Related papers: Kernelizations for the hybridization number proble…
Kernelization is a formalization of efficient preprocessing for NP-hard problems using the framework of parameterized complexity. Among open problems in kernelization it has been asked many times whether there are deterministic polynomial…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be…
Parallel fixed-parameter tractability studies how parameterized problems can be solved in parallel. A surprisingly large number of parameterized problems admit a high level of parallelization, but this does not mean that we can also…
We introduce a graph partitioning problem motivated by computational topology and propose two algorithms that produce approximate solutions. Specifically, given a weighted, undirected graph $G$ and a positive integer $k$, we desire to find…
For all integers $k\geq 3$, we give an $O(n^4)$ time algorithm for the problem whose instance is a graph $G$ of girth at least $k$ together with $k$ vertices and whose question is "Does $G$ contains an induced subgraph containing the $k$…
We study the kernel complexity of constraint satisfaction problems over a finite domain, parameterized by the number of variables, whose constraint language consists of two relations: the non-equality relation and an additional…
The notion of a (polynomial) kernelization from parameterized complexity is a well-studied model for efficient preprocessing for hard computational problems. By now, it is quite well understood which parameterized problems do or…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
A kernelization is an efficient algorithm that given an instance of a parameterized problem returns an equivalent instance of size bounded by some function of the input parameter value. It is quite well understood which problems do or…
Two kinds of approximation algorithms exist for the k-BALANCED PARTITIONING problem: those that are fast but compute unsatisfying approximation ratios, and those that guarantee high quality ratios but are slow. In this paper we prove that…
Several computational problems in phylogenetic reconstruction can be formulated as restrictions of the following general problem: given a formula in conjunctive normal form where the literals are rooted triples, is there a rooted binary…
We present a geometric formulation of the Multiple Kernel Learning (MKL) problem. To do so, we reinterpret the problem of learning kernel weights as searching for a kernel that maximizes the minimum (kernel) distance between two convex…
In the Vector Connectivity problem we are given an undirected graph $G=(V,E)$, a demand function $\phi\colon V\to\{0,\ldots,d\}$, and an integer $k$. The question is whether there exists a set $S$ of at most $k$ vertices such that every…
Enumerative kernelization is a recent and promising area sitting at the intersection of parameterized complexity and enumeration algorithms. Its study began with the paper of Creignou et al. [Theory Comput. Syst., 2017], and development in…
The Maximum Agreement Forest problem has been extensively studied in phylogenetics. Most previous work is on two binary phylogenetic trees. In this paper, we study a generalized version of the problem: the Maximum Agreement Forest problem…
The storage capacity of a graph measures the maximum amount of information that can be stored across its vertices, such that the information at any vertex can be recovered from the information stored at its neighborhood. The study of this…
Given a set $X$ of species, a phylogenetic tree is an unrooted binary tree whose leaves are bijectively labelled by $X$. Such trees can be used to show the way species evolve over time. One way of understanding how topologically different…
Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…
The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work…