This thesis discusses Kaplan, a free conformer searching package, available at github.com/PeaWagon/Kaplan / Conformer searching algorithms find minima in the Potential Energy Surface (PES) of a molecule, usually by following a torsion-driven approach. The minima represent conformers, which are interchangeable via free rotation around bonds. Conformers can be used as input to computational analyses, such as drug design, that can convey molecular reactivity, structure, and function. With an increasing number of rotatable bonds, finding optima in the PES becomes more complicated, as the dimensionality explodes. Kaplan is a new, free and open-source software package written by the author that uses a ring-based Evolutionary Algorithm (EA) to find conformers. The ring, which contains population members (or pmems), is designed to allow initial PES exploration, followed by exploitation of individual energy wells, such that the most energetically-favourable structures are returned. The strengths and weaknesses of existing publicly available conformer searchers are discussed, including Balloon, RDKit, Openbabel, Confab, Frog2, and Kaplan. Since RDKit is usually considered to be the best free package for conformer searching, its conformers for the amino acids were optimised using the MMFF94 forcefield and compared to the conformers generated by Kaplan. Amino acid conformers are well characterised, and provide insight for protein substructure. Of the 20 molecules, Kaplan found a lower energy minima for 12 of the structures and tied for 5 of them. Kaplan allows the user to specify which dihedrals (by atom indices) to optimise and angles to use, a feature that is not offered by other programs. The results from Kaplan were compared to a known dataset of amino acid conformers. Kaplan identified all 57 conformers of methionine to within 1.2Å, and found identical conformers for the 5 lowest-energy structures (i.e. within 0.083Å), following forcefield optimisation. / Thesis / Master of Science (MSc) / A conformer search affords the low-energy arrangements of atoms that can be obtained via rotation around bonds. Conformers provide insight about the chemical reactivity and physical properties of a molecule. With increasing molecule size, the number of possible conformers increases exponentially. To search the space of possible conformers, this thesis presents Kaplan, which is a software package that implements a novel directed, stochastic, sampling technique based on an Evolutionary Algorithm (EA). Kaplan uses a special type of EA that stores sets of conformers in a ring-based structure. Unlike other conformer-specific packages, Kaplan provides the means to analyse and interact with found conformers. Known conformers of amino acids are used to verify Kaplan. Other tools for generating conformers are discussed, including a comparison of freely available software. Kaplan effectively finds the conformers of small molecules, but requires additional parametrisation to find the conformers of mid-sized molecules, such as Penta-Alanine.

Durante las últimas décadas el desarrollo de la bioinformática nos ha permitido lograr una mayor comprensión de los procesos biológicos que ocurren con nuestras células a nivel molecular. Al respecto, las mejoras e innovaciones en la tecnología continúan estimulando la mejora en la calidad de los datos biológicos que pueden ser obtenidos a nivel genómico. En tal sentido, grandes volúmenes de información pueden ser encontrados en formas de anotaciones o bases de datos computacionales. Estos conjuntos de datos, apropiadamente combinados, tienen el potencial de posibilitar descubrimientos novedosos que lleven a avances en campos tan relevantes para el desarrollo nacional como son la biotecnología o la medicina post-genómica. En particular, esta tesis se centra en la investigación de técnicas de aprendizaje automático y computación evolutiva para la inferencia de redes regulatorias de genes a partir de datos de expresión de genes, a nivel de genomas completos. Una red regulatoria de genes es una colección de segmentos de ADN (ácido desoxirribonucleico) en una célula que interactúan unos con otros (indirectamente a través del producto de su expresión) y con otras sustancias en la célula, gobernando así las tasas de transcripción de los genes de la red en ARNm (ácido ribonucleico mensajero). La principal contribución de esta tesis esta relacionada con el desarrollo de metodologías computacionales que asistan, a expertos en bioinformática, en la ingeniería inversa de las redes regulatorias de genes. En tal sentido, se desarrollaron algoritmos de computación evolutiva que permiten la identificación de grupos de genes co-expresados bajo ciertos subconjuntos de condiciones experimentales. Estos algoritmos se aplican sobre datos de expresión de genes, y optimizan características deseables desde el punto de vista biológico, posibilitando la obtención de relaciones de co-expresión relevantes. Tales algoritmos fueron cuidadosamente validados por medio de comparaciones con otras técnicas similares disponibles en la literatura, realizando estudios con datos reales y sintéticos a fin de mostrar la utilidad de la información extraída. Además, se desarrolló un algoritmo de inferencia que permite la extracción de potenciales relaciones causa-efecto entre genes, tanto simultáneas como también aquellas diferidas en el tiempo. Este algoritmo es una evolución de una técnica presentada con anterioridad, e incorpora características novedosas como la posibilidad de