Related papers: Chaining with overlaps revisited
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…
Longest common extension queries (LCE queries) and runs are ubiquitous in algorithmic stringology. Linear-time algorithms computing runs and preprocessing for constant-time LCE queries have been known for over a decade. However, these…
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…
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 $Z$…
A necklace is an equivalence class of words of length $n$ over an alphabet under the cyclic shift (rotation) operation. As a classical object, there have been many algorithmic results for key operations on necklaces, including counting,…
This paper focuses on the problem of coflow scheduling with precedence constraints in identical parallel networks, which is a well-known $\mathcal{NP}$-hard problem. Coflow is a relatively new network abstraction used to characterize…
Overlapping clusters are common in models of many practical data-segmentation applications. Suppose we are given $n$ elements to be clustered into $k$ possibly overlapping clusters, and an oracle that can interactively answer queries of the…
Finding the longest common subsequence in $k$-length substrings (LCS$k$) is a recently proposed problem motivated by computational biology. This is a generalization of the well-known LCS problem in which matching symbols from two sequences…
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…
We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
Two strings of the same length are said to Cartesian-tree match (CT-match) if their Cartesian-trees are isomorphic [Park et al., TCS 2020]. Cartesian-tree matching is a natural model that allows for capturing similarities of numerical…
Sublinear time algorithms for approximating maximum matching size have long been studied. Much of the progress over the last two decades on this problem has been on the algorithmic side. For instance, an algorithm of Behnezhad [FOCS'21]…
We consider the problem of finding \textit{semi-matching} in bipartite graphs which is also extensively studied under various names in the scheduling literature. We give faster algorithms for both weighted and unweighted case. For the…
We study the problem of computing a longest increasing subsequence in a sequence $S$ of $n$ distinct elements in the presence of persistent comparison errors. In this model, every comparison between two elements can return the wrong result…
We consider the problem of scheduling $n$ precedence-constrained jobs on $m$ uniformly-related machines in the presence of an arbitrary, fixed communication delay $\rho$. We consider a model that allows job duplication, i.e. processing of…
The 2-LCPS problem, first introduced by Chowdhury et al. [Fundam. Inform., 129(4):329-340, 2014], asks one to compute (the length of) a longest palindromic common subsequence between two given strings $A$ and $B$. We show that the 2-LCPS…
A fundamental problem in shape matching and geometric similarity is computing the maximum area overlap between two polygons under translation. For general simple polygons, the best-known algorithm runs in $O((nm)^2 \log(nm))$ time [Mount,…
We consider the longest common subsequence (LCS) problem with the restriction that the common subsequence is required to consist of at least $k$ length substrings. First, we show an $O(mn)$ time algorithm for the problem which gives a…
A central problem in scheduling is to schedule $n$ unit size jobs with precedence constraints on $m$ identical machines so as to minimize the makespan. For $m=3$, it is not even known if the problem is NP-hard and this is one of the last…