Related papers: Quantum Algorithm for the Shortest Superstring Pro…
We consider the following problem: Given a set S of at most n elements from a universe of size m, represent it in memory as a bit string so that membership queries of the form "Is x in S?" can be answered by making at most t probes into the…
Suppose we want to seek the longest common subsequences (LCSs) of two strings as informative patterns that explain the relationship between the strings. The dynamic programming algorithm gives us a table from which all LCSs can be extracted…
Minimizers sampling is one of the most widely-used mechanisms for sampling strings [Roberts et al., Bioinformatics 2004]. Let $S=S[1]\ldots S[n]$ be a string over a totally ordered alphabet $\Sigma$. Further let $w\geq 2$ and $k\geq 1$ be…
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…
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using 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…
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…
Designing short DNA words is a problem of constructing a set (i.e., code) of n DNA strings (i.e., words) with the minimum length such that the Hamming distance between each pair of words is at least k and the n words satisfy a set of…
Quantum state preparation (QSP) is a key component in many quantum algorithms. In particular, the problem of sparse QSP (SQSP) $\unicode{x2013}$ the task of preparing the states with only a small number of non-zero amplitudes…
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,…
Compared to general quantum states, the sparse states arise more frequently in the field of quantum computation. In this work, we consider the preparation for $n$-qubit sparse quantum states with $s$ non-zero amplitudes and propose two…
We study the problem of cutting a length-$n$ string of positive real numbers into $k$ pieces so that every piece has sum at least $b$. The problem can also be phrased as transforming such a string into a new one by merging adjacent numbers.…
Subset Sum is a classical optimization problem taught to undergraduates as an example of an NP-hard problem, which is amenable to dynamic programming, yielding polynomial running time if the input numbers are relatively small. Formally,…
Quantum state tomography (QST) is one of the fundamental problems in quantum information. Among various metrics, sample complexity is widely used to evaluate QST algorithms. While multi-copy measurements are known to achieve optimal sample…
We investigate the longest common substring problem for encoded sequences and its asymptotic behaviour. The main result is a strong law of large numbers for a re-scaled version of this quantity, which presents an explicit relation with the…
We consider the problem of finding, given two documents of total length $n$, a longest string occurring as a substring of both documents. This problem, known as the Longest Common Substring (LCS) problem, has a classic $O(n)$-time solution…
Quantum signal processing (QSP) provides a systematic framework for implementing a polynomial transformation of a linear operator, and unifies nearly all known quantum algorithms. In parallel, recent works have developed randomized…
Given $m$ documents of total length $n$, we consider the problem of finding a longest string common to at least $d \geq 2$ of the documents. This problem is known as the \emph{longest common substring (LCS) problem} and has a classic $O(n)$…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
Here we study the complexity of string problems as a function of the size of a program that generates input. We consider straight-line programs (SLP), since all algorithms on SLP-generated strings could be applied to processing…