inferir reglas con múltiples retardos en el tiempo, a nivel genoma completo, e integrando múltiples conjuntos de datos. La técnica se validó mostrando su eficacia respecto de otros enfoques relevantes de la literatura. También se estudiaron los resultados obtenidos a partir de conjuntos de datos reales en términos de su relevancia biológica, exponiendo la viabilidad de la información inferida. Finalmente, estos algoritmos se integraron en una plataforma de software que facilita la utilización de estas técnicas permitiendo la inferencia, manipulación y visualización de redes regulatorias de genes. / In recent decades, the development of bioinformatics has allowed us to achieve a greater understanding of the biological processes that occur at the molecular level in our cells. In this regard, the improvements and innovations in technology continue to boost the improvement in the quality of the biological data that can be obtained at the genomic level. In this regard, large volumes of information can be found in forms of ontology's or computer databases. These datasets, appropriately combined, have the potential to enable novel discoveries that lead to progress in relevant fields to national development such as biotechnology and post-genomic medicine. In particular, this thesis focuses on the research of machine learning techniques and evolutionary computation for the inference of gene regulatory networks from gene expression data at genome-wide levels. A gene regulatory network is a collection of segments of DNA (deoxyribonucleic acid) in a cell which interact with each other (indirectly through their products of expression) and with other substances in the cell, thereby governing the rates of network genes transcription into mRNA (messenger ribonucleic acid). The main contribution of this thesis is related to the development of computational methodologies to attend experts in bioinformatics in the reverse engineering of gene regulatory networks. In this sense, evolutionary algorithms that allow the identification of groups of coexpressed genes under certain subsets of experimental conditions were developed. These algorithms are applied to gene expression data, and optimize desirable characteristics from the biological point of view, allowing the inference of relevant co-expression relationships. Such algorithms were carefully validated by the comparison with other similar techniques available in the literature, conducting studies with real and synthetic data in order to show the usefulness of the information extracted. Furthermore, an inference algorithm that allows the extraction of potential cause-effect relationships between genes, both simultaneous and time-delayed, were developed. This algorithm is an evolution of a previous approach, and incorporates new features such as the ability to infer rules with multiple time delays, at genome-wide level, and integrating multiple datasets. The technique was validated by showing its effectiveness over other relevant approaches in the literature. The results obtained from real datasets were also studied in terms of their biological relevance by exposing the viability of the inferred information. Finally, these algorithms were integrated into a software platform that facilitates the use of these techniques allowing the inference, manipulation and visualization of gene regulatory networks.

Firms specializing in the construction of large commercial buildings and factories must often design and build steel structural components as a part of each project. Such firms must purchase large steel plates, cut them into pieces and then weld the pieces into H-beams and other construction components. The details of the order and the production operation are specified in the "cutting plan." This dissertation focuses on solving this "cutting plan generation" problem with the goal of minimizing cost. Two solution approaches are proposed in this dissertation: a multi-expert system and an evolutionary algorithm. The expert system extends the field by relying on the knowledge of multiple experts. Furthermore, unlike traditional rule-base expert systems, this expert system (XS) uses procedural rules to capture and represent experts' knowledge. The second solution method, called CPGEA, involves development of an evolutionary algorithm based on Falkenauer's grouping genetic algorithm. A series of experiments is designed and performed to investigate the efficiency and effectiveness of the proposed approaches. Two types of data are used in the experiments. Historical data are real data provided by a construction company. Solutions developed manually and implemented are available. In addition, simulated data has been generated to more fully test the solution methods. Experiments are performed to optimize CPGEA parameters as well as to compare the approaches to each other, to known solutions and to theoretical bounds developed in this dissertation. Both approaches show excellent results in solving historical cases with an average cost 1% above the lower bound of the optimal solution. However, as revealed by experiments with simulated problems, the performance decreases in cases where the optimal solution includes multiple identical plates. The performance of the XS is affected by this problem characteristic more than that of CPGEA. While CPGEA is more robust in effectively solving a range of problems, the XS requires substantially less processing time. Both approaches can be useful in different practical situations. / Ph. D.

