Related papers: Computing Quartet Distance is Equivalent to Counti…
Let $m$ and $n$ be the numbers of vertices of two polygonal curves in $\mathbb{R}^d$ for any fixed $d$ such that $m \leq n$. Since it was known in 1995 how to compute the Fr\'{e}chet distance of these two curves in $O(mn\log (mn))$ time, it…
The degree distribution of an ordered tree $T$ with $n$ nodes is $\vec{n} = (n_0,\ldots,n_{n-1})$, where $n_i$ is the number of nodes in $T$ with $i$ children. Let $\mathcal{N}(\vec{n})$ be the number of trees with degree distribution…
Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…
We show a simple generalization of the quantum walk algorithm for search in backtracking trees by Montanaro (ToC 2018) to the case where vertices can have different times of computation. If a vertex $v$ in the tree of depth $D$ is computed…
The path-difference metric is one of the oldest distances for the comparison of fully resolved phylogenetic trees, but its statistical properties are still quite unknown. In this paper we compute the mean value of the square of the…
The closest pair problem is a fundamental problem of computational geometry: given a set of $n$ points in a $d$-dimensional space, find a pair with the smallest distance. A classical algorithm taught in introductory courses solves this…
Given a set $P$ of $n$ points and a set $S$ of $n$ segments in the plane, we consider the problem of computing for each segment of $S$ its closest point in $P$. The previously best algorithm solves the problem in $n^{4/3}2^{O(\log^*n)}$…
The Tree Evaluation Problem ($\mathsf{TreeEval}$) is a computational problem originally proposed as a candidate to prove a separation between complexity classes $\mathsf{P}$ and $\mathsf{L}$. Recently, this problem has gained significant…
A trie $\mathcal{T}$ is a rooted tree such that each edge is labeled by a single character from the alphabet, and the labels of out-going edges from the same node are mutually distinct. Given a trie $\mathcal{T}$ with $n$ edges, we show how…
A consensus tree is a phylogenetic tree that captures the similarity between a set of conflicting phylogenetic trees. The problem of computing a consensus tree is a major step in phylogenetic tree reconstruction. It also finds applications…
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…
Optimal decision tree (\odt) is a fundamental problem arising in applications such as active learning, entity identification, and medical diagnosis. An instance of \odt is given by $m$ hypotheses, out of which an unknown ``true'' hypothesis…
Dual-tree algorithms are a widely used class of branch-and-bound algorithms. Unfortunately, developing dual-tree algorithms for use with different trees and problems is often complex and burdensome. We introduce a four-part logical split:…
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…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
We present an algorithm that, with high probability, generates a random spanning tree from an edge-weighted undirected graph in $\tilde{O}(n^{4/3}m^{1/2}+n^{2})$ time (The $\tilde{O}(\cdot)$ notation hides $\operatorname{polylog}(n)$…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…
We consider a classical k-center problem in trees. Let T be a tree of n vertices and every vertex has a nonnegative weight. The problem is to find k centers on the edges of T such that the maximum weighted distance from all vertices to…
The Fr\'echet distance is a popular distance measure between trajectories or curves in space, or between walks in graphs. We study computing the Fr\'echet distance between walks in the $d$-dimensional grid graphs, i.e. $\mathbb{Z}^d$ where…
We give an O(sqrt n log n)-query quantum algorithm for evaluating size-n AND-OR formulas. Its running time is poly-logarithmically greater after efficient preprocessing. Unlike previous approaches, the algorithm is based on a quantum walk…