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The Minimum Linear Arrangement problem (MLA) consists of finding a mapping $\pi$ from vertices of a graph to distinct integers that minimizes $\sum_{\{u,v\}\in E}|\pi(u) - \pi(v)|$. In that setting, vertices are often assumed to lie on a…
Multiple sequence alignment is increasingly important to bioinformatics, with several applications ranging from phylogenetic analyses to domain identification. There are several ways to perform multiple sequence alignment, an important way…
Min-Cut queries are fundamental: Preprocess an undirected edge-weighted graph, to quickly report a minimum-weight cut that separates a query pair of nodes $s,t$. The best data structure known for this problem simply builds a cut-equivalent…
The problem of determining the configuration of points from partial distance information, known as the Euclidean Distance Geometry (EDG) problem, is fundamental to many tasks in the applied sciences. In this paper, we propose two algorithms…
The path-difference metric is one of the oldest and most popular distances for the comparison of phylogenetic trees, but its statistical properties are still quite unknown. In this paper we compute the expected value under the Yule model of…
We augment a tree $T$ with a shortcut $pq$ to minimize the largest distance between any two points along the resulting augmented tree $T+pq$. We study this problem in a continuous and geometric setting where $T$ is a geometric tree in the…
Computing the Euclidean minimum spanning tree (EMST) is a computationally demanding step of many algorithms. While work-efficient serial and multithreaded algorithms for computing EMST are known, designing an efficient GPU algorithm is…
Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean distance between…
We present a deterministic algorithm for computing the sensitivity of a minimum spanning tree (MST) or shortest path tree in $O(m\log\alpha(m,n))$ time, where $\alpha$ is the inverse-Ackermann function. This improves upon a long standing…
In the Euclidean Steiner Tree problem, we are given as input a set of points (called terminals) in the $\ell_2$-metric space and the goal is to find the minimum-cost tree connecting them. Additional points (called Steiner points) from the…
In this paper, we consider Steiner forest and its generalizations, prize-collecting Steiner forest and k-Steiner forest, when the vertices of the input graph are points in the Euclidean plane and the lengths are Euclidean distances. First,…
We introduce stronger notions for approximate single-source shortest-path distances, show how to efficiently compute them from weaker standard notions, and demonstrate the algorithmic power of these new notions and transformations. One…
Stochastic algorithms, especially stochastic gradient descent (SGD), have proven to be the go-to methods in data science and machine learning. In recent years, the stochastic proximal point algorithm (SPPA) emerged, and it was shown to be…
We give a randomized O(n polylog n)-time approximation scheme for the Steiner forest problem in the Euclidean plane. For every fixed eps > 0 and given n terminals in the plane with connection requests between some pairs of terminals, our…
A planar orthogonal drawing {\Gamma} of a connected planar graph G is a geometric representation of G such that the vertices are drawn as distinct points of the plane, the edges are drawn as chains of horizontal and vertical segments, and…
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…
The linearized Bregman iterations (LBreI) and its variants are powerful tools for finding sparse or low-rank solutions to underdetermined linear systems. In this study, we propose a cut-and-project perspective for the linearized Bregman…
The paper introduces a special case of the Euclidean distance matrix completion problem (edmcp) of interest in statistical data analysis where only the minimal spanning tree distances are given and the matrix completion must preserve the…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…