Evolutionary Search Techniques with Strong Heuristics for Multi-Objective Feature Selection in Software Product Lines

Software design is a process of trading off competing objectives. If the user objective space is rich, then we should use optimizers that can fully exploit that richness. For example, this study configures software product lines (expressed as feature models) using various search-based software engineering methods. Our main result is that as we increase the number of optimization objectives, the methods in widespread use (e.g. NSGA-II, SPEA2) perform much worse than IBEA (Indicator-Based Evolutionary Algorithm). IBEA works best since it makes most use of user preference knowledge. Hence it does better on the standard measures (hypervolume and spread) but it also generates far more products with 0 violations of domain constraints. We also present significant improvements to IBEA\u27s performance by employing three strong heuristic techniques that we call PUSH, PULL, and seeding. The PUSH technique forces the evolutionary search to respect certain rules and dependencies defined by the feature models, while the PULL technique gives higher weight to constraint satisfaction as an optimization objective and thus achieves a higher percentage of fully-compliant configurations within shorter runtimes. The seeding technique helps in guiding very large feature models to correct configurations very early in the optimization process. Our conclusion is that the methods we apply in search-based software engineering need to be carefully chosen, particularly when studying complex decision spaces with many optimization objectives. Also, we conclude that search methods must be customized to fit the problem at hand. Specifically, the evolutionary search must respect domain constraints

Modelling and multiobjective optimization for simulation of cyanobacterial metabolism

The present thesis is devoted to the development of models and algorithms to improve metabolic simulations of cyanobacterial metabolism. Cyanobacteria are photosynthetic bacteria of great biotechnological interest to the development of sustainable bio-based manufacturing processes. For this purpose, it is fundamental to understand metabolic behaviour of these organisms, and constraint-based metabolic modelling techniques offer a platform for analysis and assessment of cell's metabolic functionality. Reliable simulations are needed to enhance the applicability of the results, and this is the main goal of this thesis. This dissertation has been structured in three parts. The first part is devoted to introduce needed fundamentals of the disciplines that are combined in this work: metabolic modelling, cyanobacterial metabolism and multi-objective optimisation. In the second part the reconstruction and update of metabolic models of two cyanobacterial strains is addressed. These models are then used to perform metabolic simulations with the application of the classic Flux Balance Analysis (FBA) methodology. The studies conducted in this part are useful to illustrate the uses and applications of metabolic simulations for the analysis of living organisms. And at the same time they serve to identify important limitations of classic simulation techniques based on mono-objective linear optimisation that motivate the search of new strategies. Finally, in the third part a novel approach is defined based on the application of multi-objective optimisation procedures to metabolic modelling. Main steps in the definition of multi-objective problem and the description of an optimisation algorithm that ensure the applicability of the obtained results, as well as the multi-criteria analysis of the solutions are covered. The resulting tool allows the definition of non-linear objective functions and constraints, as well as the analysis of multiple Pareto-optimal solutions. It avoids some of the main drawbacks of classic methodologies, leading to more flexible simulations and more realistic results. Overall this thesis contributes to the advance in the study of cyanobacterial metabolism by means of definition of models and strategies that improve plasticity and predictive capacities of metabolic simulations.La presente tesis está dedicada al desarrollo de modelos y algoritmos para mejorar las simulaciones metabólicas de cianobacterias. Las cianobacterias son bacterias fotosintéticas de gran interés biotecnológico para el desarrollo de bioprocesos productivos sostenibles. Para este propósito, es fundamental entender el comportamiento metabólico de estos organismos, y el modelado metabólico basado en restricciones ofrece una plataforma para el análisis y la evaluación de las funcionalidades