Related papers: Approximating General Metric Distances Between a P…

Given a set of strings over a specified alphabet, identifying a median or consensus string that minimizes the total distance to all input strings is a fundamental data aggregation problem. When the Hamming distance is considered as the…

Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…

We propose a new $(1+O(\varepsilon))$-approximation algorithm with $O(n+ 1/\varepsilon^{\frac{(d-1)}{2}})$ running time for computing the diameter of a set of $n$ points in the $d$-dimensional Euclidean space for a fixed dimension $d$,…

We study approximation algorithms for the following geometric version of the maximum coverage problem: Let $\mathcal{P}$ be a set of $n$ weighted points in the plane. Let $D$ represent a planar object, such as a rectangle, or a disk. We…

Edit distance is a measure of similarity of two strings based on the minimum number of character insertions, deletions, and substitutions required to transform one string into the other. The edit distance can be computed exactly using a…

Consider a set $P$ of $n$ points in $\mathbb{R}^d$. In the discrete median line segment problem, the objective is to find a line segment bounded by a pair of points in $P$ such that the sum of the Euclidean distances from $P$ to the line…

In this paper, we study the problem of computing the diameter of a set of $n$ points in $d$-dimensional Euclidean space for a fixed dimension $d$, and propose a new $(1+\varepsilon)$-approximation algorithm with $O(n+ 1/\varepsilon^{d-1})$…

Real-world data often comes in compressed form. Analyzing compressed data directly (without decompressing it) can save space and time by orders of magnitude. In this work, we focus on fundamental sequence comparison problems and try to…

We give a dimensionality reduction procedure to approximate the sum of distances of a given set of $n$ points in $R^d$ to any "shape" that lies in a $k$-dimensional subspace. Here, by "shape" we mean any set of points in $R^d$. Our…

A weighted string over an alphabet of size $\sigma$ is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices or uncertain sequences,…

For two d-dimensional point sets A, B of size up to n, the Chamfer distance from A to B is defined as CH(A,B) = \sum_{a \in A} \min_{b \in B} \|a-b\|. The Chamfer distance is a widely used measure for quantifying dissimilarity between sets…

In this paper we present a simple linear-time algorithm constructing a context-free grammar of size O(g log(N/g)) for the input string, where N is the size of the input string and g the size of the optimal grammar generating this string.…

In this paper, a fully compressed pattern matching problem is studied. The compression is represented by straight-line programs (SLPs), i.e. a context-free grammars generating exactly one string; the term fully means that both the pattern…

We study algorithms for approximating pairwise similarity matrices that arise in natural language processing. Generally, computing a similarity matrix for $n$ data points requires $\Omega(n^2)$ similarity computations. This quadratic…

Given a pair of strings, the problems of computing their Longest Common Subsequence and Edit Distance have been extensively studied for decades. For exact algorithms, LCS and Edit Distance (with character insertions and deletions) are…

We survey the emerging area of compression-based, parameter-free, similarity distance measures useful in data-mining, pattern recognition, learning and automatic semantics extraction. Given a family of distances on a set of objects, a…

The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. The ACS can be computed in O(n) space and time, where n=x+y is the input size. The compressed string matching is the study of…

We show how to compute for $n$-vertex planar graphs in $O(n^{11/6}{\rm polylog}(n))$ expected time the diameter and the sum of the pairwise distances. The algorithms work for directed graphs with real weights and no negative cycles. In…

Persistent homology allows us to create topological summaries of complex data. In order to analyse these statistically, we need to choose a topological summary and a relevant metric space in which this topological summary exists. While…

The metric sketching problem is defined as follows. Given a metric on $n$ points, and $\epsilon>0$, we wish to produce a small size data structure (sketch) that, given any pair of point indices, recovers the distance between the points up…