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Briefings in Bioinformatics

Quantum computing in bioinformatics: a systematic review mapping

Katarzyna Nałęcz-Charkiewicz, Kamil Charkiewicz, Robert Marek Nowak

Published Jul 25, 2024• 52 citations
Publisher

Abstract

The field of quantum computing (QC) is expanding, with efforts being made to apply it to areas previously covered by classical algorithms and methods. Bioinformatics is one such domain that is developing in terms of QC. This article offers a broad mapping review of methods and algorithms of QC in bioinformatics, marking the first of its kind. It presents an overview of the domain and aids researchers in identifying further research directions in the early stages of this field of knowledge. The work presented here shows the current state-of-the-art solutions, focuses on general future directions, and highlights the limitations of current methods. The gathered data includes a comprehensive list of identified methods along with descriptions, classifications, and elaborations of their advantages and disadvantages. Results are presented not just in a descriptive table but also in an aggregated and visual format.

DOI
10.1093/bib/bbae391

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The field of quantum computing (QC) is expanding, with efforts being made to apply it to areas previously covered by classical algorithms and methods. Bioinformatics is one such domain that is developing in terms of QC. This article offers a broad mapping review of methods and algorithms of QC in bioinformatics, marking the first of its kind. It presents an overview of the domain and aids researchers in identifying further research directions in the early stages of this field of knowledge. The work presented here shows the current state-of-the-art solutions, focuses on general future directions, and highlights the limitations of current methods. The gathered data includes a comprehensive list of identified methods along with descriptions, classifications, and elaborations of their advantages and disadvantages. Results are presented not just in a descriptive table but also in an aggregated and visual format.
Modern bioinformatics faces escalating challenges stemming from both the inherent computational hardness of many fundamental problems and the rapidly growing scale and complexity of biological data, increasingly limiting the effectiveness of classical computational approaches. Quantum computing has emerged as a promising paradigm for addressing these challenges by enabling alternative problem representations and novel search strategies for exploring complex solution spaces. This systematic review provides a structured overview of the emerging field of quantum bioinformatics and aims to supplement recent reviews on this topic in the journal by providing an updated and structured synthesis of current research. We systematically collect and organize existing studies across 10 bioinformatics domains to identify research trends, dominant themes, and recurring methodological patterns. The review examines quantum and hybrid quantum-classical approaches, problem formulations, and encoding strategies, with particular attention to the constraints of noisy intermediate-scale quantum devices, including noise, limited scalability, and the need for error mitigation. We further synthesize reported limitations, open challenges, and prospective research directions.
Abstract Quantum computing (QC) is an emerging paradigm with the potential to offer significant computational advantage over conventional classical computing by exploiting quantum‐mechanical principles such as entanglement and superposition. It is anticipated that this computational advantage of QC will help to solve many complex and computationally intractable problems in several application domains such as drug design, data science, clean energy, finance, industrial chemical development, secure communications, and quantum chemistry. In recent years, tremendous progress in both quantum hardware development and quantum software/algorithm has brought QC much closer to reality. Indeed, the demonstration of quantum supremacy marks a significant milestone in the Noisy Intermediate Scale Quantum (NISQ) era—the next logical step being the quantum advantage whereby quantum computers solve a real‐world problem much more efficiently than classical computing. As the quantum devices are expected to steadily scale up in the next few years, quantum decoherence and qubit interconnectivity are two of the major challenges to achieve quantum advantage in the NISQ era. QC is a highly topical and fast‐moving field of research with significant ongoing progress in all facets. A systematic review of the existing literature on QC will be invaluable to understand the state‐of‐the‐art of this emerging field and identify open challenges for the QC community to address in the coming years. This article presents a comprehensive review of QC literature and proposes taxonomy of QC. The proposed taxonomy is used to map various related studies to identify the research gaps. A detailed overview of quantum software tools and technologies, post‐quantum cryptography, and quantum computer hardware development captures the current state‐of‐the‐art in the respective areas. The article identifies and highlights various open challenges and promising future directions for research and innovation in QC.