metabólicas de las células. Se necesitan simulaciones fidedignas para aumentar la aplicabilidad de los resultados, y este es el objetivo principal de esta tesis. Esta disertación se ha estructurado en tres partes. La primera parte está dedicada a introducir los fundamentos necesarios de las disciplinas que se combinan en este trabajo: el modelado metabólico, el metabolismo de cianobacterias, y la optimización multiobjetivo. En la segunda parte, se encara la reconstrucción y la actualización de los modelos metabólicos de dos cepas de cianobacterias. Estos modelos se usan después para llevar a cabo simulaciones metabólicas con la aplicación de la metodología clásica Flux Balance Analysis (FBA). Los estudios realizados en esta parte son útiles para ilustrar los usos y aplicaciones de las simulaciones metabólicas para el análisis de los organismos vivos. Y al mismo tiempo sirven para identificar importantes limitaciones de las técnicas clásicas de simulación basadas en optimización lineal mono-objetivo que motivan la búsqueda de nuevas estrategias. Finalmente, en la tercera parte, se define una nueva aproximación basada en la aplicación al modelado metabólico de procedimientos de optimización multiobjetivo. Se cubren los principales pasos en la definición de un problema multiobjetivo y la descripción de un algoritmo de optimización que aseguren la aplicabilidad de los resultados obtenidos, así como el análisis multi-criterio de las soluciones. La herramienta resultante permite la definición de funciones objetivo y restricciones no lineales, así como el análisis de múltiples soluciones en el sentido de Pareto. Esta herramienta evita algunos de los principales inconvenientes de las metodologías clásicas, lo que lleva a obtener simulaciones más flexibles y resultados más realistas. En conjunto, esta tesis contribuye al avance en el estudio del metabolismo de cianobacterias por medio de la definición de modelos y estrategias que mejoran la plasticidad y las capacidades predictivas de las simulaciones metabólicas.La present tesi està dedicada al desenvolupament de models i algorismes per a millorar les simulacions metabòliques de cianobacteris. Els cianobacteris són bacteris fotosintètics de gran interés biotecnològic per al desenvolupament de bioprocessos productius sostenibles. Per a aquest propòsit, és fonamental entendre el comportament metabòlic d'aquests organismes, i el modelatge metabòlic basat en restriccions ofereix una plataforma per a l'anàlisi i l'avaluació de les funcionalitats metabòliques de les cèl·lules. Es necessiten simulacions fidedignes per a augmentar l'aplicabilitat dels resultats, i aquest és l'objectiu principal d'aquesta tesi. Aquesta dissertació s'ha estructurat en tres parts. La primera part està dedicada a introduir els fonaments necessaris de les disciplines que es combinen en aquest treball: el modelatge metabòlic, el metabolisme de cianobacteris i l'optimització multiobjectiu. En la segona part, s'adreça la reconstrucció i l'actualització dels models metabòlics de dos soques de cianobacteris. Aquests models s'empren després per a portar a terme simulacions metabòliques amb l'aplicació de la metodologia clàssica Flux Balance Analysis (FBA). Els estudis realitzats en aquesta part són útils per a il·lustrar els usos i aplicacions de les simulacions metabòliques per a l'anàlisi dels organismes vius. I al mateix temps serveixen per a identificar importants limitacions de les tècniques clàssiques de simulació basades en optimització lineal mono-objectiu que motiven la cerca de noves estratègies. Finalment, en la tercera part, es defineix una nova aproximació basada en l'aplicació al modelatge metabòlic de procediments d'optimització multiobjectiu. Es cobreixen els principals passos en la definició d'un problema multiobjectiu i la descripció d'un algorisme d'optimització que asseguren l'aplicabilitat dels resultats obtinguts, així com l'anàlisi multi-criteri de les solucions. La ferramenta resultant permet la definició de funcions objectiu i restriccions no lineals, així com l'anàlisi de múltiples solucions òptimes en el sentit de Pareto. Aquesta ferramenta evita alguns dels principals inconvenients de les metodologies clàssiques, el que porta a obtenir simulacions més flexibles i resultats més realistes. En conjunt, aquesta tesi contribueix a l'avanç en l'estudi del metabolisme de cianobacteris per mitjà de la definició de models i estratègies que milloren la plasticitat i les capacitats predictives de les simulacions metabòliques.Siurana Paula, M. (2017). Modelling and multiobjective optimization for simulation of cyanobacterial metabolism [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/9057

