Related papers: Near-Linear Time Edit Distance for Indel Channels

Analyzing high-dimensional data with manifold learning algorithms often requires searching for the nearest neighbors of all observations. This presents a computational bottleneck in statistical manifold learning when observations of…

Edit Distance is a classic family of dynamic programming problems, among which Time Warp Edit Distance refines the problem with the notion of a metric and temporal elasticity. A novel Improved Time Warp Edit Distance algorithm that is both…

We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have…

We consider the approximate pattern matching problem under the edit distance. Given a text $T$ of length $n$, a pattern $P$ of length $m$, and a threshold $k$, the task is to find the starting positions of all substrings of $T$ that can be…

We study the online variant of the language distance problem for two classical formal languages, the language of palindromes and the language of squares, and for the two most fundamental distances, the Hamming distance and the edit…

Edit-distance-based string similarity search has many applications such as spell correction, data de-duplication, and sequence alignment. However, computing edit distance is known to have high complexity, which makes string similarity…

We revisit a fundamental problem in string matching: given a pattern of length m and a text of length n, both over an alphabet of size $\sigma$, compute the Hamming distance between the pattern and the text at every location. Several…

In a way similar to the string-to-string correction problem we address time series similarity in the light of a time-series-to-time-series-correction problem for which the similarity between two time series is measured as the minimum cost…

We study the problem of edit similarity joins, where given a set of strings and a threshold value $K$, we want to output all pairs of strings whose edit distances are at most $K$. Edit similarity join is a fundamental problem in data…

In this paper we investigate the \emph{approximate string matching problem} when the allowed edit operations are \emph{non-overlapping unbalanced translocations of adjacent factors}. Such kind of edit operations take place when two adjacent…

In this article we consider the graph alignment problem from the perspective of high-dimensional statistics: we aim to estimate an unknown permutation $\pi^*$ from the observation of two correlated random adjacency matrices $A_1$, $A_2$. We…

Recently, Musco and Woodruff (FOCS, 2017) showed that given an $n \times n$ positive semidefinite (PSD) matrix $A$, it is possible to compute a $(1+\epsilon)$-approximate relative-error low-rank approximation to $A$ by querying…

We consider the problem of computing L1-distances between every pair ofcprobability densities from a given family. We point out that the technique of Cauchy random projections (Indyk'06) in this context turns into stochastic integrals with…

Consider the following distance query for an $n$-node graph $G$ undergoing edge insertions and deletions: given two sets of nodes $I$ and $J$, return the distances between every pair of nodes in $I\times J$. This query is rather general and…

Given a sequence $s_1$ of $n$ letters drawn i.i.d. from an alphabet of size $\sigma$ and a mutated substring $s_2$ of length $m < n$, we often want to recover the mutation history that generated $s_2$ from $s_1$. Modern sequence aligners…

In this paper, we consider a generalized longest common subsequence problem, in which a constraining sequence of length $s$ must be included as a substring and the other constraining sequence of length $t$ must be excluded as a subsequence…

We revisit the complexity of the classical Interval Scheduling in the dynamic setting. In this problem, the goal is to maintain a set of intervals under insertions and deletions and report the size of the maximum size subset of pairwise…

We consider approximation of diameter of a set $S$ of $n$ points in dimension $m$. E$\tilde{g}$ecio$\tilde{g}$lu and Kalantari \cite{kal} have shown that given any $p \in S$, by computing its farthest in $S$, say $q$, and in turn the…

Motivated by comparative genomics, Chen et al. [9] introduced the Maximum Duo-preservation String Mapping (MDSM) problem in which we are given two strings $s_1$ and $s_2$ from the same alphabet and the goal is to find a mapping $\pi$…

Stochastic versions of proximal methods have gained much attention in statistics and machine learning. These algorithms tend to admit simple, scalable forms, and enjoy numerical stability via implicit updates. In this work, we propose and…