16,662 research outputs found
Faster Approximate String Matching for Short Patterns
We study the classical approximate string matching problem, that is, given
strings and and an error threshold , find all ending positions of
substrings of whose edit distance to is at most . Let and
have lengths and , respectively. On a standard unit-cost word RAM with
word size we present an algorithm using time When is
short, namely, or this
improves the previously best known time bounds for the problem. The result is
achieved using a novel implementation of the Landau-Vishkin algorithm based on
tabulation and word-level parallelism.Comment: To appear in Theory of Computing System
Improved bounds for testing Dyck languages
In this paper we consider the problem of deciding membership in Dyck
languages, a fundamental family of context-free languages, comprised of
well-balanced strings of parentheses. In this problem we are given a string of
length in the alphabet of parentheses of types and must decide if it is
well-balanced. We consider this problem in the property testing setting, where
one would like to make the decision while querying as few characters of the
input as possible.
Property testing of strings for Dyck language membership for , with a
number of queries independent of the input size , was provided in [Alon,
Krivelevich, Newman and Szegedy, SICOMP 2001]. Property testing of strings for
Dyck language membership for was first investigated in [Parnas, Ron
and Rubinfeld, RSA 2003]. They showed an upper bound and a lower bound for
distinguishing strings belonging to the language from strings that are far (in
terms of the Hamming distance) from the language, which are respectively (up to
polylogarithmic factors) the power and the power of the input size
.
Here we improve the power of in both bounds. For the upper bound, we
introduce a recursion technique, that together with a refinement of the methods
in the original work provides a test for any power of larger than .
For the lower bound, we introduce a new problem called Truestring Equivalence,
which is easily reducible to the -type Dyck language property testing
problem. For this new problem, we show a lower bound of to the power of
Constant-factor approximation of near-linear edit distance in near-linear time
We show that the edit distance between two strings of length can be
computed within a factor of in time as long as
the edit distance is at least for some .Comment: 40 pages, 4 figure
An output-sensitive algorithm for the minimization of 2-dimensional String Covers
String covers are a powerful tool for analyzing the quasi-periodicity of
1-dimensional data and find applications in automata theory, computational
biology, coding and the analysis of transactional data. A \emph{cover} of a
string is a string for which every letter of lies within some
occurrence of . String covers have been generalized in many ways, leading to
\emph{k-covers}, \emph{-covers}, \emph{approximate covers} and were
studied in different contexts such as \emph{indeterminate strings}.
In this paper we generalize string covers to the context of 2-dimensional
data, such as images. We show how they can be used for the extraction of
textures from images and identification of primitive cells in lattice data.
This has interesting applications in image compression, procedural terrain
generation and crystallography
Edit Distance: Sketching, Streaming and Document Exchange
We show that in the document exchange problem, where Alice holds and Bob holds , Alice can send Bob a message of
size bits such that Bob can recover using the
message and his input if the edit distance between and is no more
than , and output "error" otherwise. Both the encoding and decoding can be
done in time . This result significantly
improves the previous communication bounds under polynomial encoding/decoding
time. We also show that in the referee model, where Alice and Bob hold and
respectively, they can compute sketches of and of sizes
bits (the encoding), and send to the referee, who can
then compute the edit distance between and together with all the edit
operations if the edit distance is no more than , and output "error"
otherwise (the decoding). To the best of our knowledge, this is the first
result for sketching edit distance using bits.
Moreover, the encoding phase of our sketching algorithm can be performed by
scanning the input string in one pass. Thus our sketching algorithm also
implies the first streaming algorithm for computing edit distance and all the
edits exactly using bits of space.Comment: Full version of an article to be presented at the 57th Annual IEEE
Symposium on Foundations of Computer Science (FOCS 2016
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