Related papers: A Linear Time Quantum Algorithm for Pairwise Seque…
We describe a quantum algorithm based on an interior point method for solving a linear program with $n$ inequality constraints on $d$ variables. The algorithm explicitly returns a feasible solution that is $\varepsilon$-close to optimal,…
Grover's algorithm is a well-known unstructured quantum search algorithm run on quantum computers. It constructs an oracle and calls the oracle O($\sqrt N$) times to locate specific data out of N unsorted data. This represents a quadratic…
The $d$-dimensional pattern matching problem is to find an occurrence of a pattern of length $m \times \dots \times m$ within a text of length $n \times \dots \times n$, with $n \ge m$. This task models various problems in text and image…
The search task is one of the most difficult when it comes to execution speed, and reducing the latter is important both when working with large data and with small samples, if they need to be processed frequently and in a limited time.…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Seeking the equivalent entities among multi-source Knowledge Graphs (KGs) is the pivotal step to KGs integration, also known as \emph{entity alignment} (EA). However, most existing EA methods are inefficient and poor in scalability. A…
We propose two quantum algorithms for a problem in bioinformatics, position weight matrix (PWM) matching, which aims to find segments (sequence motifs) in a biological sequence such as DNA and protein that have high scores defined by the…
Quantum computing promises to improve the information processing power to levels unreachable by classical computation. Quantum walks are heading the development of quantum algorithms for searching information on graphs more efficiently than…
The subject of this paper is to study conformance checking for timed models, that is, process models that consider both the sequence of events in a process as well as the timestamps at which each event is recorded. Time-aware process mining…
A quantum computer encodes information in quantum states and runs quantum algorithms to surpass the classical counterparts by exploiting quantum superposition and quantum correlation. Grover's quantum search algorithm is a typical quantum…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
In this paper we present a novel quantum algorithm, namely the quantum grid search algorithm, to solve a special search problem. Suppose $ k $ non-empty buckets are given, such that each bucket contains some marked and some unmarked items.…
Satisfiability (SAT) is a central problem in computer science, and advances in SAT-solving algorithms have a far-reaching impact across many fields. Recent works have proposed quantum SAT solvers based on Grover's algorithm, a quantum…
Quantum partial search algorithm is approximate search. It aims to find a target block (which has the target items). It runs a little faster than full Grover search. In this paper, we consider quantum partial search algorithm for multiple…
Network alignment generalizes and unifies several approaches for forming a matching or alignment between the vertices of two graphs. We study a mathematical programming framework for network alignment problem and a sparse variation of it…
The use of Hirschberg algorithm reduces the spatial cost of recovering the Longest Common Subsequence to linear space. The same technique can be applied to similar problems like Sequence Alignment. However, the price to pay is a duplication…
Quantum contextuality is a limitation on deterministic hidden variable models, testable in measurement scenarios where outcomes differ under quantum or classical descriptions due to a common set of constraints. When considering measurements…
Continuous-time quantum walks provide a natural framework to tackle the fundamental problem of finding a node among a set of marked nodes in a graph, known as spatial search. Whether spatial search by continuous-time quantum walk provides a…
Quantum random walks on graphs have been shown to display many interesting properties, including exponentially fast hitting times when compared with their classical counterparts. However, it is still unclear how to use these novel…