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We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
Propositional linear time temporal logic (LTL) is the standard temporal logic for computing applications and many reasoning techniques and tools have been developed for it. Tableaux for deciding satisfiability have existed since the 1980s.…
We present a new algorithm for generating a uniformly random spanning tree in an undirected graph. Our algorithm samples such a tree in expected $\tilde{O}(m^{4/3})$ time. This improves over the best previously known bound of…
The palindromic tree (a.k.a. eertree) for a string $S$ of length $n$ is a tree-like data structure that represents the set of all distinct palindromic substrings of $S$, using $O(n)$ space [Rubinchik and Shur, 2018]. It is known that, when…
A \emph{tree cut-sparsifier} $T$ of quality $\alpha$ of a graph $G$ is a single tree that preserves the capacities of all cuts in the graph up to a factor of $\alpha$. A \emph{tree flow-sparsifier} $T$ of quality $\alpha$ guarantees that…
In the PATH COVER problem, one asks to cover the vertices of a graph using the smallest possible number of (not necessarily disjoint) paths. While the variant where the paths need to be pairwise vertex-disjoint, which we call PATH…
Alphabetic codes and binary search trees are combinatorial structures that abstract search procedures in ordered sets endowed with probability distributions. In this paper, we design new linear-time algorithms to construct alphabetic codes,…
We provide the first algorithm for computing an optimal tree decomposition for a given graph $G$ that runs in single exponential time in the feedback vertex number of $G$, that is, in time $2^{O(\text{fvn}(G))}\cdot n^{O(1)}$, where…
In this paper, we present fixed-parameter tractability algorithms for both the undirected and directed versions of the Spanning Tree Isomorphism Problem, parameterized by the size $k$ of a redundant set. A redundant set is a collection of…
We study the problem of computing the tightest upper and lower bounds on the probability that the sum of $n$ dependent Bernoulli random variables exceeds an integer $k$. Under knowledge of all pairs of bivariate distributions denoted by a…
Cographs have always been a research target in areas such as coloring, graph decomposition, and spectral theory. In this work, we present an algorithm to generate all unlabeled cographs with $n$ vertices, based on the generation of cotrees.…
We present algorithms that run in linear time on pointer machines for a collection of problems, each of which either directly or indirectly requires the evaluation of a function defined on paths in a tree. These problems previously had…
Various specifiable combinatorial structures, with d extensive parameters, can be exactly sampled both by the recursive method, with linear arithmetic complexity if a heavy preprocessing is performed, or by the Boltzmann method, with…
Arising from structural graph theory, treewidth has become a focus of study in fixed-parameter tractable algorithms in various communities including combinatorics, integer-linear programming, and numerical analysis. Many NP-hard problems…
Graph Isomorphism (GI) is a fundamental algorithmic problem. Amongst graph classes for which the computational complexity of GI has been resolved, trees are arguably the most fundamental. Tree Isomorphism is complete for deterministic…
We show that the problem of constructing tree-structured descriptions of data layouts that are optimal with respect to space or other criteria from given sequences of displacements, can be solved in polynomial time. The problem is relevant…
The simulation of electrical discharges has been attracting a great deal of attention. In such simulations, the electric field computation dominates the computational time. In this paper, we propose a fast tree algorithm that helps to…
Boltzmann samplers and the recursive method are prominent algorithmic frameworks for the approximate-size and exact-size random generation of large combinatorial structures, such as maps, tilings, RNA sequences or various tree-like…
Various combinatorial classes such as outerplanar graphs and maps, series-parallel graphs, substitution-closed classes of permutations and many more allow bijective encodings by so-called enriched trees, which are rooted trees with…
We present an algorithm that enumerates all the minimal triangulations of a graph in incremental polynomial time. Consequently, we get an algorithm for enumerating all the proper tree decompositions, in incremental polynomial time, where…