Related papers: Approximating the Longest Common Subsequence probl…
In this paper we address the constrained longest common subsequence problem. Given two sequences $X$, $Y$ and a constrained sequence $P$, a sequence $Z$ is a constrained longest common subsequence for $X$ and $Y$ with respect to $P$ if $Z$…
In this paper, we study parallel algorithms for the correlation clustering problem, where every pair of two different entities is labeled with similar or dissimilar. The goal is to partition the entities into clusters to minimize the number…
Computation on compressed strings is one of the key approaches to processing massive data sets. We consider local subsequence recognition problems on strings compressed by straight-line programs (SLP), which is closely related to…
The fundamental sparsest cut problem takes as input a graph $G$ together with the edge costs and demands, and seeks a cut that minimizes the ratio between the costs and demands across the cuts. For $n$-node graphs~$G$ of treewidth~$k$,…
In this paper, we provide new approximation algorithms for dynamic variations of the longest increasing subsequence (\textsf{LIS}) problem, and the complementary distance to monotonicity (\textsf{DTM}) problem. In this setting, operations…
We present an algorithm for approximating the edit distance between two strings of length $n$ in time $n^{1+\varepsilon}$ up to a constant factor, for any $\varepsilon>0$. Our result completes a research direction set forth in the recent…
The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. The ACS can be computed in O(n) space and time, where n=x+y is the input size. The compressed string matching is the study of…
In the Shortest Common Superstring problem (SCS), one needs to find the shortest superstring for a set of strings. While SCS is NP-hard and MAX-SNP-hard, the Greedy Algorithm "choose two strings with the largest overlap; merge them; repeat"…
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…
In many applications, it is necessary to determine the string similarity. Edit distance[WF74] approach is a classic method to determine Field Similarity. A well known dynamic programming algorithm [GUS97] is used to calculate edit distance…
A longest common extension (LCE) query on a string computes the length of the longest common suffix or prefix at two given positions. A dynamic LCE algorithm maintains a data structure that allows efficient LCE queries on a string that can…
This study investigates whether reoptimization can help in solving the closest substring problem. We are dealing with the following reoptimization scenario. Suppose, we have an optimal l-length closest substring of a given set of sequences…
Maximal Common Subsequences (MCSs) between two strings X and Y are subsequences of both X and Y that are maximal under inclusion. MCSs relax and generalize the well known and widely used concept of Longest Common Subsequences (LCSs), which…
The nature of the alignment with gaps corresponding to a longest common subsequence (LCS) of two independent iid random sequences drawn from a finite alphabet is investigated. It is shown that such an optimal alignment typically matches…
Given a sequence of integers, we want to find a longest increasing subsequence of the sequence. It is known that this problem can be solved in $O(n \log n)$ time and space. Our goal in this paper is to reduce the space consumption while…
In this paper, we propose a data structure, a quadruple neighbor list (QN-list, for short), to support real time queries of all longest increasing subsequence (LIS) and LIS with constraints over sequential data streams. The QN-List built by…
This paper performs the analysis necessary to bound the running time of known, efficient algorithms for generating all longest common subsequences. That is, we bound the running time as a function of input size for algorithms with time…
This study develops an algorithm to solve a variation of the Shortest Common Superstring (SCS) problem. There are two modifications to the base SCS problem. First, one string in the set S is allowed to have up to K mistakes, defined as not…
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…
The problem of the fluctuation of the Longest Common Subsequence (LCS) of two i.i.d. sequences of length $n>0$ has been open for decades. There exist contradicting conjectures on the topic. Chvatal and Sankoff conjectured in 1975 that…