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Interpreting three-leaf binary trees or {\em rooted triples} as constraints yields an entailment relation, whereby binary trees satisfying some rooted triples must also thus satisfy others, and thence a closure operator, which is known to…
We prove the following theorem. Given a planar graph $G$ and an integer $k$, it is possible in polynomial time to randomly sample a subset $A$ of vertices of $G$ with the following properties: (i) $A$ induces a subgraph of $G$ of treewidth…
When $k|n$, the tree $\mathrm{Comb}_{n,k}$ consists of a path containing $n/k$ vertices, each of whose vertices has a disjoint path length $k-1$ beginning at it. We show that, for any $k=k(n)$ and $\epsilon>0$, the binomial random graph…
We study the problem of finding small trees. Classical network design problems are considered with the additional constraint that only a specified number $k$ of nodes are required to be connected in the solution. A prototypical example is…
In this paper, we provide a polynomial time algorithm to calculate the probability of a {\it ranked} gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The…
We prove the following result about approximating the maximum independent set in a graph. Informally, we show that any approximation algorithm with a ``non-trivial'' approximation ratio (as a function of the number of vertices of the input…
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…
We investigate the tractability of a simple fusion of two fundamental structures on graphs, a spanning tree and a perfect matching. Specifically, we consider the following problem: given an edge-weighted graph, find a minimum-weight…
We consider the problem of computing a Steiner tree of minimum cost under a hop constraint which requires the depth of the tree to be at most $k$. Our main result is an exact algorithm for metrics induced by graphs with bounded treewidth…
It is known that a graph isomorphism testing algorithm is polynomially equivalent to a detecting of a graph non-trivial automorphism algorithm. The polynomiality of the latter algorithm, is obtained by consideration of symmetry properties…
Trigraph list homomorphism problems (also known as list matrix partition problems) have generated recent interest, partly because there are concrete problems that are not known to be polynomial time solvable or NP-complete. Thus while…
An $r$-uniform hypergraph $H$ consists of a set of vertices $V$ and a set of edges whose elements are $r$-subsets of $V$. We define a hypertree to be a connected hypergraph which contains no cycles. A hypertree spans a hypergraph $H$ if it…
In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…
Many complex questions in biology, physics, and mathematics can be mapped to the graph isomorphism problem and the closely related graph automorphism problem. In particular, these problems appear in the context of network visualization,…
Given a directed graph $D=(V,A)$ with a set of $d$ specified vertices $S=\{s_1,...,s_d\}\subseteq V$ and a function $f\colon S \to \mathbb{Z}_+$ where $\mathbb{Z}_+$ denotes the set of non-negative integers, we consider the problem which…
We consider the problem of finding a subgraph of a given graph which minimizes the sum of given functions at vertices evaluated at their subgraph degrees. While the problem is NP-hard already when all functions are the same, we show that it…
Given a directed graph $G$ on $n$ vertices with a special vertex $s$, the directed minimum degree spanning tree problem requires computing a incoming spanning tree rooted at $s$ whose maximum tree in-degree is the smallest among all such…
We give an algorithm that, for every fixed k, decides isomorphism of graphs of rank width at most k in polynomial time. As the clique width of a graph is bounded in terms of its rank width, we also obtain a polynomial time isomorphism test…
Considering the worst-case scenario, junction tree algorithm remains the most general solution for exact MAP inference with polynomial run-time guarantees. Unfortunately, its main tractability assumption requires the treewidth of a…
Graph searches and the corresponding search trees can exhibit important structural properties and are used in various graph algorithms. The problem of deciding whether a given spanning tree of a graph is a search tree of a particular search…