Related papers: A quadratic kernel for computing the hybridization…

With the advent of kernel methods, automating the task of specifying a suitable kernel has become increasingly important. In this context, the Multiple Kernel Learning (MKL) problem of finding a combination of pre-specified base kernels…

Kernelization---a mathematical key concept for provably effective polynomial-time preprocessing of NP-hard problems---plays a central role in parameterized complexity and has triggered an extensive line of research. This is in part due to a…

The maximum agreement forest (MAF) problem in phylogenetics takes as input a set t >= 2 of binary phylogenetic trees T on the same set of taxa X. It asks for a partition of X into the smallest number of blocks such that the subtrees induced…

We show that two important problems that have applications in computational biology are ASP-complete, which implies that, given a solution to a problem, it is NP-complete to decide if another solution exists. We show first that a variation…

What is the minimal information that a robot must retain to achieve its task? To design economical robots, the literature dealing with reduction of combinatorial filters approaches this problem algorithmically. As lossless state compression…

The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes.…

An enumeration kernel as defined by Creignou et al. [Theory Comput. Syst. 2017] for a parameterized enumeration problem consists of an algorithm that transforms each instance into one whose size is bounded by the parameter plus a…

Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…

A hierarchical, reversible mapping between levels of tree structured computation, applicable for structuring the Quantum Computation algorithm for NP-complete problem is presented. It is proven that confining the state of a quantum computer…

We consider the well-studied problem of finding a spanning tree with minimum average distance between vertex pairs (called a MAD tree). This is a classic network design problem which is known to be NP-hard. While approximation algorithms…

The Treewidth-2 Vertex Deletion problem asks whether a set of at most $t$ vertices can be removed from a graph, such that the resulting graph has treewidth at most two. A graph has treewidth at most two if and only if it does not contain a…

Counting the number of answers to conjunctive queries is a fundamental problem in databases that, under standard assumptions, does not have an efficient solution. The issue is inherently #P-hard, extending even to classes of acyclic…

While every rooted binary phylogenetic tree is determined by its set of displayed rooted triples, such a result does not hold for an arbitrary rooted binary phylogenetic network. In particular, there exist two non-isomorphic 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…

We develop a technique that we call Conflict Packing in the context of kernelization, obtaining (and improving) several polynomial kernels for editing problems on dense instances. We apply this technique on several well-studied problems:…

When modeling an application of practical relevance as an instance of a combinatorial problem X, we are often interested not merely in finding one optimal solution for that instance, but in finding a sufficiently diverse collection of good…

Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…

We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…

Tree kernels are fundamental tools that have been leveraged in many applications, particularly those based on machine learning for Natural Language Processing tasks. In this paper, we devise a parallel implementation of the sequential…

The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…