Tesis por compendio / Water is an essential resource from an environmental, biological, economic or social point of view. In basin management, the irregular distribution in time and in space of this resource is well known. This issue is worsened by extreme climate conditions, generating drought periods or flood events. For both situations, optimal management is necessary. In one case, different water uses should be supplied efficiently using the available surface and groundwater resources. In another case, the most important goal is to avoid damages in flood areas, including the loss of human lives, but also to optimize the revenue of energy production in hydropower plants, or in other uses. The approach presented in this thesis proposes to obtain optimal management rules in water resource systems. With this aim, evolutionary algorithms were combined with simulation models. The first ones, as optimization tools, are responsible for guiding the process iterations. In each iteration, a new management rule is defined in the simulation model, which is computed to comprehend the situation of the system after applying this new management. For testing the proposed methodology, four evolutionary algorithms were assessed combining them with two simulation models. The methodology was implemented in four real case studies. This thesis is presented as a compendium of five manuscripts: three scientific papers published in journals (which are indexed in the Journal Citation Report), another under review, and the last manuscript from Conference Proceedings. In the first manuscript, the Pikaia optimization algorithm was combined with the network flow SIMGES simulation model for obtaining four different types of optimal management rules in the Júcar River Basin. In addition, the parameters of the Pikaia algorithm were also analyzed to identify the best combination of them to use in the optimization process. In the second scientific paper, the multi-objective NSGA-II algorithm was assessed to obtain a parametric management rule in the Mijares River basin. In this case, the same simulation model was linked with the evolutionary algorithm. In the Conference manuscript, an in-depth analysis of the Tirso-Flumendosa-Campidano (TFM) system using different scenarios and comparing three water simulation models for water resources management was developed. The third published manuscript presented the assessment and comparison of two evolutionary algorithms for obtaining optimal rules in the TFM system using SIMGES model. The algorithms assessed were the SCE-UA and the Scatter Search. In this research paper, the parameters of both algorithms were also analyzed as it was done with the Pikaia algorithm. The management rules in the three first manuscripts were focused to avoid or minimize deficits in urban and agrarian demands and, in some case studies, also to minimize the water pumped. Finally, in the last document, two of the algorithms used in previous manuscripts were assessed, the mono-objective SCE-UA and the multi-objective NSGA-II. For this research, the algorithms were combined with RS MINERVE software to manage flood events in Visp River basin minimizing damages in risk areas and losses in hydropower plants. Results reached in the five manuscripts demonstrate the validity of the approach. In all the case studies and with the different evolutionary algorithms assessed, the obtained management rules achieved a better system management than the base scenario of each case. These results usually mean a decrease of the economic costs in the management of water resources. However, comparing the four algorithms assessed, SCE-UA algorithm proved to be the most efficient due to the different stop/convergence criteria and its formulation. Nevertheless, NSGA-II is the most recommended due to its multi-objective search focus on the enhancement of different objectives with the same importance where the decision makers can make the best decision for the management of the system. / El agua es un recurso esencial desde el punto de vista ambiental, biológico, económico o social. En la gestión de cuencas, es bien conocido que la distribución del recurso en el tiempo y el espacio es irregular. Este problema se agrava debido a condiciones climáticas extremas, generando períodos de sequía o inundaciones. Para ambas situaciones, una gestión óptima es necesaria. En un caso, el suministro de agua a los diferentes usos del sistema debe realizarte eficientemente empleando los recursos disponibles, tanto superficiales como subterráneos. En el otro caso, el objetivo más importante es evitar daños en las zonas de inundación, incluyendo la pérdida de vidas humanas, pero al mismo tiempo, optimizar los beneficios de centrales hidroeléctricas, o de otros usos. El enfoque presentado en esta tesis propone la obtención de reglas de gestión óptimas en sistemas reales de recursos hídricos. Con este objetivo, se combinaron algoritmos evolutivos con modelos de simulación. Los primeros, como herramientas de optimización, encargados de guiar las iteraciones del proceso. En cada iteración se define una nueva regla de gestión en el modelo de simulación, que se evalúa para conocer la situación del sistema después de aplicar esta nueva gestión. Para probar la metodología propuesta, se evaluaron cuatro algoritmos evolutivos combinándolos con dos modelos de simulación. La metodología se implementó en cuatro casos de estudio reales. Esta tesis se presenta como un compendio de cinco publicaciones: tres de ellas en revistas indexadas en el Journal Citation Report, otra en revisión y la última como publicación de un congreso. En el primer manuscrito, el algoritmo de optimización Pikaia se combinó con el modelo de simulación SIMGES para obtener reglas de gestión óptimas en la cuenca del río Júcar. Además, se analizaron los parámetros del algoritmo para identificar la mejor combinación de los mismos en el proceso de optimización. El segundo artículo evaluó el algoritmo multi-objetivo NSGA-II para obtener una regla de gestión paramétrica en la cuenca del río Mijares. En el trabajo presentado en el congreso se desarrolló un análisis en profundidad del sistema Tirso-Flumendosa-Campidano utilizando diferentes escenarios y comparando tres modelos