Evolutionary Computation

This book presents several recent advances on Evolutionary Computation, specially evolution-based optimization methods and hybrid algorithms for several applications, from optimization and learning to pattern recognition and bioinformatics. This book also presents new algorithms based on several analogies and metafores, where one of them is based on philosophy, specifically on the philosophy of praxis and dialectics. In this book it is also presented interesting applications on bioinformatics, specially the use of particle swarms to discover gene expression patterns in DNA microarrays. Therefore, this book features representative work on the field of evolutionary computation and applied sciences. The intended audience is graduate, undergraduate, researchers, and anyone who wishes to become familiar with the latest research work on this field

Towards Sustainable Freight Energy Management - Development of a Strategic Decision Support Tool

Freight transportation, in its current shape and form, is on a highly unsustainable trajectory. Global demand for freight is ever increasing, while this demand is predominantly serviced by inefficient, fossil fuel dependent transportation options. The management of energy use in freight transportation has been identified as a significant opportunity to improve the sustainability of the freight sector. Given the vast amount of energy mitigation measures and policies to choose from to attempt this, decision-makers need support and guidance in terms of selecting which policies to adopt – they are faced with a complex and demanding problem. These complexities result, in part, from the vast range, scope and extent of measures to be considered by decision-makers. The tool developed needs to encompass a suitable methodology for comparing proverbial apples to oranges in a fair and unbiased manner, despite the development of one consistent assessment metric that can accommodate this level of diversity being problematic. Further to this, decision-makers need insight into the extent of implementation that is required for each measure. Because the level of implementation of each measure is variable and the extent to which each adopted measure will be implemented in the network needs to be specified, the number of potential measure implementation combinations that decision-makers need to consider is infinite, adding further complexity to the problem. Freight energy management measures cannot, and should not, be evaluated in isolation. The knock-on effects of measure adoption on the performance of other measures need to be considered. Measures are not all independent and decision-makers need to take these dependencies and their ramifications into account. In addition, there is dimensionality to be accounted for in terms of each measure, because one measure can be applied in a variable manner across different components of the freight network. A unique and independent decision needs to be made on the application of a measure for each of these network components (for example for each mode). Decisions on freight transportation impact all three traditional pillars of sustainability: social, environmental and economic. Measure impacts, thus, need to be assessed over multiple criteria. Decisions will affect a variety of stakeholders and outcomes must be acceptable to a range of interested parties. Sustainability criteria are often in conflict with one another, implying that there are trade-offs to be negotiated by the decision-makers. Decision-makers, thus, need to propose system alterations, or a portfolio of system alterations, that achieve improvements in some sustainability respects, whilst maintaining a balance between all other sustainability aspects. Moreover, the magnitude of impacts (be it positive or negative) of a measure on the sustainability criteria is variable, adding additional dimensionality to the problem. The aim of the research presented in this dissertation was to develop a decision support tool which addresses the complexities involved in the formulation of freight transport energy management strategies on behalf of the decision-makers, facilitating the development of holistic, sustainable and comprehensive freight management policy by government level decision-makers. The Freight Transport Energy Management Tool (FTEMT) was developed in response to this research objective, using a standardised operations research approach as a roadmap for its development. Following a standardised operations research approach to model development provides a structure where stakeholder participation can be encouraged at all the key stages in the decision-making process; it offers a logical basis for proposing solutions and for assessing any proposed suggestions by others; it ensures that the appraisal of alternative solutions is conducted in a logical, consistent and comprehensive manner against the full set of objectives; and it provides a means for assessing whether the implemented instruments have performed as predicted, enabling the improvement of the model being developed. The FTEMT can be classified as a simulation optimisation model, which is a combination between multi-objective optimisation and simulation. The simulation component provides a suitably accurate representation of the freight system and affords the ability to approximate the effect that measure implementation will have on the sustainability objectives, whilst the optimisation component provides the ability to effectively explore the decision space and reduces the number of alternative options (and, therefore, the complexity) that decision-makers need to consider. It is this simulation optimisation backbone of the FTEMT that enables the tool to address all the complexities surrounding the problem, enabling the decision support produced by the FTEMT to provide the information necessary for decision-makers to steer the freight transport sector towards true sustainability. Although this problem originates from the domain of sustainable transportation planning, the combination of operations research and transport modelling knowledge applied proved essential in developing a decision support tool that is able to generate adequate decision support on the problem. To demonstrate the use and usefulness of the decision support system developed, a fictitious case study version of the FTEMT was modelled and is discussed throughout this dissertation. Results from the case study implementation were used to verify and validate the tool, to demonstrate the decision support generated and to illustrate how this decision support can be interpreted and incorporated into a decision-making process. Outputs from the case study FTEMT proved the tool to be operationally valid, as it successfully achieved its stated objectives (the FTEMT unearths a Pareto set of solutions close to the true efficient frontier through the exploration of different energy management measure combinations). Explained in short, the value of using the FTEMT to generate decision support is that it explores the decision space and reduces the number of decision alternatives that decision-makers need to consider to a manageable number of solutions, all of which represent harmonic measure combinations geared toward optimal performance in terms of the entire spectrum of the problem objectives. These solutions are developed taking all the complexity issues surrounding the problem into account. Decision-makers can, thus, have confidence that the acceptance of any one of the solutions proposed by the FTEMT will be a responsible and sound decision. As an additional benefit, preferences and strategic priorities of the decision-makers can be factored in when selecting a preferred decision alternative for implementation. Decision-makers must debate the trade-offs between solutions and need to determine what they are willing to sacrifice to realise what gain, but they are afforded the opportunity to select solutions that show the greatest alignment with their official mandates. The structure of the FTEMT developed and described in this dissertation presents a practical methodology for producing decision support on the development of sound freight energy management policy. This work serves as a basis to stimulate further scholarship and expands upon the collective knowledge on the topic, by proposing an approach that is able to address the full scale of complexities involved in the production of such decision support

XXI Workshop de Investigadores en Ciencias de la Computación - WICC 2019: libro de actas

Trabajos presentados en el XXI Workshop de Investigadores en Ciencias de la Computación (WICC), celebrado en la provincia de San Juan los días 25 y 26 de abril 2019, organizado por la Red de Universidades con Carreras en Informática (RedUNCI) y la Facultad de Ciencias Exactas, Físicas y Naturales de la Universidad Nacional de San Juan.Red de Universidades con Carreras en Informátic

XXI Workshop de Investigadores en Ciencias de la Computación - WICC 2019: libro de actas

Trabajos presentados en el XXI Workshop de Investigadores en Ciencias de la Computación (WICC), celebrado en la provincia de San Juan los días 25 y 26 de abril 2019, organizado por la Red de Universidades con Carreras en Informática (RedUNCI) y la Facultad de Ciencias Exactas, Físicas y Naturales de la Universidad Nacional de San Juan.Red de Universidades con Carreras en Informátic