Related papers: Linear Time Inference of Strings from Cover Arrays…
In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…
An absent word of a word y of length n is a word that does not occur in y. It is a minimal absent word if all its proper factors occur in y. Minimal absent words have been computed in genomes of organisms from all domains of life; their…
Given two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the…
In this paper, we provide the first provable linear-time (in the number of non-zero entries of the input) algorithm for approximately solving the generalized trust region subproblem (GTRS) of minimizing a quadratic function over a quadratic…
We present two variations of Duval's algorithm for computing the Lyndon factorization of a word. The first algorithm is designed for the case of small alphabets and is able to skip a significant portion of the characters of the string, for…
A technique using a systolic array structure is proposed for solving the common approximate substring (CAS) problem. This approach extends the technique introduced in earlier work from the computation of the edit-distance between two…
Suppose an oracle knows a string $S$ that is unknown to us and that we want to determine. The oracle can answer queries of the form "Is $s$ a substring of $S$?". In 1995, Skiena and Sundaram showed that, in the worst case, any algorithm…
This paper investigates the number of quantum queries made to solve the problem of reconstructing an unknown string from its substrings in a certain query model. More concretely, the goal of the problem is to identify an unknown string $S$…
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…
The anchor words algorithm performs provably efficient topic model inference by finding an approximate convex hull in a high-dimensional word co-occurrence space. However, the existing greedy algorithm often selects poor anchor words,…
We generalize the problem of reconstructing strings from their substring compositions first introduced by Acharya et al. in 2015 motivated by polymer-based advanced data storage systems utilizing mass spectrometry. Namely, we see strings as…
In this paper we propose a new, more appropriate definition of regular and indeterminate strings. A regular string is one that is "isomorphic" to a string whose entries all consist of a single letter, but which nevertheless may itself…
Given an arbitrary bitstream, we consider the problem of finding the longest substring whose ratio of ones to zeroes equals a given value. The central result of this paper is an algorithm that solves this problem in linear time. The method…
A Lyndon word is a primitive string which is lexicographically smallest among cyclic permutations of its characters. Lyndon words are used for constructing bases in free Lie algebras, constructing de Bruijn sequences, finding the…
Bille and G{\o}rtz (2011) recently introduced the problem of substring range counting, for which we are asked to store compactly a string $S$ of $n$ characters with integer labels in ([0, u]), such that later, given an interval ([a, b]) and…
In this paper we show the usability of the Gray code with constant weight words for computing linear combinations of codewords. This can lead to a big improvement of the computation time for finding the minimum distance of a code. We have…
In this paper, we propose a probabilistic algorithm suitable for any linear code $C$ to determine whether a given vector $\mathbf{x}$ belongs to $ C$. The algorithm achieves $O(n\log n)$ time complexity, $ O(n^2)$ space complexity and with…
The minimum common string partition problem is an NP-hard combinatorial optimization problem with applications in computational biology. In this work we propose the first integer linear programming model for solving this problem. Moreover,…
The problem of reconstructing strings from their substring spectra has a long history and in its most simple incarnation asks for determining under which conditions the spectrum uniquely determines the string. We study the problem of coded…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. Sampled string…