de simulación para la gestión de los recursos hídricos. En el tercer manuscrito publicado se evaluó y comparó dos algoritmos evolutivos (SCE-UA y Scatter Search) para obtener reglas de gestión óptimas en el sistema Tirso-Flumendosa-Campidano. En dicha investigación también se analizaron los parámetros de ambos algoritmos. Las reglas de gestión de estas cuatro publicaciones se enfocaron en evitar o minimizar los déficits de las demandas urbanas y agrarias y, en ciertos casos, también en minimizar el caudal bombeado, utilizando para ello el modelo de simulación SIMGES. Finalmente, en la última publicación se evaluó el algoritmo mono-objetivo SCE-UA y el multi-objetivo NSGA-II. Para esta investigación, los algoritmos se combinaron con el software RS MINERVE para gestionar los eventos de inundación en la cuenca del río Visp minimizando los daños en las zonas de riesgo y las pérdidas en las centrales hidroeléctricas. Los resultados obtenidos en las cinco publicaciones demuestran la validez del enfoque. En todos los casos de estudio y, con los diferentes algoritmos evolutivos evaluados, las reglas de gestión obtenidas lograron una mejor gestión del sistema que el escenario base de cada caso. Estos resultados suelen representar una disminución de los costes económicos en la gestión de los recursos hídricos. Comparando los cuatro algoritmos, el SCE-UA demostró ser el más eficiente debido a los diferentes criterios de convergencia. No obstante, el NSGA-II es el más recomendado debido a su búsqueda multi-objetivo enfocada en la mejora, con la misma importancia, de diferentes objetivos, donde los tomadores de decisiones pueden sel / L'aigua és un recurs essencial des del punt de vista ambiental, biològic, econòmic o social. En la gestió de conques, és ben conegut que la distribució del recurs en el temps i l'espai és irregular. Este problema s'agreuja a causa de condicions climàtiques extremes, generant períodes de sequera o inundacions. Per a ambdúes situacions, una gestió òptima és necessària. En un cas, el subministrament d'aigua als diferents usos del sistema ha de realitzar-se eficientment utilitzant els recursos disponibles, tant superficials com subterranis. En l'altre cas, l'objectiu més important és evitar danys en les zones d'inundació, incloent la pèrdua de vides humanes, però al mateix temps, optimitzar els beneficis de centrals hidroelèctriques, o d'altres usos. La proposta d'esta tesi és l'obtenció de regles de gestió òptimes en sistemes reals de recursos hídrics. Amb este objectiu, es van combinar algoritmes evolutius amb models de simulació. Els primers, com a ferramentes d'optimització, encarregats de guiar les iteracions del procés. En cada iteració es definix una nova regla de gestió en el model de simulació, que s'avalua per a conéixer la situació del sistema després d'aplicar esta nova gestió. Per a provar la metodologia proposada, es van avaluar quatre algoritmes evolutius combinant-los amb dos models de simulació. La metodologia es va implementar en quatre casos d'estudi reals. Esta tesi es presenta com un compendi de cinc publicacions: tres d'elles en revistes indexades en el Journal Citation Report, una altra en revisió i l'última com a publicació d'un congrés. En el primer manuscrit, l'algoritme d'optimització Pikaia es va combinar amb el model de simulació SIMGES per a obtindre regles de gestió òptimes en la conca del riu Xúquer. A més, es van analitzar els paràmetres de l'algoritme per a identificar la millor combinació dels mateixos en el procés d'optimització. El segon article va avaluar l'algoritme multi-objectiu NSGA-II per a obtindre una regla de gestió paramètrica en la conca del riu Millars. En el treball presentat en el congrés es va desenvolupar una anàlisi en profunditat del sistema Tirso-Flumendosa-Campidano utilitzant diferents escenaris i comparant tres models de simulació per a la gestió dels recursos hídrics. En el tercer manuscrit publicat es va avaluar i va comparar dos algoritmes evolutius (SCE-UA i Scatter Search) per a obtindre regles de gestió òptimes en el sistema Tirso-Flumendosa-Campidano. En dita investigació també es van analitzar els paràmetres d'ambdós algoritmes. Les regles de gestió d'estes quatre publicacions es van enfocar a evitar o minimitzar els dèficits de les demandes urbanes i agràries i, en certs casos, també a minimitzar el cabal bombejat, utilitzant per a això el model de simulació SIMGES. Finalment, en l'última publicació es va avaluar l'algoritme mono-objectiu SCE-UA i el multi-objetiu NSGA-II. Per a esta investigació, els algoritmes es van combinar amb el programa RS MINERVE per a gestionar els esdeveniments d'inundació en la conca del riu Visp minimitzant els danys en les zones de risc i les pèrdues en les centrals hidroelèctriques. Els resultats obtinguts en les cinc publicacions demostren la validesa de la metodología. En tots els casos d'estudi i, amb els diferents algoritmes evolutius avaluats, les regles de gestió obtingudes van aconseguir una millor gestió del sistema que l'escenari base de cada cas. Estos resultats solen representar una disminució dels costos econòmics en la gestió dels recursos hídrics. Comparant els quatre algoritmes, el SCE-UA va demostrar ser el més eficient a causa dels diferents criteris de convergència. No obstant això, el NSGA-II és el més recomanat a causa de la seua cerca multi-objectiu enfocada en la millora, amb la mateixa importància, de diferents objectius, on els decisors poden seleccionar la millor opció per a la gestió del sistema. / Lerma Elvira, N. (2017). Assessment and implementation of evolutionary algorithms for optimal management rules design in water resources systems [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/90547 / Compendio

The complex refractive index is reported at room temperature for CdxZn1_xO thin film alloys for Cd composition up to 0.16. The CdxZn1_xO epilayers were grown by molecular-beam epitaxy on smooth ZnO/GaN/sapphire lattice templates. Transmission spectra were recorded by spectrophotometry in the 350-800nm wavelength range. The refractive index and extinction coefficient were derived by an evolutionary algorithm, which optimizes the Sellmeier and Forouhi-Bloomer dispersion models by a least-squares fitting to the experimental data.

