Related papers: Semi-local string comparison: algorithmic techniqu…
In this paper we study the fundamental problem of maintaining a dynamic collection of strings under the following operations: concat - concatenates two strings, split - splits a string into two at a given position, compare - finds the…
In this paper, we revisit the much studied LCS problem for two given sequences. Based on the algorithm of Iliopoulos and Rahman for solving the LCS problem, we have suggested 3 new improved algorithms. We first reformulate the problem in a…
The aim of this Lecture Note is to introduce the Signal Processing (SP) community to a powerful yet still under-utilised tool: the semiparametric statistics. In short, the semiparametric framework allows us to estimate or perform hypothesis…
We study distributed algorithms for string matching problem in presence of wildcard characters. Given a string T (a text), we look for all occurrences of another string P (a pattern) as a substring of string T . Each wildcard character in…
The Shortest Common Superstring (SCS) problem asks for the shortest string that contains each of a given set of strings as a substring. Its reverse-complement variant, the Shortest Common Superstring problem with Reverse Complements…
The Longest Common Increasing Subsequence problem (LCIS) is a natural variant of the celebrated Longest Common Subsequence (LCS) problem. For LCIS, as well as for LCS, there is an $O(n^2)$-time algorithm and a SETH-based conditional lower…
Given $m$ documents of total length $n$, we consider the problem of finding a longest string common to at least $d \geq 2$ of the documents. This problem is known as the \emph{longest common substring (LCS) problem} and has a classic $O(n)$…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
A technique using a systolic array structure is proposed for solving the common approximate substring (CAS) problem. This approach extends the technique introduced in earlier work from the computation of the edit-distance between two…
The constrained LCS problem asks one to find a longest common subsequence of two input strings $A$ and $B$ with some constraints. The STR-IC-LCS problem is a variant of the constrained LCS problem, where the solution must include a given…
This paper addresses the Longest Filled Common Subsequence (LFCS) problem, a challenging NP-hard problem with applications in bioinformatics, including gene mutation prediction and genomic data reconstruction. Existing approaches, including…
Measuring similarities between strings is central for many established and fast growing research areas including information retrieval, biology, and natural language processing. The traditional approach for string similarity measurements is…
We present novel randomized approximation schemes for the Edit Distance (ED) problem and the Longest Common Subsequence (LCS) problem that, for any constant $\epsilon>0$, compute a $(1+\epsilon)$-approximation for ED and a…
We propose efficient algorithms for enumerating maximal common subsequences (MCSs) of two strings. Efficiency of the algorithms are estimated by the preprocessing-time, space, and delay-time complexities. One algorithm prepares a…
Given a set of pattern strings $\mathcal{P}=\{P_1, P_2,\ldots P_k\}$ and a text string $S$, the classic dictionary matching problem is to report all occurrences of each pattern in $S$. We study the dictionary problem in the compressed…
Let $X_1, X_2, ..., X_s$ and $Y_1, Y_2, ..., Y_t$ be strings over an alphabet $\Sigma$, where $s$ and $t$ are positive integers. The longest common subsequence and substring problem for multiple strings $X_1, X_2, ..., X_s$ and $Y_1, Y_2,…
In this paper, we study a series of algorithmic problems related to the subsequences occurring in the strings of a given language, under the assumption that this language is succinctly represented by a grammar generating it, or an automaton…
We study quantum algorithms for several fundamental string problems, including Longest Common Substring, Lexicographically Minimal String Rotation, and Longest Square Substring. These problems have been widely studied in the stringology…
The longest square subsequence (LSS) problem consists of computing a longest subsequence of a given string $S$ that is a square, i.e., a longest subsequence of form $XX$ appearing in $S$. It is known that an LSS of a string $S$ of length…
For a set of mulitple sequences, their patterns,Longest Common Subsequences (LCS) and Shortest Common Supersequences (SCS) represent different aspects of these sequences profile, and they can all be used for biological sequence comparisons…