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We develop a time-optimal $O(mn^2)$-time algorithm to construct the subtree prune-regraft (SPR) graph on a collection of m phylogenetic trees with n leaves. This improves on the previous bound of $O(mn^3)$. Such graphs are used to better…
The transversal hypergraph problem is the task of enumerating the minimal hitting sets of a hypergraph. It is a long-standing open question whether this can be done in output-polynomial time. For hypergraphs whose solutions have bounded…
Subgraph enumeration problems ask to output all subgraphs of an input graph that belongs to the specified graph class or satisfy the given constraint. These problems have been widely studied in theoretical computer science. As far, many…
We consider the problem of computing the diameter of a unicycle graph (i.e., a graph with a unique cycle). We present an O(n) time algorithm for the problem, where n is the number of vertices of the graph. This improves the previous best…
A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graph where the edges are labeled with different types of opening and closing parentheses, and the reachability information is computed…
The quartet distance is a measure of similarity used to compare two unrooted phylogenetic trees on the same set of $n$ leaves, defined as the number of subsets of four leaves related by a different topology in both trees. After a series of…
The classic algorithm of Viterbi computes the most likely path in a Hidden Markov Model (HMM) that results in a given sequence of observations. It runs in time $O(Tn^2)$ given a sequence of $T$ observations from a HMM with $n$ states.…
In the Densest k-Subgraph problem, given a graph G and a parameter k, one needs to find a subgraph of G induced on k vertices that contains the largest number of edges. There is a significant gap between the best known upper and lower…
Recently, \citeauthor*{akbari2021locality}~(ICALP 2023) studied the locality of graph problems in distributed, sequential, dynamic, and online settings from a {unified} point of view. They designed a novel $O(\log n)$-locality deterministic…
Mining cohesive subgraphs from a graph is a fundamental problem in graph data analysis. One notable cohesive structure is $\gamma$-quasi-clique (QC), where each vertex connects at least a fraction $\gamma$ of the other vertices inside.…
The \emph{maximal $k$-edge-connected subgraphs} problem is a classical graph clustering problem studied since the 70's. Surprisingly, no non-trivial technique for this problem in weighted graphs is known: a very straightforward…
This paper is about: (1) bounds on the number of cliques in a graph in a particular class, and (2) algorithms for listing all cliques in a graph. We present a simple algorithm that lists all cliques in an $n$-vertex graph in O(n) time per…
Given an $n$-vertex $m$-edge graph $G$ with non negative edge-weights, the girth of $G$ is the weight of a shortest cycle in $G$. For any graph $G$ with polynomially bounded integer weights, we present a deterministic algorithm that…
We concentrate on some recent results of Egawa and Ozeki [J. Graph Theory, 2015 and Combinatorica, 2014], and He et al. [J. Graph Theory, 2002]. We give shorter proofs and polynomial time algorithms as well. We present two new proofs for…
In this paper, we consider the problem of finding a cycle of length $2k$ (a $C_{2k}$) in an undirected graph $G$ with $n$ nodes and $m$ edges for constant $k\ge2$. A classic result by Bondy and Simonovits [J.Comb.Th.'74] implies that if $m…
We consider the (exact, minimum) $k$-cut problem: given a graph and an integer $k$, delete a minimum-weight set of edges so that the remaining graph has at least $k$ connected components. This problem is a natural generalization of the…
Given a graph of which the n vertices form a regular two-dimensional grid, and in which each (possibly weighted and/or directed) edge connects a vertex to one of its eight neighbours, the following can be done in O(scan(n)) I/Os, provided M…
We present subquadratic algorithms in the algebraic decision-tree model for several \textsc{3Sum}-hard geometric problems, all of which can be reduced to the following question: Given two sets $A$, $B$, each consisting of $n$ pairwise…
Listing dense subgraphs in large graphs plays a key task in varieties of network analysis applications like community detection. Clique, as the densest model, has been widely investigated. However, in practice, communities rarely form as…
We study the knapsack problem with graph theoretic constraints. That is, we assume that there exists a graph structure on the set of items of knapsack and the solution also needs to satisfy certain graph theoretic properties on top of…