The automatic synthesis of embodied creatures through artificial evolution has become a key area of research in robotics, artificial life and the cognitive sciences. However, the research has mainly focused on genetic encodings and fitness functions. Considerably less has been said about the role of controllers and how they affect the evolution of morphologies and behaviors in artificial creatures. Furthermore, the evolutionary algorithms used to evolve the controllers and morphologies are pre-dominantly based on a single objective or a weighted combination of multiple objectives, and a large majority of the behaviors evolved are for wheeled or abstract artifacts. In this thesis, we present a systematic study of evolving artificial neural network (ANN) controllers for the legged locomotion of embodied organisms. A virtual but physically accurate world is used to simulate the evolution of locomotion behavior in a quadruped creature. An algorithm using a self-adaptive Pareto multi-objective evolutionary optimization approach is developed. The experiments are designed to address five research aims investigating: (1) the search space characteristics associated with four classes of ANNs with different connectivity types, (2) the effect of selection pressure from a self-adaptive Pareto approach on the nature of the locomotion behavior and capacity (VC-dimension) of the ANN controller generated, (3) the effciency of the proposed approach against more conventional methods of evolutionary optimization in terms of computational cost and quality of solutions, (4) a multi-objective approach towards the comparison of evolved creature complexities, (5) the impact of relaxing certain morphological constraints on evolving locomotion controllers. The results showed that: (1) the search space is highly heterogeneous with both rugged and smooth landscape regions, (2) pure reactive controllers not requiring any hidden layer transformations were able to produce sufficiently good legged locomotion, (3) the proposed approach yielded competitive locomotion controllers while requiring significantly less computational cost, (4) multi-objectivity provided a practical and mathematically-founded methodology for comparing the complexities of evolved creatures, (5) co-evolution of morphology and mind produced significantly different creature designs that were able to generate similarly good locomotion behaviors. These findings attest that a Pareto multi-objective paradigm can spawn highly beneficial robotics and virtual reality applications.

[pt] Através das técnicas utilizadas em Identificação de Sistemas é possível obter um modelo matemático para um sistema dinâmico somente a partir de dados medidos de suas entradas e saídas. Por possuírem comportamento naturalmente dinâmico e um procedimento de treinamento simples e rápido, o uso de redes neurais do tipo Echo State Networks (ESNs) é vantajoso nesta área. Entretanto, as ESNs possuem hiperparâmetros que devem ser ajustados para que obtenham um bom desempenho em uma dada tarefa, além do fato de que a inicialização aleatória de pesos da camada interna destas redes (reservatório) nem sempre ser a ideal em termos de desempenho. Por teoricamente conseguirem obter boas soluções com poucas avaliações, o AEIQ-R (Algoritmo Evolutivo com Inspiração Quântica e Representação Real) e a estratégia evolucionária com adaptação da matriz de covariâncias (CMA-ES) representam alternativas de algoritmos evolutivos que permitem lidar de maneira eficiente com a otimização de hiperparâmetros e/ou pesos desta rede. Sendo assim, este trabalho propõe um modelo neuroevolucionário que define automaticamente uma ESN para aplicações de Identificação de Sistemas. O modelo inicialmente foca na otimização dos hiperparâmetros da ESN utilizando o AEIQ-R ou o CMA-ES, e, num segundo momento, seleciona o reservatório mais adequado para esta rede, o que pode ser feito através de uma segunda otimização focada no ajuste de alguns pesos do reservatório ou por uma escolha simples baseando-se em redes com reservatórios aleatórios. O método proposto foi aplicado a 9 problemas benchmark da área de Identificação de Sistemas, apresentando bons resultados quando comparados com modelos tradicionais. / [en] Through System Identification techniques is possible to obtain a mathematical model for a dynamic system from its input/output data. Due to their intrinsic dynamic behavior and simple and fast training procedure, the use of Echo State Networks, which are a kind of neural networks, for System Identification is advantageous. However, ESNs have global parameters that should be tuned in order to improve their performance in a determined task. Besides, a random reservoir may not be ideal in terms of performance. Due to their theoretical ability of obtaining good solutions with few evaluations, the Real Coded Quantum-Inspired Evolutionary Algorithm (QIEA-R) and the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) represent efficient alternatives of evolutionary algorithms for optimizing ESN global parameters and/or weights. Thus, this work proposes a neuro-evolutionary method that automatically defines an ESN for System Identification problems. The method initially focuses in finding the best ESN global parameters by using the QIEA-R or the CMA-ES, then, in a second moment, in selecting its best reservoir, which can be done by a second optimization focused on some reservoir weights or by doing a simple choice based on networks with random reservoirs. The method was applied to 9 benchmark problems in System Identification, showing good results when compared to traditional methods.

