An out-tree $T$ of a directed graph $D$ is a rooted tree subgraph with all arcs directed outwards from the root. An out-branching is a spanning out-tree. By $l(D)$ and $l_s(D)$ we denote the maximum number of leaves over all out-trees and out-branchings of $D$, respectively.
We give fixed parameter tractable algorithms for deciding whether $l_s(D)\geq k$ and whether $l(D)\geq k$ for a digraph $D$ on $n$ vertices, both with time complexity $2^{O(k\log k)} \cdot n^{O(1)}$. This improves on previous algorithms with complexity $2^{O(k^3\log k)} \cdot n^{O(1)}$ and $2^{O(k\log^2 k)} \cdot n^{O(1)}$, respectively.
To obtain the complexity bound in the case of out-branchings, we prove that when all arcs of $D$ are part of at least one out-branching, $l_s(D)\geq l(D)/3$. The second bound we prove in this paper states that for strongly connected digraphs $D$ with minimum in-degree 3, $l_s(D)\geq Θ(\sqrt{n})$, where previously $l_s(D)\geq Θ(\sqrt[3]{n})$ was the best known bound. This bound is tight, and also holds for the larger class of digraphs with minimum in-degree 3 in which every arc is part of at least one out-branching.
Given a directed graph $G=(V,A)$, the Directed Maximum Leaf Spanning Tree problem asks to compute a directed spanning tree (i.e., an out-branching) with as many leaves as possible. By designing a Branch-and-Reduced algorithm combined with the Measure & Conquer technique for running time analysis, we show that the problem can be solved in time $\Oh^*(1.9043^n)$ using polynomial space. Hitherto, there have been only few examples. Provided exponential space this run time upper bound can be lowered to $\Oh^*(1.8139^n)$.
An out-branching of a directed graph is a rooted spanning tree with all arcs directed outwards from the root. We consider the problem of deciding whether a given directed graph D has an out-branching with at least k leaves (Directed Spanning k-Leaf). We prove that this problem is fixed parameter tractable, when k is chosen as the parameter. Previously this was only known for restricted classes of directed graphs. The main new ingredient in our approach is a lemma that shows that given a locally optimal out-branching of a directed graph in which every arc is part of at least one out-branching, …
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 improve known parameterized algorithms and combinatorial bounds on the number of leaves in out-branchings. We show that \begin{itemize} \item every strongly connected digraph $D$ of order $n$ with minimum in-degree at least 3 has an out-branching with at least $(n/4)^{1/3}-1$ leaves; \item if a strongly connected digraph $D$ does not contain an out-branching with $k$ leaves, then the pathwidth of its und…
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…
A minimum dominating set for a digraph (directed graph) is a smallest set of vertices such that each vertex either belongs to this set or has at least one parent vertex in this set. We solve this hard combinatorial optimization problem approximately by a local algorithm of generalized leaf removal and by a message-passing algorithm of belief propagation. These algorithms can construct near-optimal dominating sets or even exact minimum dominating sets for random digraphs and also for real-world digraph instances. We further develop a core percolation theory and a replica-symmetric spin glass th…
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…
Given a digraph $D$, the Minimum Leaf Out-Branching problem (MinLOB) is the problem of finding in $D$ an out-branching with the minimum possible number of leaves, i.e., vertices of out-degree 0. Gutin, Razgon and Kim (2008) proved that MinLOB is polynomial time solvable for acyclic digraphs which are exactly the digraphs of directed path-width (DAG-width, directed tree-width, respectively) 0. We investigate how much one can extend this polynomiality result. We prove that already for digraphs of directed path-width (directed tree-width, DAG-width, respectively) 1, MinLOB is NP-hard. On the othe…
Institute of Mathematics；Statistics. University of S \ a o Paulo. S \ a o Paulo, Brazil；Center for Mathematics. Computing；Cognition. Federal University of ABC. Santo Andr \'e , S \ a o Paulo, Brazil
