Related papers: Chaining with overlaps revisited
Two strings are considered to have parameterized matching when there exists a bijection of the parameterized alphabet onto itself such that it transforms one string to another. Parameterized matching has application in software duplication…
Given $n$ intervals on a line $\ell$, we consider the problem of moving these intervals on $\ell$ such that no two intervals overlap and the maximum moving distance of the intervals is minimized. The difficulty for solving the problem lies…
Determining whether an unordered collection of overlapping substrings (called shingles) can be uniquely decoded into a consistent string is a problem that lies within the foundation of a broad assortment of disciplines ranging from…
Recently, Armstrong, Guzm\'an, and Sing Long (2021), presented an optimal $O(n^2)$ time algorithm for strict circular seriation (called also the recognition of strict quasi-circular Robinson spaces). In this paper, we give a very simple…
We present linear time {\it in-place} algorithms for several basic and fundamental graph problems including the well-known graph search methods (like depth-first search, breadth-first search, maximum cardinality search), connectivity…
We study the classical scheduling problem on parallel machines %with precedence constraints where the precedence graph has the bounded depth $h$. Our goal is to minimize the maximum completion time. We focus on developing approximation…
We consider the problem of efficiently scheduling jobs with precedence constraints on a set of identical machines in the presence of a uniform communication delay. Such precedence-constrained jobs can be modeled as a directed acyclic graph,…
This paper studies a scheduling problem in a parallel machine setting, where each machine must adhere to a predetermined fixed order for processing the jobs. Given $n$ jobs, each with processing times and deadlines, we aim to minimize the…
We present a sorting algorithm for the case of recurrent random comparison errors. The algorithm essentially achieves simultaneously good properties of previous algorithms for sorting $n$ distinct elements in this model. In particular, it…
Given two convex polygons $P$ and $Q$ with $n$ and $m$ edges, the maximum overlap problem is to find a translation of $P$ that maximizes the area of its intersection with $Q$. We give the first randomized algorithm for this problem with…
The hierarchical overlap graph (HOG) is a graph that encodes overlaps from a given set P of n strings, as the overlap graph does. A best known algorithm constructs HOG in O(||P|| log n) time and O(||P||) space, where ||P|| is the sum of…
Sequence Alignment is the process of aligning biological sequences in order to identify similarities between multiple sequences. In this paper, a Quantum Algorithm for finding the optimal alignment between DNA sequences has been…
Recently Kubica et al. (Inf. Process. Let., 2013) and Kim et al. (submitted to Theor. Comp. Sci.) introduced order-preserving pattern matching. In this problem we are looking for consecutive substrings of the text that have the same "shape"…
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…
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…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
We consider the problem of sorting $n$ elements subject to persistent random comparison errors. In this problem, each comparison between two elements can be wrong with some fixed (small) probability $p$, and comparing the same pair of…
We study fully dynamic algorithms for maximum matching. This is a well-studied problem, known to admit several update-time/approximation trade-offs. For instance, it is known how to maintain a 1/2-approximate matching in $\log^{O(1)} n$…
We study the non-overlapping indexing problem: Given a text T, preprocess it so that you can answer queries of the form: given a pattern P, report the maximal set of non-overlapping occurrences of P in T. A generalization of this problem is…
In the classic longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, over an alphabet of size $\sigma$, and we are asked to find a longest string occurring as a fragment of both $S$ and…