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

Metaheurísticas, optimización multiobjetivo y paralelismo para descubrir motifs en secuencias de ADN

La resolución de problemas complejos mediante técnicas evolutivas es uno de los aspectos más investigados en Informática. El objetivo principal de esta tesis doctoral es desarrollar nuevos algoritmos capaces de resolver estos problemas con el menor tiempo computacional posible, mejorando la calidad de los resultados obtenidos por los métodos ya existentes. Para ello, combinamos tres conceptos importantes: metaheurísticas, optimización multiobjetivo y paralelismo. Con este fin, primero buscamos un problema de optimización importante que aún no fuese resuelto de forma eficiente y encontramos el Problema del Descubrimiento de Motifs (PDM). El PDM tiene como objetivo descubrir pequeños patrones repetidos (motifs) en conjuntos de secuencias de ADN que puedan poseer cierto significado biológico. Para abordarlo, definimos una formulación multiobjetivo adecuada a los requerimientos del mundo real, implementamos un total de diez algoritmos de distinta naturaleza (población, trayectoria, inteligencia colectiva...), analizando aspectos como la capacidad de escalar y converger. Finalmente, diseñamos diversas técnicas paralelas, haciendo uso de entornos de programación como OpenMP y MPI, que tratan de combinar las propiedades de varias metaheurísticas en una única aplicación. Los resultados obtenidos son estudiados en detalle a través de la aplicación de numerosos test estadísticos, y las predicciones son comparadas con las descubiertas por un total de trece herramientas biológicas bien conocidas en la literatura. Las conclusiones obtenidas demuestran que la utilización de la optimización multiobjetivo en técnicas metaheurísticas favorece el descubrimiento de soluciones de calidad y que el paralelismo es útil para combinar las propiedades evolutivas de diferentes algoritmos.The resolution of complex problems by using evolutionary algorithms is one of the most researched issues in Computer Science. The main goal of this thesis is directly related with the development of new algorithms that can solve this kind of problems with the least possible computational time, improving the results achieved by the existing methods. To this end, we combine three important concepts: metaheuristics, multiobjective optimization, and parallelism. For doing this, we first look for a significant optimization problem that had not been solved in an efficient way and we find the Motif Discovery Problem (MDP). MDP aims to discover over-represented short patterns (motifs) in a set of DNA sequences that may have some biological significance. To address it, we defined a multiobjective formulation adjusted to the real-world biological requirements, we implemented a total of ten algorithms of different nature (population, trajectory, collective intelligence...), analyzing aspects such as the ability to scale and converge. Finally, we designed parallel techniques, by using parallel and distributed programming environments as OpenMP and MPI, which try to combine the properties of several metaheuristics in a single application. The obtained results are discussed in detail through numerous statistical tests, and the achieved predictions are compared with those discovered by a total of thirteen well-known biological tools. The drawn conclusions demonstrate that using multiobjective optimization in metaheuristic techniques favors the discovery of quality solutions, and that parallelism is useful for combining the properties of different evolutionary algorithms.Ministerio de Economía y Competitividad - FEDER (TIN2008-06491-C04-04; TIN2012-30685) Gobierno de Extremadura (GR10025-TIC015

A Comprehensive Survey on Particle Swarm Optimization Algorithm and Its Applications

Particle swarm optimization (PSO) is a heuristic global optimization method, proposed originally by Kennedy and Eberhart in 1995. It is now one of the most commonly used optimization techniques. This survey presented a comprehensive investigation of PSO. On one hand, we provided advances with PSO, including its modifications (including quantum-behaved PSO, bare-bones PSO, chaotic PSO, and fuzzy PSO), population topology (as fully connected, von Neumann, ring, star, random, etc.), hybridization (with genetic algorithm, simulated annealing, Tabu search, artificial immune system, ant colony algorithm, artificial bee colony, differential evolution, harmonic search, and biogeography-based optimization), extensions (to multiobjective, constrained, discrete, and binary optimization), theoretical analysis (parameter selection and tuning, and convergence analysis), and parallel implementation (in multicore, multiprocessor, GPU, and cloud computing forms). On the other hand, we offered a survey on applications of PSO to the following eight fields: electrical and electronic engineering, automation control systems, communication theory, operations research, mechanical engineering, fuel and energy, medicine, chemistry, and biology. It is hoped that this survey would be beneficial for the researchers studying PSO algorithms

Evolutionary Computation 2020

Intelligent optimization is based on the mechanism of computational intelligence to refine a suitable feature model, design an effective optimization algorithm, and then to obtain an optimal or satisfactory solution to a complex problem. Intelligent algorithms are key tools to ensure global optimization quality, fast optimization efficiency and robust optimization performance. Intelligent optimization algorithms have been studied by many researchers, leading to improvements in the performance of algorithms such as the evolutionary algorithm, whale optimization algorithm, differential evolution algorithm, and particle swarm optimization. Studies in this arena have also resulted in breakthroughs in solving complex problems including the green shop scheduling problem, the severe nonlinear problem in one-dimensional geodesic electromagnetic inversion, error and bug finding problem in software, the 0-1 backpack problem, traveler problem, and logistics distribution center siting problem. The editors are confident that this book can open a new avenue for further improvement and discoveries in the area of intelligent algorithms. The book is a valuable resource for researchers interested in understanding the principles and design of intelligent algorithms

