Related papers: A Polynomial Kernel For Multicut In Trees
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
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…
The Steiner Multicut problem asks, given an undirected graph G, terminals sets T1,...,Tt $\subseteq$ V(G) of size at most p, and an integer k, whether there is a set S of at most k edges or nodes s.t. of each set Ti at least one pair of…
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…
In the Block Graph Deletion problem, we are given a graph $G$ on $n$ vertices and a positive integer $k$, and the objective is to check whether it is possible to delete at most $k$ vertices from $G$ to make it a block graph, i.e., a graph…
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…
We define the (random) $k$-cut number of a rooted graph to model the difficulty of the destruction of a resilient network. The process is as the cut model of Meir and Moon except now a node must be cut $k$ times before it is destroyed. The…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
The $P_2$-packing problem asks for whether a graph contains $k$ vertex-disjoint paths each of length two. We continue the study of its kernelization algorithms, and develop a $5k$-vertex kernel.
This paper investigates the execution of tree-shaped task graphs using multiple processors. Each edge of such a tree represents a large IO file. A task can only be executed if all input and output files fit into memory, and a file can only…
We give a kernel with $O(k^7)$ vertices for Trivially Perfect Editing, the problem of adding or removing at most $k$ edges in order to make a given graph trivially perfect. This answers in affirmative an open question posed by Nastos and…
Given two rooted, ordered, and labeled trees $P$ and $T$ the tree inclusion problem is to determine if $P$ can be obtained from $T$ by deleting nodes in $T$. This problem has recently been recognized as an important query primitive in XML…
A subgraph $T$ of a digraph $D$ is an {\em out-branching} if $T$ is an oriented spanning tree with only one vertex of in-degree zero (called the {\em root}). The vertices of $T$ of out-degree zero are {\em leaves}. In the {\sc Directed…
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…
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…
A graph is distance-hereditary if for any pair of vertices, their distance in every connected induced subgraph containing both vertices is the same as their distance in the original graph. The Distance-Hereditary Vertex Deletion problem…
The Subset Feedback Vertex Set problem generalizes the classical Feedback Vertex Set problem and asks, for a given undirected graph $G=(V,E)$, a set $S \subseteq V$, and an integer $k$, whether there exists a set $X$ of at most $k$ vertices…
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…
A soft tree is an actively studied variant of a decision tree that updates splitting rules using the gradient method. Although soft trees can take various architectures, their impact is not theoretically well known. In this paper, we…
Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…