Related papers: Quantum gate algorithm for reference-guided DNA se…
We propose a modified MSA algorithm on quantum annealers with applications in areas of bioinformatics and genetic sequencing. To understand the human genome, researchers compare extensive sets of these genetic sequences -- or their protein…
The field of quantum computing has grown from concept to demonstration devices over the past 20 years. Universal quantum computing offers efficiency in approaching problems of scientific and commercial interest, such as factoring large…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
Quantum computing is a popular topic in computer science, which has recently attracted many studies in various areas such as machine learning and network. However, the topic of quantum data structures seems neglected. There is an open…
Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of…
Quantum computing has noteworthy speedup over classical computing by taking advantage of quantum parallelism, i.e., the superposition of states. In particular, quantum search is widely used in various computationally hard problems. Grover's…
For strings of letters from a small alphabet, such as DNA sequences, we present a quantum encoding that empirically provides a strong correlation between the Levenshtein edit distance and the fidelity between quantum states defined by the…
Protein folding processes are a vital aspect of molecular biology that is hard to simulate with conventional computers. Quantum algorithms have been proven superior for certain problems and may help tackle this complex life science…
De novo DNA sequence assembly is based on finding paths in overlap graphs, which is a NP-hard problem. We developed a quantum algorithm for de novo assembly based on quantum walks in graphs. The overlap graph is partitioned repeatedly to…
DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings. Assessment of variants in such sequencing data is commonly implemented through Bayesian heuristic algorithms. Machine learning has shown…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
We develop a new class of genetic algorithm that computationally determines efficient pulse sequences to implement a quantum gate U in a three-qubit system. The method is shown to be quite general, and the same algorithm can be used to…
Genetic algorithms, which mimic evolutionary processes to solve optimization problems, can be enhanced by using powerful semi-local search algorithms as mutation operators. Here, we introduce reverse quantum annealing, a class of quantum…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
Reconstructing DNA sequences without a reference, known as de novo assembly, is a complex computational task involving the alignment of overlapping fragments. To address this problem, a usual strategy is to map the assembly to a Quadratic…
Quantum computers provide a fundamentally new computing paradigm that promises to revolutionize our ability to solve broad classes of problems. Surprisingly, the basic mathematical structures of gate-based quantum computing, such as unitary…
With the rapid increase of available digital data, DNA storage is identified as a storage media with high density and capability of long-term preservation, especially for archival storage systems. However, the encoding density (i.e., how…
Quantum computers process information with the laws of quantum mechanics. Current quantum hardware is noisy, can only store information for a short time, and is limited to a few quantum bits, i.e., qubits, typically arranged in a planar…
We propose a scalable scheme for optical quantum computing using measurement-induced continuous-variable quantum gates in a loop-based architecture. Here, time-bin-encoded quantum information in a single spatial mode is deterministically…