Related papers: Accelerating De Novo Genome Assembly via Quantum-A…
Quantum computation, in particular Grover's algorithm, has aroused a great deal of interest since it allows for a quadratic speedup to be obtained in search procedures. Classical search procedures for an $N$ element database require at most…
In just the last decade, a multitude of bio-technologies and software pipelines have emerged to revolutionize genomics. To further their central goal, they aim to accelerate and improve the quality of de novo whole-genome assembly starting…
Quantum machines are among the most promising technologies expected to provide significant improvements in the following years. However, bridging the gap between real-world applications and their implementation on quantum hardware is still…
A random-key genetic algorithm is an evolutionary metaheuristic for discrete and global optimization. Each solution is encoded as a vector of N random keys, where a random key is a real number randomly generated in the continuous interval…
DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past…
Sequence Alignment is the process of aligning biological sequences in order to identify similarities between multiple sequences. In this paper, a Quantum Algorithm for finding the optimal alignment between DNA sequences has been…
Quantum metrology plays a fundamental role in many scientific areas. However, the complexity of engineering entangled probes and the external noise raise technological barriers for realizing the expected precision of the to-be-estimated…
The Hybrid Genetic Optimisation framework (HYGO) is introduced to meet the pressing need for efficient and unified optimisation frameworks that support both parametric and functional learning in complex engineering problems. Evolutionary…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
Co-crystallization is an accessible way to control physicochemical characteristics of organic crystals, which finds many biomedical applications. In this work, we present Generative Method for Co-crystal Design (GEMCODE), a novel pipeline…
Optimization drives advances in quantum science and machine learning, yet most generative models aim to mimic data rather than to discover optimal answers to challenging problems. Here we present a variational generative optimization…
Join order optimization is among the most crucial query optimization problems, and its central position is also evident in the new research field where quantum computing is applied to database optimization and data management. In the field,…
Long-distance quantum communication via entanglement distribution is of great importance for the quantum internet. However, scaling up to such long distances has proved challenging due to the loss of photons, which grows exponentially with…
Motivation: Second generation sequencing technology makes it feasible for many researches to obtain enough sequence reads to attempt the de novo assembly of higher eukaryotes (including mammals). De novo assembly not only provides a tool…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
Genetic Programming is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use Genetic Programming to develop surrogate models to mitigate…
In topologically-protected quantum computation, quantum gates can be carried out by adiabatically braiding two-dimensional quasiparticles, reminiscent of entangled world lines. Bonesteel et al. [Phys. Rev. Lett. 95, 140503 (2005)], as well…
In this article, we present QuASeR, a reference-free DNA sequence reconstruction implementation via de novo assembly on both gate-based and quantum annealing platforms. Each one of the four steps of the implementation (TSP, QUBO,…
Among the genetic algorithms generally used for optimization problems in the recent decades, quantum-inspired variants are known for fast and high-fitness convergence and small resource requirement. Here the application to the patient…
Quantum oracles play key roles in the studies of quantum computation and quantum information. But implementing quantum oracles efficiently with universal quantum gates is a hard work. Motivated by genetic programming, this paper proposes a…