Related papers: Improved Approximation Algorithms and Hardness Res…

Consensus problems for strings and sequences appear in numerous application contexts, ranging from bioinformatics over data mining to machine learning. Closing some gaps in the literature, we show that several fundamental problems in this…

A fundamental property of DNA is that the reverse complement (RC) of a sequence often carries identical biological meaning. However, state-of-the-art DNA language models frequently fail to capture this symmetry, producing inconsistent…

In this paper, we consider a generalized longest common subsequence problem, the string-excluding constrained LCS problem. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a constraint string $P$ of length $r$, the…

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 study the approximability of two related problems on graphs with $n$ nodes and $m$ edges: $n$-Pairs Shortest Paths ($n$-PSP), where the goal is to find a shortest path between $O(n)$ prespecified pairs, and All Node Shortest Cycles…

Compressive Sensing (CS) theory states that real-world signals can often be recovered from much fewer measurements than those suggested by the Shannon sampling theorem. Nevertheless, recoverability does not only depend on the signal, but…

The longest common subsequence (LCS) is a fundamental problem in string processing which has numerous algorithmic studies, extensions, and applications. A sequence $u_1, \ldots, u_f$ of $f$ strings s said to be an ($f$-)segmentation of a…

Longest common subsequence (LCS) is one of the most fundamental problems in combinatorial optimization. Apart from theoretical importance, LCS has enormous applications in bioinformatics, revision control systems, and data comparison…

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…

DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…

We revisit the classic combinatorial pattern matching problem of finding a longest common subsequence (LCS). For strings $x$ and $y$ of length $n$, a textbook algorithm solves LCS in time $O(n^2)$, but although much effort has been spent,…

Partial Set Cover (PSC) is a generalization of the well-studied Set Cover problem (SC). In PSC the input consists of an integer $k$ and a set system $(U,S)$ where $U$ is a finite set, and $S \subseteq 2^U$ is a collection of subsets of $U$.…

This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…

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…

Compressed Sensing (CS) is an effective approach to reduce the required number of samples for reconstructing a sparse signal in an a priori basis, but may suffer severely from the issue of basis mismatch. In this paper we study the problem…

In the dynamic set cover (SC) problem, the input is a dynamic universe of at most $n$ elements and a fixed collection of $m$ sets, where each element belongs to at most $f$ sets and each set has cost in $[1/C, 1]$. The objective is to…

A classical measure of string comparison is given by the longest common subsequence (LCS) problem on a pair of strings. We consider its generalisation, called the semi-local LCS problem, which arises naturally in many string-related…

Given a static reference string $R$ and a source string $S$, a relative compression of $S$ with respect to $R$ is an encoding of $S$ as a sequence of references to substrings of $R$. Relative compression schemes are a classic model of…

In this paper, we consider a generalized longest common subsequence problem with multiple substring exclusion constrains. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constrains $P=\{P_1,...,P_d\}$ of…

One of the basic tasks in bioinformatics is localizing a short subsequence $S$, read while sequencing, in a long reference sequence $R$, like the human geneome. A natural rapid approach would be finding a hash value for $S$ and compare it…