The explosive growth of genomic information calls for computational methods to handle complex sequence analysis and genome assembly assays. Based on the principles of superposition and entanglement, quantum computing represents an another way of computation to achieve potentially faster and more efficient operations than classical systems. This article offers a comparative overview of 4 major studies dedicated to the use of QC in genomics, spanning theoretical algorithmical conceptualization, systematic literature mapping, analyses on practical challenges in QC-aided genomics and hybrid Q-C designs. The review indicates that there is potential for significant speed-up based on theoretical formulation, while current applications are limited by hardware resource constraint, data-loading latency and scalability. Hybrid models, in particular those that hybridize quantum annealing with classical optimization, seem to offer the most practicable route to near-term genomic computing. The analysis also shines a light on the increasingly pivotal positions that quantum-inspired approaches and hybrid orchestration systems are playing as crucial stepping stones towards full-quantum advantage. The results suggest that quantum computing is in its infancy as far as genomic analysis is concerned but the potential seems to be promising for future bioinformatics research and applications. Such opportunities are only accessible with further advancements in quantum hardware, data encoding and benchmark development.
Quantum technologies have become powerful tools for a wide range of application disciplines, which tend to range from chemistry to agriculture, natural language processing, and healthcare due to exponentially growing computational power and advancement in machine learning algorithms. Furthermore, the processing of classical data and machine learning algorithms in the quantum domain has given rise to an emerging field like quantum machine learning. Recently, quantum machine learning, become a quite challenging field in case of healthcare applications. As a result, quantum machine learning has become a common and effective technique for data processing and classification across a wide range of domains. Consequently, quantum machine learning is the most commonly used application of quantum computing. The main objective of this work is to present a brief overview of current state-of-the-art published articles between 2013 and 2021 to identify, analyze, and classify the different QML algorithms and applications in the biomedical field. Furthermore, the approach adheres to the requirements for conducting systematic literature review techniques such as research questions and quality metrics of the articles. Initially, we discovered 3149 articles, excluded the 2847 papers, and read the 121 full papers. Therefore, this research compiled 30 articles that comply with the quantum machine learning models, and quantum circuits are using biomedical data. Eventually, this article provides a broad overview of quantum machine learning limitations and future prospects.
We use the benefits and components of classical computers every day. However, there are many types of problems which, as they grow in size, their computational complexity grows larger than classical computers will ever be able to solve. Quantum computing (QC) is a computation model that uses quantum physical properties to solve such problems. QC is at the early stage of large-scale adoption in various industry domains to take advantage of the algorithmic speed-ups it has to offer. It can be applied in a variety of areas, such as computer science, mathematics, chemical and biochemical engineering, and the financial industry. The main goal of this paper is to give an overview to chemical and biochemical researchers and engineers who may not be familiar with quantum computation. Thus, the paper begins by explaining the fundamental concepts of QC. The second contribution this publication tries to tackle is the fact that the chemical engineering literature still lacks a comprehensive review of the recent advances of QC. Therefore, this article reviews and summarizes the state of the art to gain insight into how quantum computation can benefit and optimize chemical engineering issues. A bibliography analysis covers the comprehensive literature in QC and analyzes quantum computing research in chemical engineering on various publication topics, using Clarivate analytics covering the years 1990 to 2020. After the bibliographic analysis, relevant applications of QC in chemical and biochemical engineering are highlighted and a conclusion offers an outlook of future directions within the field.
Abstract Quantum computing has emerged as a promising field with the potential to revolutionize information processing and storage. Understanding its current state and research trajectory is crucial. This study aims to map the current literature on quantum computing, to identify how quantum computing is being used in solving quantum software problems and improving quantum algorithms. Moreover, it examines evaluation parameters and the challenges faced in this field. A systematic mapping study was conducted using the SCOPUS database, including all papers up to December 2024. Relevant articles were selected based on inclusion criteria, and a content analysis was performed to categorize and synthesize the findings. Information was gathered from 33 primary studies. Findings show that quantum computing is mainly applied in machine learning and optimization, though classical methods still outperform it. IBM Quantum is the most used platform. Research focuses on algorithm efficiency, verification over validation, and resource optimization, but lacks standardized evaluation methods. Key limitations include hardware constraints, noise, and scalability, while challenges involve integration, error correction, and problem formulation. Quantum computing continues to face significant technological challenges, but current research lays the groundwork for future advances. More practical studies on real hardware and strategies to improve the implementation and performance of quantum algorithms are needed. Effective evaluation, verification, and validation of quantum solutions must be further investigated.