Related papers: A Practical O(R\log\log n+n) time Algorithm for Co…
We consider two closely related problems of text indexing in a sub-linear working space. The first problem is the Sparse Suffix Tree (SST) construction of a set of suffixes $B$ using only $O(|B|)$ words of space. The second problem is the…
We study the Multiple Cluster Scheduling problem and the Multiple Strip Packing problem. For both problems, there is no algorithm with approximation ratio better than $2$ unless $P = NP$. In this paper, we present an algorithm with…
We revisit two well-known algorithmic problems on strings: computing a shortest unique substring (SUS) and a shortest absent substring (SAS) of a string $S$ of length $n$. Both problems admit folklore $\mathcal{O}(n)$-time solutions using…
Let $S$ be a string of length $n$ over an alphabet $\Sigma$ and let $Q$ be a subset of $\Sigma$ of size $q \geq 2$. The 'co-occurrence problem' is to construct a compact data structure that supports the following query: given an integer $w$…
In this paper, we consider the ``Shortest Superstring Problem''(SSP) or the ``Shortest Common Superstring Problem''(SCS). The problem is as follows. For a positive integer $n$, a sequence of n strings $S=(s^1,\dots,s^n)$ is given. We should…
Consider two independent random strings having same length and taking values uniformly in a common finite alphabet. We study the order of the variance of the length of the longest common subsequences (LCS) of these strings when long blocks,…
We revisit the problem of maintaining the longest increasing subsequence (LIS) of an array under (i) inserting an element, and (ii) deleting an element of an array. In a recent breakthrough, Mitzenmacher and Seddighin [STOC 2020] designed…
In the area of Pattern Recognition and Matching, finding a Longest Common Subsequence plays an important role. In this paper, we have proposed one algorithm based on parallel computation. We have used OpenMP API package as middleware to…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
The string indexing problem is a fundamental computational problem with numerous applications, including information retrieval and bioinformatics. It aims to efficiently solve the pattern matching problem: given a text T of length n for…
The notion of the cover is a generalization of a period of a string, and there are linear time algorithms for finding the shortest cover. The seed is a more complicated generalization of periodicity, it is a cover of a superstring of a…
The Shortest Common Superstring problem (SCS) consists, for a set of strings S = {s_1,...,s_n}, in finding a minimum length string that contains all s_i, 1<= i <= n, as substrings. While a 2+11/30 approximation ratio algorithm has recently…
Colinear chaining is a classical heuristic for sequence alignment and is widely used in modern practical aligners. Jain et al. (J. Comput. Biol. 2022) proposed an $O(n \log^3 n)$ time algorithm to chain a set of $n$ anchors so that the…
Given two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the…
There are efficient dynamic programming solutions to the computation of the Edit Distance from $S\in[1..\sigma]^n$ to $T\in[1..\sigma]^m$, for many natural subsets of edit operations, typically in time within $O(nm)$ in the worst-case over…
Given several number sequences, determining the longest common subsequence is a classical problem in computer science. This problem has applications in bioinformatics, especially determining transposable genes. Nevertheless, related works…
We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal $O(n)$ time and space algorithm that can find an SUS for every location of a string of size $n$. Our algorithm significantly…
We investigate the asymptotic standard deviation of the Longest Common Subsequence (LCS) of two independent i.i.d. sequences of length n. The first sequence is drawn from a three letter alphabet {0,1,a}, whilst the second sequence is…
Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can…
Correlation Clustering is a fundamental and widely-studied problem in unsupervised learning and data mining. The input is a graph and the goal is to construct a clustering minimizing the number of inter-cluster edges plus the number of…