Applied Metaheuristic Computing

For decades, Applied Metaheuristic Computing (AMC) has been a prevailing optimization technique for tackling perplexing engineering and business problems, such as scheduling, routing, ordering, bin packing, assignment, facility layout planning, among others. This is partly because the classic exact methods are constrained with prior assumptions, and partly due to the heuristics being problem-dependent and lacking generalization. AMC, on the contrary, guides the course of low-level heuristics to search beyond the local optimality, which impairs the capability of traditional computation methods. This topic series has collected quality papers proposing cutting-edge methodology and innovative applications which drive the advances of AMC

The use of computational intelligence for security in named data networking

Information-Centric Networking (ICN) has recently been considered as a promising paradigm for the next-generation Internet, shifting from the sender-driven end-to-end communication paradigma to a receiver-driven content retrieval paradigm. In ICN, content -rather than hosts, like in IP-based design- plays the central role in the communications. This change from host-centric to content-centric has several significant advantages such as network load reduction, low dissemination latency, scalability, etc. One of the main design requirements for the ICN architectures -since the beginning of their design- has been strong security. Named Data Networking (NDN) (also referred to as Content-Centric Networking (CCN) or Data-Centric Networking (DCN)) is one of these architectures that are the focus of an ongoing research effort that aims to become the way Internet will operate in the future. Existing research into security of NDN is at an early stage and many designs are still incomplete. To make NDN a fully working system at Internet scale, there are still many missing pieces to be filled in. In this dissertation, we study the four most important security issues in NDN in order to defense against new forms of -potentially unknown- attacks, ensure privacy, achieve high availability, and block malicious network traffics belonging to attackers or at least limit their effectiveness, i.e., anomaly detection, DoS/DDoS attacks, congestion control, and cache pollution attacks. In order to protect NDN infrastructure, we need flexible, adaptable and robust defense systems which can make intelligent -and real-time- decisions to enable network entities to behave in an adaptive and intelligent manner. In this context, the characteristics of Computational Intelligence (CI) methods such as adaption, fault tolerance, high computational speed and error resilient against noisy information, make them suitable to be applied to the problem of NDN security, which can highlight promising new research directions. Hence, we suggest new hybrid CI-based methods to make NDN a more reliable and viable architecture for the future Internet.Information-Centric Networking (ICN) ha sido recientemente considerado como un paradigma prometedor parala nueva generación de Internet, pasando del paradigma de la comunicación de extremo a extremo impulsada por el emisora un paradigma de obtención de contenidos impulsada por el receptor. En ICN, el contenido (más que los nodos, como sucede en redes IPactuales) juega el papel central en las comunicaciones. Este cambio de "host-centric" a "content-centric" tiene varias ventajas importantes como la reducción de la carga de red, la baja latencia, escalabilidad, etc. Uno de los principales requisitos de diseño para las arquitecturas ICN (ya desde el principiode su diseño) ha sido una fuerte seguridad. Named Data Networking (NDN) (también conocida como Content-Centric Networking (CCN) o Data-Centric Networking (DCN)) es una de estas arquitecturas que son objetode investigación y que tiene como objetivo convertirse en la forma en que Internet funcionará en el futuro. Laseguridad de NDN está aún en una etapa inicial. Para hacer NDN un sistema totalmente funcional a escala de Internet, todavía hay muchas piezas que faltan por diseñar. Enesta tesis, estudiamos los cuatro problemas de seguridad más importantes de NDN, para defendersecontra nuevas formas de ataques (incluyendo los potencialmente desconocidos), asegurar la privacidad, lograr una alta disponibilidad, y bloquear los tráficos de red maliciosos o al menos limitar su eficacia. Estos cuatro problemas son: detección de anomalías, ataques DoS / DDoS, control de congestión y ataques de contaminación caché. Para solventar tales problemas necesitamos sistemas de defensa flexibles, adaptables y robustos que puedantomar decisiones inteligentes en tiempo real para permitir a las entidades de red que se comporten de manera rápida e inteligente. Es por ello que utilizamos Inteligencia Computacional (IC), ya que sus características (la adaptación, la tolerancia a fallos, alta velocidad de cálculo y funcionamiento adecuado con información con altos niveles de ruido), la hace adecuada para ser aplicada al problema de la seguridad ND

Applied Methuerstic computing

For decades, Applied Metaheuristic Computing (AMC) has been a prevailing optimization technique for tackling perplexing engineering and business problems, such as scheduling, routing, ordering, bin packing, assignment, facility layout planning, among others. This is partly because the classic exact methods are constrained with prior assumptions, and partly due to the heuristics being problem-dependent and lacking generalization. AMC, on the contrary, guides the course of low-level heuristics to search beyond the local optimality, which impairs the capability of traditional computation methods. This topic series has collected quality papers proposing cutting-edge methodology and innovative applications which drive the advances of AMC

