Related papers: An $O(n \log n)$ time Algorithm for computing the …
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
We describe a $O(\log n )$-approximation algorithm for computing the homotopic \Frechet distance between two polygonal curves that lie on the boundary of a triangulated topological disk. Prior to this work, algorithms were known only for…
In 1996, Bodlaender showed the celebrated result that an optimal tree decomposition of a graph of bounded treewidth can be found in linear time. The algorithm is based on an algorithm of Bodlaender and Kloks that computes an optimal tree…
The tree-metric theorem provides a necessary and sufficient condition for a dissimilarity matrix to be a tree metric, and has served as the foundation for numerous distance-based reconstruction methods in phylogenetics. Our main result is…
We introduce a scale-free method for testing the proportionality of branch lengths between two phylogenetic trees that have the same topology and contain the same set of taxa. This method scales both trees to a total length of 1 and sums up…
Net-trees are a general purpose data structure for metric data that have been used to solve a wide range of algorithmic problems. We give a simple randomized algorithm to construct net-trees on doubling metrics using $O(n\log n)$ time in…
Unbreakable decomposition, introduced by Cygan et al. (SICOMP'19) and Cygan et al. (TALG'20), has proven to be one of the most powerful tools for parameterized graph cut problems in recent years. Unfortunately, all known constructions…
An added edge to a graph is called an inset edge. Predicting k inset edges which minimize the average distance of a graph is known to be NP-Hard. When k = 1 the complexity of the problem is polynomial. In this paper, we further find the…
The interleaving distance is a key tool for comparing merge trees, which provide topological summaries of scalar functions. In this work, we define an average merge tree for a pair of merge trees using the interleaving distance. Since such…
Resistance distance computation is a fundamental problem in graph analysis, yet existing random walk-based methods are limited to approximate solutions and suffer from poor efficiency on small-treewidth graphs (e.g., road networks). In…
There are few, if any, algorithms in statistical phylogenetics which are used more heavily than Felsenstein's 1973 pruning method for computing the likelihood of a tree. We present LvD, (Likelihood via Decomposition), an alternative to…
Computing optimal transport (OT) distances such as the earth mover's distance is a fundamental problem in machine learning, statistics, and computer vision. In this paper, we study the problem of approximating the general OT distance…
Let $P$ be a simple polygon of $n$ vertices. We consider two-point $L_1$ shortest path queries in $P$. We build a data structure of $O(n)$ size in $O(n)$ time such that given any two query points $s$ and $t$, the length of an $L_1$ shortest…
In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…
In machine learning and particularly in topological data analysis, $\epsilon$-graphs are important tools but are generally hard to compute as the distance calculation between n points takes time O(n^2) classically. Recently, quantum…
We present $O(\log^2 \log n)$ time 3-coloring, maximal independent set and maximal matching algorithms for trees in the Massively Parallel Computation (MPC) model. Our algorithms are deterministic, apply to arbitrary-degree trees and work…
We define, analyze, and give efficient algorithms for two kinds of distance measures for rooted and unrooted phylogenies. For rooted trees, our measures are based on the topologies the input trees induce on triplets; that is, on…
Distance covariance and distance correlation have been widely adopted in measuring dependence of a pair of random variables or random vectors. If the computation of distance covariance and distance correlation is implemented directly…
The treedepth of a graph $G$ is the least possible depth of an elimination forest of $G$: a rooted forest on the same vertex set where every pair of vertices adjacent in $G$ is bound by the ancestor/descendant relation. We propose an…
Reachability is the problem of deciding whether there is a path from one vertex to the other in the graph. Standard graph traversal algorithms such as DFS and BFS take linear time to decide reachability however their space complexity is…