Related papers: Approximating the Longest Common Subsequence probl…
The index coding problem is concerned with broadcasting encoded information to a collection of receivers in a way that enables each receiver to discover its required data based on its side information, which comprises the data required by…
In this paper, we study edit distance (ED) and longest common subsequence (LCS) in the asymmetric streaming model, introduced by Saks and Seshadhri [SS13]. As an intermediate model between the random access model and the streaming model,…
A pangenome captures the genetic diversity across multiple individuals simultaneously, providing a more comprehensive reference for genome analysis than a single linear genome, which may introduce allele bias. A widely adopted pangenome…
The Shortest Common Superstring (SCS) problem asks for the shortest string that contains each of a given set of strings as a substring. Its reverse-complement variant, the Shortest Common Superstring problem with Reverse Complements…
For a set of mulitple sequences, their patterns,Longest Common Subsequences (LCS) and Shortest Common Supersequences (SCS) represent different aspects of these sequences profile, and they can all be used for biological sequence comparisons…
We study the precedence-constrained resource scheduling problem [SICOMP'75]. There are $n$ jobs where each job takes a certain time to finish and has a resource requirement throughout the execution time. There are precedence among the jobs.…
We overcome two major bottlenecks in the study of low rank approximation by assuming the low rank factors themselves are sparse. Specifically, (1) for low rank approximation with spectral norm error, we show how to improve the best known…
Least squares approximation is a technique to find an approximate solution to a system of linear equations that has no exact solution. In a typical setting, one lets $n$ be the number of constraints and $d$ be the number of variables, with…
We present an algorithm computing the longest periodic subsequence of a string of length $n$ in $O(n^7)$ time with $O(n^4)$ words of space. We obtain improvements when restricting the exponents or extending the search allowing the reported…
Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that…
Finding the densest subgraph (DS) from a graph is a fundamental problem in graph databases. The DS obtained, which reveals closely related entities, has been found to be useful in various application domains such as e-commerce, social…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
We consider the Abelian longest common factor problem in two scenarios: when input strings are uncompressed and are of size $n$, and when the input strings are run-length encoded and their compressed representations have size at most $m$.…
In this paper, we study a class of approximation problems, appearing in data approximation and signal processing. The approximations are constructed as combinations of polynomial splines (piecewise polynomials), whose parameters are subject…
In the $k$-edge-connected spanning subgraph ($k$ECSS) problem, our goal is to compute a minimum-cost sub-network that is resilient against up to $k$ link failures: Given an $n$-node $m$-edge graph with a cost function on the edges, our goal…
The Shortest Superstring Problem (SSP) consists, for a set of strings S = {s_1,...,s_n}, to find a minimum length string that contains all s_i, 1 <= i <= k, as substrings. This problem is proved to be NP-Complete and APX-hard. Guaranteed…
Let $\Sigma$ be an alphabet. For two strings $X$, $Y$, and a constrained string $P$ over the alphabet $\Sigma$, the constrained longest common subsequence and substring problem for two strings $X$ and $Y$ with respect to $P$ is to find a…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
In this paper we initiate the study of computing a maximal (not necessarily maximum) repeating pattern in a single input string, where the corresponding problems have been studied (e.g., a maximal common subsequence) only in two or more…
Approximating a univariate function on the interval $[-1,1]$ with a polynomial is among the most classical problems in numerical analysis. When the function evaluations come with noise, a least-squares fit is known to reduce the effect of…