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 …
How heavy independent sets help to find arborescences with many leaves in DAGs
Institute of Mathematics；Statistics. University of S \ a o Paulo. S \ a o Paulo, Brazil；Center for Mathematics. Computing；Cognition. Federal University of ABC. Santo Andr \'e , S \ a o Paulo, Brazil
We consider construction of the suffix tree and the directed acyclic word graph (DAWG) indexing data structures for a collection $\mathcal{T}$ of texts, where a new symbol may be appended to any text in $\mathcal{T} = \{T_1, \ldots, T_K\}$, at any time. This fully-online scenario, which arises in dynamically indexing multi-sensor data, is a natural generalization of the long solved semi-online text indexing problem, where texts $T_1, \ldots, T_{k}$ are permanently fixed before the next text $T_{k+1}$ is processed for each $1 \leq k < K$. We present fully-online algorithms that construct the su…
The metric dimension of a graph is the size of the smallest set of vertices whose distances distinguish all pairs of vertices in the graph. We show that this graph invariant may be calculated by an algorithm whose running time is linear in the input graph size, added to a function of the largest possible number of leaves in a spanning tree of the graph.
A straightforward dynamic programming method for the single-source shortest paths problem (SSSP) in an edge-weighted directed acyclic graph (DAG) processes the vertices in a topologically sorted order. First, we similarly iterate this method alternatively in a breadth-first search sorted order and the reverse order on an input directed graph with both positive and negative real edge weights, $n$ vertices and $m$ edges. For a positive integer $t,$ after $O(t)$ iterations in $O(tm)$ time, we obtain for each vertex $v$ a path distance from the source to $v$ not exceeding that yielded by the short…
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 develop two different methods to achieve subexponential time parameterized algorithms for problems on sparse directed graphs. We exemplify our approaches with two well studied problems. For the first problem, {\sc $k$-Leaf Out-Branching}, which is to find an oriented spanning tree with at least $k$ leaves, we obtain an algorithm solving the problem in time $2^{O(\sqrt{k} \log k)} n+ n^{O(1)}$ on directed graphs whose underlying undirected graph excludes some fixed graph $H$ as a minor. For the special case when the input directed graph is planar, the running time can be improved to $2^{O(\s…
Moderately beyond clique-width: reduced component max-leaf and related parameters
Univ Lyon, CNRS, ENS de Lyon, Université Claude Bernard Lyon 1（里昂大学、法国国家科学研究中心、巴黎高等师范学院里昂分校、克洛德·贝尔纳里昂大学）；Institute of Informatics, University of Warsaw（华沙大学信息学研究所）；Department of Mathematics and Research Institute for Natural Sciences, Hanyang University（汉阳大学数学系与自然科学研究所）；Discrete Mathematics Group, Institute for Basic Science (IBS)（基础科学研究院离散数学组）
A graph $G$ is a $k$-leaf power if there exists a tree $T$ whose leaf set is $V(G)$, and such that $uv \in E(G)$ if and only if the distance between $u$ and $v$ in $T$ is at most $k$. The graph classes of $k$-leaf powers have several applications in computational biology, but recognizing them has remained a challenging algorithmic problem for the past two decades. The best known result is that $6$-leaf powers can be recognized in polynomial time. In this paper, we present an algorithm that decides whether a graph $G$ is a $k$-leaf power in time $O(n^{f(k)})$ for some function $f$ that depends …
I extend the methods in "Electrical Flows, Laplacian Systems, and Faster Approximation of Maximum Flow in Undirected Graphs, with Paul Christiano, Jonathan Kelner, Daniel Spielman, and Shang-Hua Teng" to directed graphs with a variation of the framework in the paper, which lead to an algorithm that approximately solves the directed max flow problem in nearly-linear time.
We develop a new technique for computing maximum flow in directed planar graphs with multiple sources and a single sink that significantly deviates from previously known techniques for flow problems. This gives rise to an O(diameter*n*log(n)) algorithm for the problem.
