Related papers: Kernelizations for the hybridization number proble…
The theory of kernelization can be used to rigorously analyze data reduction for graph coloring problems. Here, the aim is to reduce a q-Coloring input to an equivalent but smaller input whose size is provably bounded in terms of structural…
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…
We re-visit the complexity of kernelization for the $d$-Hitting Set problem. This is a classic problem in Parameterized Complexity, which encompasses several other of the most well-studied problems in this field, such as Vertex Cover,…
For a fixed finite family of graphs $\mathcal{F}$, the $\mathcal{F}$-Minor-Free Deletion problem takes as input a graph $G$ and an integer $\ell$ and asks whether there exists a set $X \subseteq V(G)$ of size at most $\ell$ such that $G-X$…
Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph…
Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees,…
In the Vertex Cover problem we are given a graph $G=(V,E)$ and an integer $k$ and have to determine whether there is a set $X\subseteq V$ of size at most $k$ such that each edge in $E$ has at least one endpoint in $X$. The problem can be…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet…
We introduce a new framework for the analysis of preprocessing routines for parameterized counting problems. Existing frameworks that encapsulate parameterized counting problems permit the usage of exponential (rather than polynomial) time…
Enumeration kernelization for parameterized enumeration problems was defined by Creignou et al. [Theory Comput. Syst. 2017] and was later refined by Golovach et al. [J. Comput. Syst. Sci. 2022, STACS 2021] to polynomial-delay enumeration…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…
$H$-Packing is the problem of finding a maximum number of vertex-disjoint copies of $H$ in a given graph $G$. $H$-Partition is the special case of finding a set of vertex-disjoint copies that cover each vertex of $G$ exactly once. Our goal…
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…
The graph crossing number problem, cr(G)<=k, asks for a drawing of a graph G in the plane with at most k edge crossings. Although this problem is in general notoriously difficult, it is fixed- parameter tractable for the parameter k…
In previous work, we gave asymptotic counting results for the number of tree-child and normal networks with $k$ reticulation vertices and explicit exponential generating functions of the counting sequences for $k=1,2,3$. The purpose of this…
Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…
It is known that any two trees on the same $n$ leaves can be displayed by a network with $n-2$ reticulations, and there are two trees that cannot be displayed by a network with fewer reticulations. But how many reticulations are needed to…
We consider the problem of embedding the Steiner points of a Steiner tree with given topology into the rectilinear plane. Thereby, the length of the path between a distinguished terminal and each other terminal must not exceed given length…