A review of population-based metaheuristics for large-scale black-box global optimization: Part A

Scalability of optimization algorithms is a major challenge in coping with the ever growing size of optimization problems in a wide range of application areas from high-dimensional machine learning to complex large-scale engineering problems. The field of large-scale global optimization is concerned with improving the scalability of global optimization algorithms, particularly population-based metaheuristics. Such metaheuristics have been successfully applied to continuous, discrete, or combinatorial problems ranging from several thousand dimensions to billions of decision variables. In this two-part survey, we review recent studies in the field of large-scale black-box global optimization to help researchers and practitioners gain a bird’s-eye view of the field, learn about its major trends, and the state-of-the-art algorithms. Part of the series covers two major algorithmic approaches to large-scale global optimization: problem decomposition and memetic algorithms. Part of the series covers a range of other algorithmic approaches to large-scale global optimization, describes a wide range of problem areas, and finally touches upon the pitfalls and challenges of current research and identifies several potential areas for future research

Foundations of Trusted Autonomy

Trusted Autonomy; Automation Technology; Autonomous Systems; Self-Governance; Trusted Autonomous Systems; Design of Algorithms and Methodologie

Predicting and characterising protein-protein complexes

Macromolecular interactions play a key role in all life processes. The construction and annotation of protein interaction networks is pivotal for the understanding of these processes, and how their perturbation leads to disease. However the extent of the human interactome and the limitations of the experimental techniques which can be brought to bear upon it necessitate theoretical approaches. Presented here are computational investigations into the interactions between biological macromolecules, focusing on the structural prediction of interactions, docking, and their kinetic and thermodynamic characterisation via empirical functions. Firstly, the use of normal modes in docking is investigated. Vibrational analysis of proteins are shown to indicate the motions which proteins are intrinsically disposed to undertake, and the use of this information to model flexible deformations upon protein-protein binding is evaluated. Subsequently SwarmDock, a docking algorithm which models flexibility as a linear combination of normal modes, is presented and benchmarked on a wide variety of test cases. This algorithm utilises state of the art energy functions and metaheuristics to navigate the free energy landscape. Information derived from Langevin dynamics simulations of encounter complex formation in the crowded cytosolic environment can be incorporated into SwarmDock and enhances its performance. Finally, a benchmark of binding free energies derived from the literature is presented. For this benchmark, a large number of molecular descriptors are derived. Machine learning methods are then applied to these in order to derive empirical binding free energy, association rate and dissociation rate functions which take account of the conformational changes which occur upon complexation

Multiobjective in-core fuel management optimisation for nuclear research reactors