Air Force Institute of Technology Research Report 2004

This report summarizes the research activities of the Air Force Institute of Technology’s Graduate School of Engineering and Management. It describes research interests and faculty expertise; lists student theses/dissertations; identifies research sponsors and contributions; and outlines the procedures for contacting the school. Included in the report are: faculty publications, conference presentations, consultations, and funded research projects. Research was conducted in the areas of Aeronautical and Astronautical Engineering, Electrical Engineering and Electro-Optics, Computer Engineering and Computer Science, Systems and Engineering Management, Operational Sciences, and Engineering Physics

New Fundamental Technologies in Data Mining

The progress of data mining technology and large public popularity establish a need for a comprehensive text on the subject. The series of books entitled by "Data Mining" address the need by presenting in-depth description of novel mining algorithms and many useful applications. In addition to understanding each section deeply, the two books present useful hints and strategies to solving problems in the following chapters. The contributing authors have highlighted many future research directions that will foster multi-disciplinary collaborations and hence will lead to significant development in the field of data mining

Evolving cell models for systems and synthetic biology

This paper proposes a new methodology for the automated design of cell models for systems and synthetic biology. Our modelling framework is based on P systems, a discrete, stochastic and modular formal modelling language. The automated design of biological models comprising the optimization of the model structure and its stochastic kinetic constants is performed using an evolutionary algorithm. The evolutionary algorithm evolves model structures by combining different modules taken from a predefined module library and then it fine-tunes the associated stochastic kinetic constants. We investigate four alternative objective functions for the fitness calculation within the evolutionary algorithm: (1) equally weighted sum method, (2) normalization method, (3) randomly weighted sum method, and (4) equally weighted product method. The effectiveness of the methodology is tested on four case studies of increasing complexity including negative and positive autoregulation as well as two gene networks implementing a pulse generator and a bandwidth detector. We provide a systematic analysis of the evolutionary algorithm’s results as well as of the resulting evolved cell models

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Cooperative Particle Swarm Optimization for Combinatorial Problems

A particularly successful line of research for numerical optimization is the well-known computational paradigm particle swarm optimization (PSO). In the PSO framework, candidate solutions are represented as particles that have a position and a velocity in a multidimensional search space. The direct representation of a candidate solution as a point that flies through hyperspace (i.e., Rn) seems to strongly predispose the PSO toward continuous optimization. However, while some attempts have been made towards developing PSO algorithms for combinatorial problems, these techniques usually encode candidate solutions as permutations instead of points in search space and rely on additional local search algorithms. In this dissertation, I present extensions to PSO that by, incorporating a cooperative strategy, allow the PSO to solve combinatorial problems. The central hypothesis is that by allowing a set of particles, rather than one single particle, to represent a candidate solution, combinatorial problems can be solved by collectively constructing solutions. The cooperative strategy partitions the problem into components where each component is optimized by an individual particle. Particles move in continuous space and communicate through a feedback mechanism. This feedback mechanism guides them in the assessment of their individual contribution to the overall solution. Three new PSO-based algorithms are proposed. Shared-space CCPSO and multispace CCPSO provide two new cooperative strategies to split the combinatorial problem, and both models are tested on proven NP-hard problems. Multimodal CCPSO extends these combinatorial PSO algorithms to efficiently sample the search space in problems with multiple global optima. Shared-space CCPSO was evaluated on an abductive problem-solving task: the construction of parsimonious set of independent hypothesis in diagnostic problems with direct causal links between disorders and manifestations. Multi-space CCPSO was used to solve a protein structure prediction subproblem, sidechain packing. Both models are evaluated against the provable optimal solutions and results show that both proposed PSO algorithms are able to find optimal or near-optimal solutions. The exploratory ability of multimodal CCPSO is assessed by evaluating both the quality and diversity of the solutions obtained in a protein sequence design problem, a highly multimodal problem. These results provide evidence that extended PSO algorithms are capable of dealing with combinatorial problems without having to hybridize the PSO with other local search techniques or sacrifice the concept of particles moving throughout a continuous search space

Mind the Gap: Developments in Autonomous Driving Research and the Sustainability Challenge

Scientific knowledge on autonomous-driving technology is expanding at a faster-than-ever pace. As a result, the likelihood of incurring information overload is particularly notable for researchers, who can struggle to overcome the gap between information processing requirements and information processing capacity. We address this issue by adopting a multi-granulation approach to latent knowledge discovery and synthesis in large-scale research domains. The proposed methodology combines citation-based community detection methods and topic modeling techniques to give a concise but comprehensive overview of how the autonomous vehicle (AV) research field is conceptually structured. Thirteen core thematic areas are extracted and presented by mining the large data-rich environments resulting from 50 years of AV research. The analysis demonstrates that this research field is strongly oriented towards examining the technological developments needed to enable the widespread rollout of AVs, whereas it largely overlooks the wide-ranging sustainability implications of this sociotechnical transition. On account of these findings, we call for a broader engagement of AV researchers with the sustainability concept and we invite them to increase their commitment to conducting systematic investigations into the sustainability of AV deployment. Sustainability research is urgently required to produce an evidence-based understanding of what new sociotechnical arrangements are needed to ensure that the systemic technological change introduced by AV-based transport systems can fulfill societal functions while meeting the urgent need for more sustainable transport solutions