The dynamical phenomena of complex networks are very difficult to predict from local information due to the rich microstructures and corresponding complex dynamics. On the other hands, it is a horrible job to compute some stochastic parameters of a large network having thousand and thousand nodes. We design several recursive algorithms for finding spanning trees having maximal leaves (MLS-trees) in investigation of topological structures of Sierpinski growing network models, and use MLS-trees to determine the kernels, dominating and balanced sets of the models. We propose a new stochastic meth…
We give an $O(n^{1.5} \log n)$ algorithm that, given a directed planar graph with arc capacities, a set of source nodes and a single sink node, finds a maximum flow from the sources to the sink . This is the first subquadratic-time strongly polynomial algorithm for the problem.
We give an O(n log^3 n) algorithm that, given an n-node directed planar graph with arc capacities, a set of source nodes, and a set of sink nodes, finds a maximum flow from the sources to the sinks. Previously, the fastest algorithms known for this problem were those for general graphs.
We give an $O(n^{1.5} \log n)$ algorithm that, given a directed planar graph with arc capacities, a set of source nodes and a set of sink nodes, finds a maximum flow from the sources to the sinks.
Given a digraph $D$, the Minimum Leaf Out-Branching problem (MinLOB) is the problem of finding in $D$ an out-branching with the minimum possible number of leaves, i.e., vertices of out-degree 0. We prove that MinLOB is polynomial-time solvable for acyclic digraphs. In general, MinLOB is NP-hard and we consider three parameterizations of MinLOB. We prove that two of them are NP-complete for every value of the parameter, but the third one is fixed-parameter tractable (FPT). The FPT parametrization is as follows: given a digraph $D$ of order $n$ and a positive integral parameter $k$, check whethe…
We study the $SIG$ dimension of trees under $L_{\infty}$ metric and answer an open problem posed by Michael and Quint (Discrete Applied Mathematics: 127, pages 447-460, 2003). Let $T$ be a tree with atleast two vertices. For each $v\in V(T)$, let leaf-degree$(v)$ denote the number of neighbours of $v$ that are leaves. We define the maximum leaf-degree as $α(T) = \max_{x \in V(T)}$ leaf-degree$(x)$. Let $S = \{v\in V(T) |$ leaf-degree$(v) = α\}$. If $|S| = 1$, we define $β(T) = α(T) - 1$. Otherwise define $β(T) = α(T)$. We show that for a tree $T$, $SIG_\infty(T) = \lceil \log_2(β+ 2)\rceil$ wh…
In this paper we present an O(n log n) algorithm for finding a maximum flow in a directed planar graph, where the vertices are subject to capacity constraints, in addition to the arcs. If the source and the sink are on the same face, then our algorithm can be implemented in O(n) time. For general (not planar) graphs, vertex capacities do not make the problem more difficult, as there is a simple reduction that eliminates vertex capacities. However, this reduction does not preserve the planarity of the graph. The essence of our algorithm is a different reduction that does preserve the planarity,…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf vertex is the parent of a tree vertex or a leaf. Up to a certain equivalence, it has been recently shown that, under two different types of weightings, edge-weighted tree-child networks are determined by their collection of distances between each pair of taxa. However, the size of these collections can be exponential in the size of the taxa set. In this paper,…
In the $k$-Leaf Out-Branching and $k$-Internal Out-Branching problems we are given a directed graph $D$ with a designated root $r$ and a nonnegative integer $k$. The question is to determine the existence of an outbranching rooted at $r$ that has at least $k$ leaves, or at least $k$ internal vertices, respectively. Both these problems were intensively studied from the points of view of parameterized complexity and kernelization, and in particular for both of them kernels with $O(k^2)$ vertices are known on general graphs. In this work we show that $k$-Leaf Out-Branching admits a kernel with $O…
In this report an entropy bound on the memory size is given for a compression method of leaf-labeled trees. The compression converts the tree into a Directed Acyclic Graph (DAG) by merging isomorphic subtrees.