Thesis (PhD)--Stellenbosch University, 2016.ENGLISH SUMMARY : The efficiency and effectiveness of fuel usage in a typical nuclear reactor is influenced by the specific arrangement of available fuel assemblies in the reactor core positions. This arrangement of assemblies is referred to as a fuel reload configuration and usually has to be determined anew for each operational cycle of a reactor. Very often, multiple objectives are pursued simultaneously when designing a reload configuration, especially in the context of nuclear research reactors. In the multiobjective in-core fuel management optimization (MICFMO) problem, the aim is to identify a Pareto optimal set of compromise or trade-off reload configurations. Such a set may then be presented to a decision maker (i.e. a nuclear reactor operator) for consideration so as to select a preferred configuration. In the first part of this dissertation, a secularization-based methodology for MICFMO is pro- posed in order to address several shortcomings associated with the popular weighting method often employed in the literature for solving the MICFMO problem. The proposed methodology has been implemented in a reactor simulation code, called the OSCAR-4 system. In order to demonstrate its practical applicability, the methodology is applied to solve several MICFMO problem instances in the context of two research reactors. In the second part of the dissertation, an extensive investigation is conducted into the suitability of several multiobjective optimization algorithms for solving the constrained MICFMO problem. The computation time required to perform the investigation is reduced through the usage of several artificial neural networks constructed in the dissertation for objective and constraint function evaluations. Eight multiobjective metaheuristics are compared in the context of a test suite of several MICFMO problem instances, based on the SAFARI-1 research reactor in South Africa. The investigation reveals that the NSGA-II, the P-ACO algorithm and the MOOCEM are generally the best-performing metaheuristics across the problem instances in the test suite, while the MOVNS algorithm also performs well in the context of bi-objective problem instances. As part of this investigation, a multiplicative penalty function (MPF) constraint handling technique is also proposed and compared to an existing constraint handling technique, called constrained-domination. The comparison reveals that the MPF technique is a competitive alternative to constrained-domination. In an attempt to raise the level of generality at which MICFMO may be performed and potentially improve the quality of optimization results, a multiobjective hyperheuristic, called the AMALGAM method, is also considered in this dissertation. This hyperheuristic incorporates multiple metaheuristic sub-algorithms simultaneously for optimization. Testing reveals that the AMALGAM method yields superior results in the majority of problem instances in the test suite, thus achieving the dual goal of raising the level of generality and of yielding improved optimization results. The method has also been implemented in the OSCAR-4 system and is applied to solve several MICFMO case study problem instances, based on two research reactors, in order to demonstrate its practical applicability. Finally, in the third part of this dissertation, a conceptual framework is proposed for an optimization-based personal decision support system, dedicated to MICFM. This framework may serve as the basis for developing a computerized tool to aid nuclear reactor operators in designing suitable reload configurations.AFRIKAANSE OPSOMMING : Die doeltreffendheid en doelmatigheid van brandstofverbruik in 'n tipiese kernreaktor word deur die spesieke rangskikking van beskikbare brandstofelemente in die laaiposisies van die reaktor beinvloed. Hierdie rangskikking staan bekend as 'n brandstof herlaaikongurasie en word gewoonlik opnuut bepaal vir elke operasionele siklus van 'n reaktor. Die gelyktydige optimering van veelvuldige doele word dikwels tydens die ontwerp van 'n herlaaikongurasie nagestreef, veral binne die konteks van navorsingsreaktore. Die doelwit van meerdoelige binne-kern brandstofbeheeroptimering (MBKBBO) is om 'n Pareto optimale versameling van herlaaikongurasieafruilings te identiseer. So 'n versameling mag dan vir oorweging (deur byvoorbeeld 'n kernreaktoroperateur) voorgele word sodat 'n voorkeurkongurasie gekies kan word. In die eerste gedeelte van hierdie proefskrif word 'n skalariseringsgebaseerde metodologie vir MBKBBO voorgestel om verskeie tekortkominge in die gewilde gewigverswaringsmetode aan te spreek. Laasgenoemde metode word gereeld in die literatuur gebruik om die MBKBBO probleem op te los. Die voorgestelde metodologie is in 'n reaktorsimulasiestelsel, bekend as die OSCAR-4 stelsel, geimplementeer. Om die praktiese toepasbaarheid daarvan te demonstreer, word die metodologie gebruik om 'n aantal MBKBBO probleemgevalle binne die konteks van twee navorsingsreaktore op te los. In die tweede gedeelte van die proefskrif word 'n uitgebreide ondersoek ingestel om die geskiktheid van verskeie meerdoelige optimeringsalgoritmes vir die oplos van die beperkte MBKBBO probleem te bepaal. Die berekeningstyd wat vir die ondersoek benodig word, word verminder deur die gebruik van kunsmatige neurale netwerke, wat in die proefskrif gekonstrueer word, om doelfunksies en beperkings te evalueer. Agt meerdoelige metaheuristieke word binne die konteks van verskeie MBKBBO toetsprobleemgevalle vergelyk wat op die SAFARI-1 navorsingsreaktor in Suid-Afrika gebaseer is. Toetse dui daarop dat die NSGA-II, die P-ACO algoritme en die MOOCEM oor die algemeen die beste oor al die toetsprobleemgevalle presteer. Die MOVNS algoritme presteer ook goed in die konteks van tweedoelige probleemgevalle. 'n Vermenigvuldigende boetefunksie (VBF) beperkinghanteringstegniek word ook voorgestel en vergelyk met 'n bestaande tegniek bekend as beperkte dominasie. Daar word bevind dat the VBF tegniek 'n mededingende alternatief tot beperkte dominasie is. 'n Poging word aangewend om die vlak van algemeenheid waarmee MBKBBO uitgevoer word, te verhoog, asook om potensieel die kwaliteit van die optimeringsresultate te verbeter. 'n Meerdoelige hiperheuristiek, bekend as die AMALGAM metode, word in die nastreef van hierdie twee doelwitte oorweeg. Die metode funksioneer deur middel van die gelyktydige insluiting van 'n aantal metaheuristieke deel-algoritmes. Toetse dui daarop dat the AMALGAM metode beter resultate vir die meerderheid van toetsprobleme lewer, en dus word die bogenoemde twee doelwitte bereik. Die metode is ook in the OSCAR-4 stelsel ge mplementeer en word gebruik om 'n aantal MBKBBO gevallestudie probleemgevalle (binne die konteks van twee navorsingsreaktore) op te los. Sodoende word die praktiese toepasbaarheid van die metode gedemonstreer. In die derde deel van die proefskrif word 'n konseptuele raamwerk laastens vir 'n optimeringsgebaseerde persoonlike besluitsteunstelsel gemik op MBKBB, voorgestel. Hierdie raamwerk mag as grondslag dien vir die ontwikkeling van 'n gerekenariseerde hulpmiddel vir kernreaktoroperateurs om aanvaarbare herlaaikongurasies te ontwerp.Doctora