Related papers: Finding Approximate Palindromes in Strings Quickly…
The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem…
An influential result by Dor, Halperin, and Zwick (FOCS 1996, SICOMP 2000) implies an algorithm that can compute approximate shortest paths for all vertex pairs in $\tilde{O}(n^{2+O\left(\frac{1}{k}\right )})$ time, ensuring that the output…
We present a near-linear time algorithm that approximates the edit distance between two strings within a polylogarithmic factor; specifically, for strings of length n and every fixed epsilon>0, it can compute a (log n)^O(1/epsilon)…
Many problems in bioinformatics are about finding strings that approximately represent a collection of given strings. We look at more general problems where some input strings can be classified as outliers. The Close to Most Strings problem…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
The palindrome pattern matching (pal-matching) is a kind of generalized pattern matching, in which two strings $x$ and $y$ of same length are considered to match (pal-match) if they have the same palindromic structures, i.e., for any…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. Sampled string…
This paper proposes a new algorithm for reducing Approximate Nearest Neighbor problem to Approximate Near Neighbor problem. The advantage of this algorithm is that it achieves O(log n) query time. As a reduction problem, the uery time…
Palindromes are popular and important objects in textual data processing, bioinformatics, and combinatorics on words. Let $S = XaY$ be a string where $X$ and $Y$ are of the same length, and $a$ is either a single character or the empty…
A run in a string is a maximal periodic substring. For example, the string $\texttt{bananatree}$ contains the runs $\texttt{anana} = (\texttt{an})^{3/2}$ and $\texttt{ee} = \texttt{e}^2$. There are less than $n$ runs in any length-$n$…
We revisit classic string problems considered in the area of parameterized complexity, and study them through the lens of dynamic data structures. That is, instead of asking for a static algorithm that solves the given instance efficiently,…
In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the…
We propose novel algorithms for sequence prediction based on ideas from stringology. These algorithms are time and space efficient and satisfy mistake bounds related to particular stringological complexity measures of the sequence. In this…
The {\em longest common subsequence (LCS)} problem is a classic and well-studied problem in computer science. LCS is a central problem in stringology and finds broad applications in text compression, error-detecting codes and biological…
We consider the approximate pattern matching problem under edit distance. In this problem we are given a pattern $P$ of length $w$ and a text $T$ of length $n$ over some alphabet $\Sigma$, and a positive integer $k$. The goal is to find all…
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…
A palindrome is a string that reads the same forward and backward. A palindromic substring $P$ of a string $S$ is called a shortest unique palindromic substring ($\mathit{SUPS}$) for an interval $[x, y]$ in $S$, if $P$ occurs exactly once…
The main subject of the paper is everywhere complex sequences. An everywhere complex sequence is a sequence that does not contain substrings of Kolmogorov complexity less than $\alpha n-O(1)$ where $n$ is the length of substring and…
This paper addresses the online exact string matching problem which consists in finding all occurrences of a given pattern p in a text t. It is an extensively studied problem in computer science, mainly due to its direct applications to…
The Longest Common Subsequence (LCS) is a fundamental string similarity measure, and computing the LCS of two strings is a classic algorithms question. A textbook dynamic programming algorithm gives an exact algorithm in quadratic time, and…