The {\sc $k$-Leaf Out-Branching} problem is to find an out-branching (i.e. a rooted oriented spanning tree) with at least $k$ leaves in a given digraph. The problem has recently received much attention from the viewpoint of parameterized algorithms {alonLNCS4596,AlonFGKS07fsttcs,BoDo2,KnLaRo}. In this paper we step aside and take a kernelization based approach to the {\sc $k$-Leaf-Out-Branching} problem. We give the first polynomial kernel for {\sc Rooted $k$-Leaf-Out-Branching}, a variant of {\sc $k$-Leaf-Out-Branching} where the root of the tree searched for is also a part of the input. Our kernel has cubic size and is obtained using extremal combinatorics.
For the {\sc $k$-Leaf-Out-Branching} problem we show that no polynomial kernel is possible unless polynomial hierarchy collapses to third level %$PH=Σ_p^3$ by applying a recent breakthrough result by Bodlaender et al. {BDFH08} in a non-trivial fashion. However our positive results for {\sc Rooted $k$-Leaf-Out-Branching} immediately imply that the seemingly intractable the {\sc $k$-Leaf-Out-Branching} problem admits a data reduction to $n$ independent $O(k^3)$ kernels. These two results, tractability and intractability side by side, are the first separating {\it many-to-one kernelization} from {\it Turing kernelization}. This answers affirmatively an open problem regarding "cheat kernelization" raised in {IWPECOPEN08}.
We consider the problem of finding a spanning tree with maximum number of leaves (MaxLeaf). A 2-approximation algorithm is known for this problem, and a 3/2-approximation algorithm when restricted to graphs where every vertex has degree 3 (cubic graphs). MaxLeaf is known to be APX-hard in general, and NP-hard for cubic graphs. We show that the problem is also APX-hard for cubic graphs. The APX-hardness of the related problem Minimum Connected Dominating Set for cubic graphs follows.
We extend the notion of lossy kernelization, introduced by Lokshtanov et al. [STOC 2017], to approximate Turing kernelization. An $α$-approximate Turing kernel for a parameterized optimization problem is a polynomial-time algorithm that, when given access to an oracle that outputs $c$-approximate solutions in $O(1)$ time, obtains an $(α\cdot c)$-approximate solution to the considered problem, using calls to the oracle of size at most $f(k)$ for some function $f$ that only depends on the parameter. Using this definition, we show that Independent Set parameterized by treewidth $\ell$ has a $(1+\…
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 $k$-Leaf} Problem, we are given a digraph $D$ and an integral parameter $k$, and we are to decide whether $D$ has an out-branching with at least $k$ leaves. Recently, Kneis et al. (2008) obtained an algorithm for the problem of running time $4^{k}\cdot n^{O(1)}$. We describe a new algorithm for the problem of running time $3.72^{k}\cdot n^{O(1)}$. In {\sc Rooted…
The {\sc Directed Maximum Leaf Out-Branching} problem is to find an out-branching (i.e. a rooted oriented spanning tree) in a given digraph with the maximum number of leaves. In this paper, we obtain two combinatorial results on the number of leaves in out-branchings. We show that - every strongly connected $n$-vertex digraph $D$ with minimum in-degree at least 3 has an out-branching with at least $(n/4)^{1/3}-1$ leaves; - if a strongly connected digraph $D$ does not contain an out-branching with $k$ leaves, then the pathwidth of its underlying graph UG($D$) is $O(k\log k)$. Moreover, if the d…
We show two results related to the Hamiltonicity and $k$-Path algorithms in undirected graphs by Björklund [FOCS'10], and Björklund et al., [arXiv'10]. First, we demonstrate that the technique used can be generalized to finding some $k$-vertex tree with $l$ leaves in an $n$-vertex undirected graph in $O^*(1.657^k2^{l/2})$ time. It can be applied as a subroutine to solve the $k$-Internal Spanning Tree ($k$-IST) problem in $O^*(\min(3.455^k, 1.946^n))$ time using polynomial space, improving upon previous algorithms for this problem. In particular, for the first time we break the natural barrier …
Let $G$ be a graph and $T_1,T_2$ be two spanning trees of $G$. We say that $T_1$ can be transformed into $T_2$ via an edge flip if there exist two edges $e \in T_1$ and $f$ in $T_2$ such that $T_2= (T_1 \setminus e) \cup f$. Since spanning trees form a matroid, one can indeed transform a spanning tree into any other via a sequence of edge flips, as observed by Ito et al. We investigate the problem of determining, given two spanning trees $T_1,T_2$ with an additional property $Π$, if there exists an edge flip transformation from $T_1$ to $T_2$ keeping property $Π$ all along. First we show that …
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of species. An agreement subtree of two evolutionary trees is an evolutionary tree which is also a topological subtree of the two given trees. We give an algorithm to determine the largest possible number of leaves in any agreement subtree of two trees T_1 and T_2 with n leaves each. If the maximum degree d of these trees is bounded by a constant, the time compl…
We study the growth of a time-ordered rooted tree by probabilistic attachment of new vertices to leaves. We construct a likelihood function of the leaves based on the connectivity of the tree. We take such connectivity to be induced by the merging of directed ordered paths from leaves to the root. Combining the likelihood with an assigned prior distribution leads to a posterior leaf distribution from which we sample attachment points for new vertices. We present computational examples of such Bayesian tree growth. Although the discussion is generic, the initial motivation for the paper is the …
We consider the parameterized version of the maximum internal spanning tree problem, which, given an $n$-vertex graph and a parameter $k$, asks for a spanning tree with at least $k$ internal vertices. Fomin et al. [J. Comput. System Sci., 79:1-6] crafted a very ingenious reduction rule, and showed that a simple application of this rule is sufficient to yield a $3k$-vertex kernel. Here we propose a novel way to use the same reduction rule, resulting in an improved $2k$-vertex kernel. Our algorithm applies first a greedy procedure consisting of a sequence of local exchange operations, which ends…
