Related papers: A New Algebraic Approach for String Reconstruction…
In this paper we develop combinatorial techniques for the case of string algebras with the aim to give a characterization of string complexes with infinite minimal projective resolution. These complexes will be called \textit{periodic…
In the standard trace reconstruction problem, the goal is to \emph{exactly} reconstruct an unknown source string $\mathsf{x} \in \{0,1\}^n$ from independent "traces", which are copies of $\mathsf{x}$ that have been corrupted by a…
In this paper we propose and study a new complexity model for approximation algorithms. The main motivation are practical problems over large data sets that need to be solved many times for different scenarios, e.g., many multicast trees…
Lexicographically minimal string rotation is a fundamental problem in string processing that has recently garnered significant attention in quantum computing. Near-optimal quantum algorithms have been proposed for solving this problem,…
Motivated by computing duplication patterns in sequences, a new fundamental problem called the longest subsequence-repeated subsequence (LSRS) is proposed. Given a sequence $S$ of length $n$, a letter-repeated subsequence is a subsequence…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
Given a pattern $p = s_1x_1s_2x_2\cdots s_{r-1}x_{r-1}s_r$ such that $x_1,x_2,\ldots,x_{r-1}\in\{x,\overset{{}_{\leftarrow}}{x}\}$, where $x$ is a variable and $\overset{{}_{\leftarrow}}{x}$ its reversal, and $s_1,s_2,\ldots,s_r$ are…
In this paper we study the fundamental problem of maintaining a dynamic collection of strings under the following operations: concat - concatenates two strings, split - splits a string into two at a given position, compare - finds the…
The theory of sequences, supported by many SMT solvers, can model program data types including bounded arrays and lists. Sequences are parameterized by the element data type and provide operations such as accessing elements, concatenation,…
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…
Chaining algorithms aim to form a semi-global alignment of two sequences based on a set of anchoring local alignments as input. Depending on the optimization criteria and the exact definition of a chain, there are several $O(n \log n)$ time…
Reconstructing continuous signals from a small number of discrete samples is a fundamental problem across science and engineering. In practice, we are often interested in signals with 'simple' Fourier structure, such as bandlimited,…
We present an online algorithm to deal with pattern matching in strings. The problem we investigate is commonly known as string matching with mismatches in which the objective is to report the number of characters that match when a pattern…
Recovering high-level type information in binaries is a key task in reverse engineering and binary analysis. Binaries contain very little explicit type information. The structure of binary code is incredibly flexible allowing for ad-hoc…
In this paper, we define the reoptimization variant of the closest substring problem (CSP) under sequence addition. We show that, even with the additional information we have about the problem instance, the problem of finding a closest…
This paper investigates the approximability of the Longest Common Subsequence (LCS) problem. The fastest algorithm for solving the LCS problem exactly runs in essentially quadratic time in the length of the input, and it is known that under…
We study the following substring suffix selection problem: given a substring of a string T of length n, compute its k-th lexicographically smallest suffix. This a natural generalization of the well-known question of computing the maximal…
Many consensus string problems are based on Hamming distance. We replace Hamming distance by the more flexible (e.g., easily coping with different input string lengths) dynamic time warping distance, best known from applications in time…
A run in a string is a maximal periodic substring. For example, the string $\texttt{bananatree}$ contains the runs $\texttt{anana} = (\texttt{an})^{3/2}$ and $\texttt{ee} = \texttt{e}^2$. There are less than $n$ runs in any length-$n$…
Generation of an (arbitrarily) long string of bits unique to a given finite-length numerical seed is of great value in the field of random number generation, computer simulations, and other areas of computer science. Extending this idea…