DNA BARCODING DENGAN ALGORITMA PARTICLE SWARM OPTIMIZATION MENGGUNAKAN APACHE SPARK SQL

Terdapat salah satu tahap dalam DNA barcoding yang masih menggunakan metode manual seperti similarity check yang mengakibatkan tahap ini ketelitian dan waktu yang cukup lama. Data sekuens DNA makhluk hidup merupakan data yang sangat banyak pada bidang biologi. Untuk itu penelitian in membuat sebuah model komputasi untuk mendapatkan DNA barcode secara cepat dan efektif dengan mengimplementasikan algoritma particle swarm optimization pada big data platform yaitu Apache Hadoop dan Apache Spark . Data yang digunakan pada penelitian kali ini adalah data RNA SARS-CoV-2. Hasil dari program yang dibangun berupa DNA barcode yang ditemukan dari sampel yang ada berserta waktu yang dibutuhkan untuk menyelesaikan kalkulasi. Dilakukan 2 skenario pengujian, skenario pertama yaitu dengan menggunakan 4 cores dan beberapa worker nodes dan yang kedua yaitu penggunaan cluster dengan 2 worker nodes dan beberapa cores. Hasil dari penelitian ini membuktikan bahwa model komputasi yang dibangun pada big data platform menunjukan adanya perkembangan fitur dan percepatan terhadap penelitian terdahulu. There is one stage in DNA barcoding that still uses manual methods such as similarity check which results in this stage of accuracy and quite a long time. DNA sequence data of living things is very much data in the field of biology. For this reason, this research creates a computational model to obtain DNA barcodes quickly and effectively by implementing the particle swarm optimization algorithm on the big data platform, Apache Hadoop, and Apache Spark. The data used in this study is SARS-CoV-2 RNA data. The results of the program that were built consisted of DNA barcodes found from the existing sample of time needed to complete calculations. The results of this study indicate that there is a significant acceleration between standalone and big data platform with 2 experimental scenarios. The first scenario is to use 4 cores and some worker nodes and the second is to use a cluster with 2 worker nodes and several cores. This research proves that the computational model built on the big data platform shows the development of features and acceleration of previous research

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

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

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

Dynamics in Logistics

This open access book highlights the interdisciplinary aspects of logistics research. Featuring empirical, methodological, and practice-oriented articles, it addresses the modelling, planning, optimization and control of processes. Chiefly focusing on supply chains, logistics networks, production systems, and systems and facilities for material flows, the respective contributions combine research on classical supply chain management, digitalized business processes, production engineering, electrical engineering, computer science and mathematical optimization. To celebrate 25 years of interdisciplinary and collaborative research conducted at the Bremen Research Cluster for Dynamics in Logistics (LogDynamics), in this book hand-picked experts currently or formerly affiliated with the Cluster provide retrospectives, present cutting-edge research, and outline future research directions

Dynamics in Logistics

This open access book highlights the interdisciplinary aspects of logistics research. Featuring empirical, methodological, and practice-oriented articles, it addresses the modelling, planning, optimization and control of processes. Chiefly focusing on supply chains, logistics networks, production systems, and systems and facilities for material flows, the respective contributions combine research on classical supply chain management, digitalized business processes, production engineering, electrical engineering, computer science and mathematical optimization. To celebrate 25 years of interdisciplinary and collaborative research conducted at the Bremen Research Cluster for Dynamics in Logistics (LogDynamics), in this book hand-picked experts currently or formerly affiliated with the Cluster provide retrospectives, present cutting-edge research, and outline future research directions

Fuelling the zero-emissions road freight of the future: routing of mobile fuellers

The future of zero-emissions road freight is closely tied to the sufficient availability of new and clean fuel options such as electricity and Hydrogen. In goods distribution using Electric Commercial Vehicles (ECVs) and Hydrogen Fuel Cell Vehicles (HFCVs) a major challenge in the transition period would pertain to their limited autonomy and scarce and unevenly distributed refuelling stations. One viable solution to facilitate and speed up the adoption of ECVs/HFCVs by logistics, however, is to get the fuel to the point where it is needed (instead of diverting the route of delivery vehicles to refuelling stations) using "Mobile Fuellers (MFs)". These are mobile battery swapping/recharging vans or mobile Hydrogen fuellers that can travel to a running ECV/HFCV to provide the fuel they require to complete their delivery routes at a rendezvous time and space. In this presentation, new vehicle routing models will be presented for a third party company that provides MF services. In the proposed problem variant, the MF provider company receives routing plans of multiple customer companies and has to design routes for a fleet of capacitated MFs that have to synchronise their routes with the running vehicles to deliver the required amount of fuel on-the-fly. This presentation will discuss and compare several mathematical models based on different business models and collaborative logistics scenarios