On the role of metaheuristic optimization in bioinformatics

Metaheuristic algorithms are employed to solve complex and large-scale optimization problems in many different fields, from transportation and smart cities to finance. This paper discusses how metaheuristic algorithms are being applied to solve different optimization problems in the area of bioinformatics. While the text provides references to many optimization problems in the area, it focuses on those that have attracted more interest from the optimization community. Among the problems analyzed, the paper discusses in more detail the molecular docking problem, the protein structure prediction, phylogenetic inference, and different string problems. In addition, references to other relevant optimization problems are also given, including those related to medical imaging or gene selection for classification. From the previous analysis, the paper generates insights on research opportunities for the Operations Research and Computer Science communities in the field of bioinformatics

Solving the DNA fragment assembly problem with a parallel discrete firefly algorithm implemented on GPU

The Deoxyribonucleic Acid Fragment Assembly Problem (DNA-FAP) consists in reconstructing a DNA chain from a set of fragments taken randomly. This problem represents an important step in the genome project. Several authors are proposed different approaches to solve the DNA-FAP. In particular, nature-inspired algorithms have been used for its resolution. Even they were obtaining good results; its computational time associated is high. The bio-inspired algorithms are iterative search processes that can explore and exploit efficiently the solution space. Firefly Algorithm is one of the recent evolutionary computing models which is inspired by the flashing light behaviour of fireflies. Recently, the Graphics Processing Units (GPUs) technology are emerge as a novel environment for a parallel implementation and execution of bio-inspired algorithms. Therefore, the use of GPU-based parallel computing it is possible as a complementary tool to speed-up the search. In this work, we design and implement a Discrete Firefly Algorithm (DFA) on a GPU architecture in order to speed-up the search process for solving the DNA Fragment Assembly Problem. Through several experiments, the efficiency of the algorithm and the quality of the results are demonstrated with the potential to applied for longer sequences or sequences of unknown length as well.Fil: Vidal, Pablo Javier. Universidad Nacional de la Patagonia Austral. Unidad Académica Caleta Olivia. Departamento de Ciencias Exactas y Naturales; Argentina. Universidad Nacional de la Patagonia Austral. Centro de Investigaciones y Transferencia Golfo San Jorge. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones y Transferencia Golfo San Jorge. Universidad Nacional de la Patagonia "San Juan Bosco". Centro de Investigaciones y Transferencia Golfo San Jorge; ArgentinaFil: Olivera, Ana Carolina. Universidad Nacional de la Patagonia Austral. Centro de Investigaciones y Transferencia Golfo San Jorge. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones y Transferencia Golfo San Jorge. Universidad Nacional de la Patagonia "San Juan Bosco". Centro de Investigaciones y Transferencia Golfo San Jorge; Argentina. Universidad Nacional de la Patagonia Austral. Unidad Académica Caleta Olivia. Departamento de Ciencias Exactas y Naturales; Argentin

Metaheuristics on quantum computers: Inspiration, simulation and real execution

Quantum-inspired metaheuristics are solvers that incorporate principles inspired from quantum mechanics into classical-approximate algorithms using non-quantum machines. Due to the uniqueness of quantum principles, the inspiration of quantum phenomena and the way it is done in fundamentally different non-quantum systems rather than real or simulated quantum computers raise important questions about these algorithms’ design and the reproducibility of their results in real or simulated quantum devices. Thus, this work’s contribution stands in a first step towards answering those questions as an attempt to identify key findings in the existing literature that should be considered or adapted in order to build hybrid or fully-quantum algorithms that can be used in quantum machines. This is done by proposing and studying four inspired, simulated and real quantum cellular genetic algorithms that, as far as the authors’ knowledge, are the first quantum structured metaheuristics studied in the three quantum realms using a quantum simulator with 32 quantum bits and a real quantum machine employing 15 superconducting quantum bits. The users’ mobility management in cellular networks is taken as a validation problem using 13 real-world instances. The comparisons have been made against 6 diverse algorithms using 9 comparison metrics. Thorough statistical tests and parameters’ sensitivity analysis have been also conducted. The experiments allowed answering several questions, including how quantum hardware influences the studied-algorithms’ search process. They also enabled opening new perspectives in quantum metaheuristics’ design.Authors acknowledge that this research is partially funded by the Universidad de Málaga, Consejería de Economía y Conocimiento de la Junta de Andalucía and FEDER under grant number UMA18-FEDERJA-003 (PRECOG); under grant PID 2020-116727RB-I00 (HUmove) funded by MCIN/AEI/10.13039/501100011033; and TAILOR ICT-48 Network (No 952215) funded by EU Horizon 2020 research and innovation programme. Funding for open access charge is supported by the Universidad de Málaga/CBUA. The authors also acknowledge that an instance studied in this work was inspired from the CRAWDAD dataset spitz/cellular. The authors acknowledge also the use of the IBMQ for this work. The views expressed are those of the authors and do not reflect the official policy or position of IBM or the IBMQ team. Finally, the authors would like to state that the views expressed are purely those of the writer and may not in any circumstances be regarded as stating an official position of the European Commission

Simulated Annealing

The book contains 15 chapters presenting recent contributions of top researchers working with Simulated Annealing (SA). Although it represents a small sample of the research activity on SA, the book will certainly serve as a valuable tool for researchers interested in getting involved in this multidisciplinary field. In fact, one of the salient features is that the book is highly multidisciplinary in terms of application areas since it assembles experts from the fields of Biology, Telecommunications, Geology, Electronics and Medicine

Computational intelligence approaches to robotics, automation, and control [Volume guest editors]

No abstract available

A Polyhedral Study of Mixed 0-1 Set

We consider a variant of the well-known single node fixed charge network flow set with constant capacities. This set arises from the relaxation of more general mixed integer sets such as lot-sizing problems with multiple suppliers. We provide a complete polyhedral characterization of the convex hull of the given set

Computational intelligence approaches to robotics, automation, and control [Volume guest editors]

No abstract available

Optimizing the DNA fragment assembly using metaheuristic-based overlap layout consensus approach

Nucleotide sequencing finds the exact order of nucleotides present in a DNA molecule. The correct DNA sequence is required to obtain the desired information about the complete genetic makeup of an organism. The DNA fragment assembly correctly combines the DNA information present in the form of fragments as a sequence. Reconstruction of the original DNA sequence from large fragments is a challenging task due to the limitations of the available technologies that reads the DNA sequence. Objective of the DNA fragment assembly is to find the correct order of the fragments which is further used in the generation of a consensus sequence that represents the original DNA sequence. Power Aware Local Search (PALS) algorithm proposed for the DNA fragment assembly is an efficient method that orders the fragments in a correct sequence by minimizing the number of contigs. This work presents a hybrid approach on the basis of Overlap Layout Consensus for the DNA fragment assembly, where Restarting and Recentering Genetic Algorithm (RRGA) with integrated PALS is utilized as an evolutionary operator. Quality of the current proposal is quantified using overlap scores and the number of contigs. This work is evaluated using 25 benchmark datasets with three types of experiments. The results are compared with four state-of-the-art methods for the same task, namely, Recentering–Restarting Genetic Algorithm variation for DNA fragment assembly, PALS, Genetic Algorithm, and Hybrid Genetic Algorithm. Results show better average performance of the proposed solution