We are motivated by a tantalizing open question in exact algorithms: can we detect whether an $n$-vertex directed graph $G$ has a Hamiltonian cycle in time significantly less than $2^n$? We present new randomized algorithms that improve upon several previous works: 1. We show that for any constant $0<λ<1$ and prime $p$ we can count the Hamiltonian cycles modulo $p^{\lfloor (1-λ)\frac{n}{3p}\rfloor}$ in expected time less than $c^n$ for a constant $c<2$ that depends only on $p$ and $λ$. Such an algorithm was previously known only for the case of counting modulo two [Björklund and Husfeldt, FOCS…
We give an algorithm to find a mincut in an $n$-vertex, $m$-edge weighted directed graph using $\tilde O(\sqrt{n})$ calls to any maxflow subroutine. Using state of the art maxflow algorithms, this yields a directed mincut algorithm that runs in $\tilde O(m\sqrt{n} + n^2)$ time. This improves on the 30 year old bound of $\tilde O(mn)$ obtained by Hao and Orlin for this problem.
A recently proposed exact algorithm for the maximum independent set problem is analyzed. The typical running time is improved exponentially in some parameter regions compared to simple binary search. The algorithm also overcomes the core transition point, where the conventional leaf removal algorithm fails, and works up to the replica symmetry breaking (RSB) transition point. This suggests that a leaf removal core itself is not enough for typical hardness in the random maximum independent set problem, providing further evidence for RSB being the obstacle for algorithms in general.
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of genes or species, and aims at finding a single tree that minimizes the leaf-removal distance to the input trees. This problem is a specific instance of the general consensus/supertree problem, widely used to combine or summarize discordant evolutionary trees. The problem we introduce is specifically tailored to address the case of discrepancies between the inp…
We introduce a novel Quadratic Unconstrained Binary Optimization (QUBO) formulation method for spanning tree problems. Instead of encoding the presence of edges in the tree individually, we opt to encode spanning trees as a permutation problem. We apply our method to four NP-hard spanning tree variants, namely the k-minimum spanning tree, degree-constrained minimum spanning tree, minimum leaf spanning tree, and maximum leaf spanning tree. Our main result is a formulation with $\mathcal{O}(|V|k)$ variables for the k-minimum spanning tree problem, beating related strategies that need $\mathcal{O…
A split-by-edges tree of a graph G on n vertices is a binary tree T where the root = V(G), every leaf is an independent set in G, and for every other node N in T with children L and R there is a pair of vertices {u, v} in N such that L = N - v, R = N - u, and uv is an edge in G. It follows from the definition that every maximal independent set in G is a leaf in T, and the maximum independent sets of G are the leaves closest to the root of T.