Algae and cyanobacteria occur naturally in source waters and are known to cause extensive problems in the drinking water treatment industry. Cyanobacteria (especially Anabaena sp. and Microcystis sp.) are responsible for many water treatment problems in drinking water treatment works (DWTW) all over the world because of their ability to produce organic compounds like cyanotoxins (e.g. microcystin) and taste and odour compounds (e.g. geosmin) that can have an adverse effect on consumer health and consumer confidence in tap water. Therefore, the monitoring of cyanobacteria in source waters entering DWTW has become an essential part of drinking water treatment management. Managers of DWTW, rely heavily on results of physical, chemical and biological water quality analyses, for their management decisions. But results of water quality analyses can be delayed from 3 hours to a few days depending on a magnitude of factors such as: sampling, distance and accessibility to laboratory, laboratory sample turn-around times, specific methods used in analyses etc. Therefore the use of on-line (in situ) instruments that can supply real-time results by the click of a button has become very popular in the past few years. On-line instruments were developed for analyses like pH, conductivity, nitrate, chlorophyll-a and cyanobacteria concentrations. Although, this real-time (on-line) data has given drinking water treatment managers a better opportunity to make sound management decisions around drinking water treatment options based on the latest possible results, it may still be “too little, too late” once a sudden cyanobacterial bloom of especially Anabaena sp. or Microcystis sp. enters the plant. Therefore the benefit for drinking water treatment management, of changing the focus from real-time results to future predictions of water quality has become apparent. The aims of this study were 1) to review the environmental variables associated with cyanobacterial blooms in the Vaal Dam, as to get background on the input variables that can be used in cyanobacterial-related forecasting models; 2) to apply rule-based Hybrid Evolutionary Algorithms (HEAs) to develop models using a) all applicable laboratory-generated data and b) on-line measureable data only, as input variables in prediction models for harmful algal blooms in the Vaal Dam; 3) to test these models with data that was not used to develop the models (so-called “unseen data”), including on-line (in situ) generated data; and 4) to incorporate selected models into two cyanobacterial incident management protocols which link to the Water Safety Plan (WSP) of a large DWTW (case study : Rand Water). During the current study physical, chemical and biological water quality data from 2000 to 2009, measured in the Vaal Dam and the 20km long canal supplying the Zuikerbosch DWTW of Rand Water, has been used to develop models for the prediction of Anabaena sp., Microcystis sp., the cyanotoxin microcystin and the taste and odour compound geosmin for different prediction or forecasting times in the source water. For the development and first stage of testing the models, 75% of the dataset was used to train the models and the remaining 25% of the dataset was used to test the models. Boot-strapping was used to determine which 75% of the dataset was to be used as the training dataset and which 25% as the testing dataset. Models were also tested with 2 to 3 years of so called “unseen data” (Vaal Dam 2010 – 2012) i.e. data not used at any stage during the model development. Fifty different models were developed for each set of “x input variables = 1 output variable” chosen beforehand. From the 50 models, the best model between the measured data and the predicted data was chosen. Sensitivity analyses were also performed on all input variables to determine the variables that have the largest impact on the result of the output. This study have shown that hybrid evolutionary algorithms can successfully be used to develop relatively accurate forecasting models, which can predict cyanobacterial cell concentrations (particularly Anabaena sp. and Microcystis sp.), as well as the cyanotoxin microcystin concentration in the Vaal Dam, for up to 21 days in advance (depending on the output variable and the model applied). The forecasting models that performed the best were those forecasting 7 days in advance (R2 = 0.86, 0.91 and 0.75 for Anabaena[7], Microcystis[7] and microcystin[7] respectively). Although no optimisation strategies were performed, the models developed during this study were generally more accurate than most models developed by other authors utilising the same concepts and even models optimised by hill climbing and/or differential evolution. It is speculated that including “initial cyanobacteria inoculum” as input variable (which is unique to this study), is most probably the reason for the better performing models. The results show that models developed from on-line (in situ) measureable data only, are almost as good as the models developed by using all possible input variables. The reason is most probably because “initial cyanobacteria inoculum” – the variable towards which the output result showed the greatest sensitivity – is included in these models. Generally models predicting Microcystis sp. in the Vaal Dam were more accurate than models predicting Anabaena sp. concentrations and models with a shorter prediction time (e.g. 7 days in advance) were statistically more accurate than models with longer prediction times (e.g. 14 or 21 days in advance). The multi-barrier approach in risk reduction, as promoted by the concept of water safety plans under the banner of the Blue Drop Certification Program, lends itself to the application of future predictions of water quality variables. In this study, prediction models of Anabaena sp., Microcystis sp. and microcystin concentrations 7 days in advance from the Vaal Dam, as well as geosmin concentration 7 days in advance from the canal were incorporated into the proposed incident management protocols. This was managed by adding an additional “Prediction Monitoring Level” to Rand Waters’ microcystin and taste and odour incident management protocols, to also include future predictions of cyanobacteria (Anabaena sp. and Microcystis sp.), microcystin and geosmin. The novelty of this study was the incorporation of future predictions into the water safety plan of a DWTW which has never been done before. This adds another barrier in the potential exposure of drinking water consumers to harmful and aesthetically unacceptable organic compounds produced by cyanobacteria. / PhD (Botany), North-West University, Potchefstroom Campus, 2015

Algae and cyanobacteria occur naturally in source waters and are known to cause extensive problems in the drinking water treatment industry. Cyanobacteria (especially Anabaena sp. and Microcystis sp.) are responsible for many water treatment problems in drinking water treatment works (DWTW) all over the world because of their ability to produce organic compounds like cyanotoxins (e.g. microcystin) and taste and odour compounds (e.g. geosmin) that can have an adverse effect on consumer health and consumer confidence in tap water. Therefore, the monitoring of cyanobacteria in source waters entering DWTW has become an essential part of drinking water treatment management. Managers of DWTW, rely heavily on results of physical, chemical and biological water quality analyses, for their management decisions. But results of water quality analyses can be delayed from 3 hours to a few days depending on a magnitude of factors such as: sampling, distance and accessibility to laboratory, laboratory sample turn-around times, specific methods used in analyses etc. Therefore the use of on-line (in situ) instruments that can supply real-time results by the click of a button has become very popular in the past few years. On-line instruments were developed for analyses like pH, conductivity, nitrate, chlorophyll-a and cyanobacteria concentrations. Although, this real-time (on-line) data has given drinking water treatment managers a better opportunity to make sound management decisions around drinking water treatment options based on the latest possible results, it may still be “too little, too late” once a sudden cyanobacterial bloom of especially Anabaena sp. or Microcystis sp. enters the plant. Therefore the benefit for drinking water treatment management, of changing the focus from real-time results to future predictions of water quality has become apparent. The aims of this study were 1) to review the environmental variables associated with cyanobacterial blooms in the Vaal Dam, as to get background on the input variables that can be used in cyanobacterial-related forecasting models; 2) to apply rule-based Hybrid Evolutionary Algorithms (HEAs) to develop models using a) all applicable laboratory-generated data and b) on-line measureable data only, as input variables in prediction models for harmful algal blooms in the Vaal Dam; 3) to test these models with data that was not used to develop the models (so-called “unseen data”), including on-line (in situ) generated data; and 4) to incorporate selected models into two cyanobacterial incident management protocols which link to the Water Safety Plan (WSP) of a large DWTW (case study : Rand Water). During the current study physical, chemical and biological water quality data from 2000 to 2009, measured in the Vaal Dam and the 20km long canal supplying the Zuikerbosch DWTW of Rand Water, has been used to develop models for the prediction of Anabaena sp., Microcystis sp., the cyanotoxin microcystin and the taste and odour compound geosmin for different prediction or forecasting times in the source water. For the development and first stage of testing the models, 75% of the dataset was used to train the models and the remaining 25% of the dataset was used to test the models. Boot-strapping was used to determine which 75% of the dataset was to be used as the training dataset and which 25% as the testing dataset. Models were also tested with 2 to 3 years of so called “unseen data” (Vaal Dam 2010 – 2012) i.e. data not used at any stage during the model development. Fifty different models were developed for each set of “x input variables = 1 output variable” chosen beforehand. From the 50 models, the best model between the measured data and the predicted data was chosen. Sensitivity analyses were also performed on all input variables to determine the variables that have the largest impact on the result of the output. This study have shown that hybrid evolutionary algorithms can successfully be used to develop relatively accurate forecasting models, which can predict cyanobacterial cell concentrations (particularly Anabaena sp. and Microcystis sp.), as well as the cyanotoxin microcystin concentration in the Vaal Dam, for up to 21 days in advance (depending on the output variable and the model applied). The forecasting models that performed the best were those forecasting 7 days