-solvers like CPLEX. Motivated by this, previous…
We study the CONNECTED \eta-TREEDEPTH DELETION problem where the input instance is an undireted graph G = (V, E) and an integer k. The objective is to decide if G has a set S \subseteq V(G) of at most k vertices such that G - S has…
Hybridization networks are representations of evolutionary histories that allow for the inclusion of reticulate events like recombinations, hybridizations, or lateral gene transfers. The recent growth in the number of hybridization network…
We consider the following problem about dispersing points. Given a set of points in the plane, the task is to identify whether by moving a small number of points by small distance, we can obtain an arrangement of points such that no pair of…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
Kernelization is an important tool in parameterized algorithmics. Given an input instance accompanied by a parameter, the goal is to compute in polynomial time an equivalent instance of the same problem such that the size of the reduced…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
Dealing with NP-hard problems, kernelization is a fundamental notion for polynomial-time data reduction with performance guarantees: in polynomial time, a problem instance is reduced to an equivalent instance with size upper-bounded by a…
Let F be a finite family of graphs. In the F-Deletion problem, one is given a graph G and an integer k, and the goal is to find k vertices whose deletion results in a graph with no minor from the family F. This may be regarded as a…
Fix an integer h>=1. In the universe of coloured trees of height at most h, we prove that for any graph decision problem defined by an MSO formula with r quantifiers, there exists a set of kernels, each of size bounded by an elementary…
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…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…