Graduate School of Information Science and Technology, The University of Tokyo（东京大学信息科学与技术研究生院）
The kernel method is a potential approach to analyzing structured data such as sequences, trees, and graphs; however, unordered trees have not been investigated extensively. Kimura et al. (2011) proposed a kernel function for unordered trees on the basis of their subpaths, which are vertical substructures of trees responsible for hierarchical information in them. Their kernel exhibits practically good performance in terms of accuracy and speed; however, linear-time computation is not guaranteed theoretically, unlike the case of the other unordered tree kernel proposed by Vishwanathan and Smola…
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 approximate within any factor of OPT^c for any constant c. In this paper we give a O(k^4) size kernel for the Tree Deletion Set problem. To the best of our knowledge our result is the first counterexample to the "conventional wisdom" that kernelization algorithms automatically provide approximation algorithms with approximation ratio close to the size of the ke…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For the purpose of validating evolutionary models, biologists check whether or not a phylogenetic tree is contained in a phylogenetic network on the same taxa. This tree containment problem is known to be NP-complete. A phylogenetic network is reticulation-visible if every reticulation node separates the root of the network from some leaves. We answer an open p…
We study the CONNECTED η-TREEDEPTH DELETION problem where the input instance is an undireted graph G = (V, E) and an integer k. The objective is to decide if G has a set S \subseteq V(G) of at most k vertices such that G - S has treedepth at most ηand G[S] is connected. As this problem naturally generalizes the well-known CONNECTED VERTEX COVER, when parameterized by solution size k, the CONNECTED η-TREEDEPTH DELETION does not admit polynomial kernel unless NP \subseteq coNP/poly. This motivates us to design an approximate kernel of polynomial size for this problem. In this paper, we show that…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the results of `experiments' on triples of leaves (a,b,c), which return the pair with the deepest least common ancestor. If the tree is assumed to be an ultrametric (i.e., all root-leaf paths have the same length), the experiment can be equivalently seen to return the closest pair of leaves. In this model, efficient algorithms are known for tree reconstruction. …
We define a search problem on trees that closely captures the backtracking behavior of all current practical graph isomorphism algorithms. Given two trees with colored leaves, the goal is to find two leaves of matching color, one in each of the trees. The trees are subject to an invariance property which promises that for every pair of leaves of equal color there must be a symmetry (or an isomorphism) that maps one leaf to the other. We describe a randomized algorithm with errors for which the number of visited leaves is quasilinear in the square root of the size of the smaller of the two tree…
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 $K_4$ minor. Hence, this problem corresponds to the NP-hard $\mathcal{F}$-Minor Cover problem with $\mathcal{F} = \{K_4\}$. For any variant of the $\mathcal{F}$-Minor Cover problem where $\mathcal{F}$ contains a planar graph, it is known that a polynomial kernel exists. I.e., a preprocessing routine that in polynomial time outputs an equivalent instance of s…
We prove that finding a rooted subtree with at least $k$ leaves in a digraph is a fixed parameter tractable problem. A similar result holds for finding rooted spanning trees with many leaves in digraphs from a wide family $\cal L$ that includes all strong and acyclic digraphs. This settles completely an open question of Fellows and solves another one for digraphs in $\cal L$. Our algorithms are based on the following combinatorial result which can be viewed as a generalization of many results for a `spanning tree with many leaves' in the undirected case, and which is interesting on its own: If…
We present a polynomial time algorithm that for any graph G and integer k >= 0, either finds a spanning tree with at least k internal vertices, or outputs a new graph G' on at most 3k vertices and an integer k' such that G has a spanning tree with at least k internal vertices if and only if G' has a spanning tree with at least k' internal vertices. In other words, we show that the Maximum Internal Spanning Tree problem parameterized by the number of internal vertices k, has a 3k-vertex kernel. Our result is based on an innovative application of a classical min-max result about hypertrees in hy…
In 2001 Allen and Steel showed that, if subtree and chain reduction rules have been applied to two unrooted phylogenetic trees, the reduced trees will have at most 28k taxa where k is the TBR (Tree Bisection and Reconnection) distance between the two trees. Here we reanalyse Allen and Steel's kernelization algorithm and prove that the reduced instances will in fact have at most 15k-9 taxa. Moreover we show, by describing a family of instances which have exactly 15k-9 taxa after reduction, that this new bound is tight. These instances also have no common clusters, showing that a third commonly-…
Throughout the last decade, we have seen much progress towards characterising and computing the minimum hybridisation number for a set P of rooted phylogenetic trees. Roughly speaking, this minimum quantifies the number of hybridisation events needed to explain a set of phylogenetic trees by simultaneously embedding them into a phylogenetic network. From a mathematical viewpoint, the notion of agreement forests is the underpinning concept for almost all results that are related to calculating the minimum hybridisation number for when |P|=2. However, despite various attempts, characterising thi…
