Edit distance cannot be computed in strongly subquadratic time (unless SETH is false)

A Backurs, P Indyk - Proceedings of the forty-seventh annual ACM …, 2015 - dl.acm.org
The edit distance (aka the Levenshtein distance) between two strings is defined as the
minimum number of insertions, deletions or substitutions of symbols needed to transform …

Quadratic conditional lower bounds for string problems and dynamic time warping

K Bringmann, M Künnemann - 2015 IEEE 56th Annual …, 2015 - ieeexplore.ieee.org
Classic similarity measures of strings are longest common subsequence and Levenshtein
distance (ie, The classic edit distance). A classic similarity measure of curves is dynamic …

If the current clique algorithms are optimal, so is Valiant's parser

A Abboud, A Backurs, VV Williams - SIAM Journal on Computing, 2018 - SIAM
The CFG recognition problem is as follows: given a context-free grammar G and a string w of
length n, decide whether w can be obtained from G. This is the most basic parsing question …

Approximating edit distance in truly subquadratic time: Quantum and mapreduce

M Boroujeni, S Ehsani, M Ghodsi… - Journal of the ACM …, 2021 - dl.acm.org
The edit distance between two strings is defined as the smallest number of insertions,
deletions, and substitutions that need to be made to transform one of the strings to another …

Distributed PCP theorems for hardness of approximation in P

A Abboud, A Rubinstein… - 2017 IEEE 58th Annual …, 2017 - ieeexplore.ieee.org
We present a new distributed model of probabilistically checkable proofs (PCP). A satisfying
assignment x∈{0, 1} n to a CNF formula φ is shared between two parties, where Alice …

Sublinear time algorithms

R Rubinfeld, A Shapira - SIAM Journal on Discrete Mathematics, 2011 - SIAM
Sublinear Time Algorithms Page 1 Copyright © by SIAM. Unauthorized reproduction of this article
is prohibited. SIAM J. DISCRETE MATH. c 2011 Society for Industrial and Applied Mathematics …

Edit distance in near-linear time: It's a constant factor

A Andoni, NS Nosatzki - 2020 IEEE 61st Annual Symposium on …, 2020 - ieeexplore.ieee.org
We present an algorithm for approximating the edit distance between two strings of length n
in time n 1+ ε, for any, up to a constant factor. Our result completes a research direction set …

Truly subcubic algorithms for language edit distance and RNA folding via fast bounded-difference min-plus product

K Bringmann, F Grandoni, B Saha, VV Williams - SIAM Journal on Computing, 2019 - SIAM
It is a major open problem whether the (\min,+)-product of two n*n matrices has a truly
subcubic (ie, O(n^3-ε) for ε>0) time algorithm; in particular, since it is equivalent to the …

Approximating edit distance in near-linear time

A Andoni, K Onak - Proceedings of the forty-first annual ACM symposium …, 2009 - dl.acm.org
We show how to compute the edit distance between two strings of length n up to a factor of 2
(O-tilde (sqrt (log n))) in n (1+ o (1)) time. This is the first sub-polynomial approximation …

Fast characterization of segmental duplications in genome assemblies

I Numanagić, AS Gökkaya, L Zhang, B Berger… - …, 2018 - academic.oup.com
Abstract Motivation Segmental duplications (SDs) or low-copy repeats, are segments of
DNA> 1 Kbp with high sequence identity that are copied to other regions of the genome …