Related papers: An $O(n \log n)$ time Algorithm for computing the …
The width measure \emph{treedepth}, also known as vertex ranking, centered coloring and elimination tree height, is a well-established notion which has recently seen a resurgence of interest. We present an algorithm which---given as input…
A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…
We present a proof that the number of breakpoints in the arrival function between two terminals in graphs of treewidth $w$ is $n^{O(\log^2 w)}$ when the edge arrival functions are piecewise linear. This is an improvement on the bound of…
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…
Given a set of pairwise disjoint polygonal obstacles in the plane, finding an obstacle-avoiding Euclidean shortest path between two points is a classical problem in computational geometry and has been studied extensively. The previous best…
The {Congested Clique} is a distributed-computing model for single-hop networks with restricted bandwidth that has been very intensively studied recently. It models a network by an $n$-vertex graph in which any pair of vertices can…
In the $2$-reachability problem we are given a directed graph $G$ and we wish to determine if there are two (edge or vertex) disjoint paths from $u$ to $v$, for a given pair of vertices $u$ and $v$. In this paper, we present an algorithm…
Consider observation data, comprised of n observation vectors with values on a set of attributes. This gives us n points in attribute space. Having data structured as a tree, implied by having our observations embedded in an ultrametric…
The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfer, viral recombination, and Markov chain Monte Carlo…
``Algorithms with predictions'', or ``learning-augmented algorithms'', has proved to be an extremely useful paradigm for combining machine learning with traditional algorithms. One of the textbook settings for this is searching a sorted…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
This paper provides a short and transparent solution for the covering cost of white-grey trees which play a crucial role in the algorithm of Bergeron {\it et al.}\ to compute the rearrangement distance between two multichromosomal genomes…
Temporal sequences of terrains arise in various application areas. To analyze them efficiently, one generally needs a suitable abstraction of the data as well as a method to compare and match them over time. In this paper we consider merge…
There exists a bijection between one stack sortable permutations --permutations which avoid the pattern 231-- and planar trees. We define an edit distance between permutations which is coherent with the standard edit distance between trees.…
This paper tightens the best known analysis of Hein's 1989 algorithm to infer the topology of a weighted tree based on the lengths of paths between its leaves. It shows that the number of length queries required for a degree-$k$ tree of $n$…
Hyperbolicity measures, in terms of (distance) metrics, how close a given graph is to being a tree. Due to its relevance in modeling real-world networks, hyperbolicity has seen intensive research over the last years. Unfortunately, the best…
In the first part of the paper, we present an (1+\mu)-approximation algorithm to the minimum-spanning tree of points in a planar arrangement of lines, where the metric is the number of crossings between the spanning tree and the lines. The…
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
In this paper, we propose new techniques for solving geometric optimization problems involving interpoint distances of a point set in the plane. Given a set $P$ of $n$ points in the plane and an integer $1 \leq k \leq \binom{n}{2}$, the…
Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…