in advance (R2 = 0.86, 0.91 and 0.75 for Anabaena[7], Microcystis[7] and microcystin[7] respectively). Although no optimisation strategies were performed, the models developed during this study were generally more accurate than most models developed by other authors utilising the same concepts and even models optimised by hill climbing and/or differential evolution. It is speculated that including “initial cyanobacteria inoculum” as input variable (which is unique to this study), is most probably the reason for the better performing models. The results show that models developed from on-line (in situ) measureable data only, are almost as good as the models developed by using all possible input variables. The reason is most probably because “initial cyanobacteria inoculum” – the variable towards which the output result showed the greatest sensitivity – is included in these models. Generally models predicting Microcystis sp. in the Vaal Dam were more accurate than models predicting Anabaena sp. concentrations and models with a shorter prediction time (e.g. 7 days in advance) were statistically more accurate than models with longer prediction times (e.g. 14 or 21 days in advance). The multi-barrier approach in risk reduction, as promoted by the concept of water safety plans under the banner of the Blue Drop Certification Program, lends itself to the application of future predictions of water quality variables. In this study, prediction models of Anabaena sp., Microcystis sp. and microcystin concentrations 7 days in advance from the Vaal Dam, as well as geosmin concentration 7 days in advance from the canal were incorporated into the proposed incident management protocols. This was managed by adding an additional “Prediction Monitoring Level” to Rand Waters’ microcystin and taste and odour incident management protocols, to also include future predictions of cyanobacteria (Anabaena sp. and Microcystis sp.), microcystin and geosmin. The novelty of this study was the incorporation of future predictions into the water safety plan of a DWTW which has never been done before. This adds another barrier in the potential exposure of drinking water consumers to harmful and aesthetically unacceptable organic compounds produced by cyanobacteria. / PhD (Botany), North-West University, Potchefstroom Campus, 2015

Dans le contexte actuel de compétitivité des marchés, la maîtrise et l'optimisation des processus de conception et de planification sont nécessaires pour garantir, d'une part la fiabilité et la qualité des produits systèmes ou services conçus et, d'autre part, le cycle de développement et les coûts. Ce constat impose de développer et d'améliorer les méthodes, modèles, techniques et outils relatifs aux processus de conception et de gestion ou de planification. Les travaux présentés dans cette thèse s'inscrivent dans ce contexte et proposent de mettre en relation ou encore de faire intéragir la configuration de produit avec la planification du projet de réalisation. Le but de ces travaux est d'apporter une aide à la décision pour le couplage de la configuration de produit et de la planification du projet associé, en exploitant deux outils issus de l'Intelligence Artificielle : les approches par contraintes et les algorithmes évolutionnaires. Cette aide à la décision est présentée en deux parties. La première partie décrit l'utilisation des approches par contraintes afin de permettre au décideur de configurer son produit et son projet de réalisation de manière simultanée et interactive. Pour ce faire, les techniques de propagation et de filtrage des contraintes sont exploitées spécifiquement. La deuxième partie s'intéresse à l'exploitation des algorithmes évolutionnaires pour optimiser l'espace de solutions selon les critères coût et délai afin de présenter au décideur, un ensemble réduit de solutions optimisées. Un algorithme SPEA2 modifié en intégrant des méthodes de filtrage dans ses opérateurs de parcours de l'espace de recherche y est présenté. Toutes nos propositions sont illustrées sur un exemple d'avion de tourisme et d'affaire. / In the actual context of market the control and optimization of design processes are essential to ensure on the one hand, the reliability and quality of products, on the other hand the development time and costs. This phenomenon involves the constant development of methodologies, in order to improve the diversity and quality of the product and at the same time to shorten their development time and decrease their cost The work presented in this thesis fits into this context and propose to associate products configuration and production process planning. The aim of this work is to provide decision support for the coupling of onfiguration products and the associate production process leveraging two tools of Artificial Intelligence : constraints approaches and evolutionary algorithms. This decision support is presented in two parts. The first part decribes the use of constraints approaches to allow decison-maker to configure product and its production process simultaneously and interactively. For this aim, propagation and filtring techniques are exploited specifically. The second part deals with the use of evolutionary algorithms to optimize the space solutions according to time and cost criteria in order to provide a small set of optimized solutions to the decision-maker. SPEA2 algorithm modified by incorporating filtering methods in its evolutionary operators. All our proposals ara illustrated on an exemple of light aitcraft.