Given a directed graph $G$ with non negative cost on the arcs, a directed tree cover of $G$ is a rooted directed tree such that either head or tail (or both of them) of every arc in $G$ is touched by $T$. The minimum directed tree cover problem (DTCP) is to find a directed tree cover of minimum cost. The problem is known to be $NP$-hard. In this paper, we show that the weighted Set Cover Problem (SCP) is a special case of DTCP. Hence, one can expect at best to approximate DTCP with the same ratio as for SCP. We show that this expectation can be satisfied in some way by designing a purely combi…
We propose a new and strengthened Branch-and-Bound (BnB) algorithm for the maximum common (connected) induced subgraph problem based on two new operators, Long-Short Memory (LSM) and Leaf vertex Union Match (LUM). Given two graphs for which we search for the maximum common (connected) induced subgraph, the first operator of LSM maintains a score for the branching node using the short-term reward of each vertex of the first graph and the long-term reward of each vertex pair of the two graphs. In this way, the BnB process learns to reduce the search tree size significantly and improve the algori…
We study the directed maximum common edge subgraph problem (DMCES) for the class of directed graphs that are finite, weakly connected, oriented, and simple. We use DMCES to define a metric on partially ordered sets that can be represented as weakly connected directed acyclic graphs. While most existing metrics assume that the underlying sets of the partial order are identical, and only the relationships between elements can differ, the metric defined here allows the partially ordered sets to be different. The proof that there is a metric based on DMCES involves the extension of the concept of …
This paper introduces a special family of randomized algorithms for Max DICUT that we call oblivious algorithms. Let the bias of a vertex be the ratio between the total weight of its outgoing edges and the total weight of all its edges. An oblivious algorithm selects at random in which side of the cut to place a vertex v, with probability that only depends on the bias of v, independently of other vertices. The reader may observe that the algorithm that ignores the bias and chooses each side with probability 1/2 has an approximation ratio of 1/4, whereas no oblivious algorithm can have an appro…
Connectivity related concepts are of fundamental interest in graph theory. The area has received extensive attention over four decades, but many problems remain unsolved, especially for directed graphs. A directed graph is 2-edge-connected (resp., 2-vertex-connected) if the removal of any edge (resp., vertex) leaves the graph strongly connected. In this paper we present improved algorithms for computing the maximal 2-edge- and 2-vertex-connected subgraphs of a given directed graph. These problems were first studied more than 35 years ago, with $\widetilde{O}(mn)$ time algorithms for graphs wit…
We present a linear-time algorithm for simplifying flow networks on directed planar graphs: Given a directed planar graph on $n$ vertices, a source vertex $s$ and a sink vertex $t$, our algorithm removes all the arcs that do not participate in any simple $s,t$-path in linear-time. The output graph produced by our algorithm satisfies the prerequisite needed by the $O(n\log n)$-time algorithm of Weihe [FOCS'94 \& JCSS'97] for computing maximum $s,t$-flow in directed planar graphs. Previously, Weihe's algorithm could not run in $O(n\log n)$-time due to the absence of the preprocessing step; all t…
We give an algorithm to find a minimum cut in an edge-weighted directed graph with $n$ vertices and $m$ edges in $\tilde O(n\cdot \max(m^{2/3}, n))$ time. This improves on the 30 year old bound of $\tilde O(nm)$ obtained by Hao and Orlin for this problem. Our main technique is to reduce the directed mincut problem to $\tilde O(\min(n/m^{1/3}, \sqrt{n}))$ calls of {\em any} maxflow subroutine. Using state-of-the-art maxflow algorithms, this yields the above running time. Our techniques also yield fast {\em approximation} algorithms for finding minimum cuts in directed graphs. For both edge and …
Given a directed graph $G$ and a parameter $k$, the {\sc Long Directed Cycle (LDC)} problem asks whether $G$ contains a simple cycle on at least $k$ vertices, while the {\sc $k$-Path} problems asks whether $G$ contains a simple path on exactly $k$ vertices. Given a deterministic (randomized) algorithm for {\sc $k$-Path} as a black box, which runs in time $t(G,k)$, we prove that {\sc LDC} can be solved in deterministic time $O^*(\max\{t(G,2k),4^{k+o(k)}\})$ (randomized time $O^*(\max\{t(G,2k),4^k\})$). In particular, we get that {\sc LDC} can be solved in randomized time $O^*(4^k)$.
We give O(log^2 n)-approximation algorithm based on the cut-matching framework of [10, 13, 14] for computing the sparsest cut on directed graphs. Our algorithm uses only O(log^2 n) single commodity max-flow computations and thus breaks the multicommodity-flow barrier for computing the sparsest cut on directed graphs
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks is to develop algorithms for building such networks by amalgamating small networks into a single large network. The level of a phylogenetic network is a measure of its deviation from being a tree; the higher the level of network, the less treelike it becomes. Various algorithms have been developed for building level-1 networks from small networks. However, …
