相关论文: A quadratic kernel for computing the hybridization…

Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks, to distinguish different networks, and to see when one…

In the Tree Deletion Set problem the input is a graph G together with an integer k. The objective is to determine whether there exists a set S of at most k vertices such that G-S is a tree. The problem is NP-complete and even NP-hard to…

Phylogenetic reconciliation seeks to explain host-symbiont co-evolution by mapping parasite trees onto host trees through events such as cospeciation, duplication, host switching, and loss. Finding an optimal reconciliation that ensures…

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…

We show that Odd Cycle Transversal and Vertex Multiway Cut admit deterministic polynomial kernels when restricted to planar graphs and parameterized by the solution size. This answers a question of Saurabh. On the way to these results, we…

We study compact straight-line embeddings of trees. We show that perfect binary trees can be embedded optimally: a tree with $n$ nodes can be drawn on a $\sqrt n$ by $\sqrt n$ grid. We also show that testing whether a given binary tree has…

We study multivariate linear tensor product problems with some special properties in the worst case setting. We consider algorithms that use finitely many continuous linear functionals. We use a unified method to investigate tractability of…

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…

We propose a novel architecture for Graph Neural Networks that is inspired by the idea behind Tree Kernels of measuring similarity between trees by taking into account their common substructures, named fragments. By imposing a series of…

Quantum computers provide an opportunity to efficiently sample from probability distributions that include non-trivial interference effects between amplitudes. Using a simple process wherein all possible state histories can be specified by…

Different sources of information might tell different stories about the evolutionary history of a given set of species. This leads to (rooted) phylogenetic trees that "disagree" on triples of species, which we call "conflict triples". An…

A graph G=(V,E) is a 3-leaf power iff there exists a tree T whose leaves are V and such that (u,v) is an edge iff u and v are at distance at most 3 in T. The 3-leaf power graph edge modification problems, i.e. edition (also known as the…

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…

This work studies the combinatorial optimization problem of finding an optimal core tensor shape, also called multilinear rank, for a size-constrained Tucker decomposition. We give an algorithm with provable approximation guarantees for its…

Modeling multiple sampling densities within a hierarchical framework enables borrowing of information across samples. These density random effects can act as kernels in latent variable models to represent exchangeable subgroups or clusters.…

Holonomic equations are recursive equations which allow computing efficiently numbers of combinatoric objects. R{\'e}my showed that the holonomic equation associated with binary trees yields an efficient linear random generator of binary…

Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods…

Tanglegrams are drawings of two rooted binary phylogenetic trees and a matching between their leaf sets. The trees are drawn crossing-free on opposite sides with their leaf sets facing each other on two vertical lines. Instead of minimizing…

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…

In this paper, we study three algorithmic problems involving computation trees: the optimization, solvability, and satisfiability problems. The solvability problem is concerned with recognizing computation trees that solve problems. The…