A multi-criteria decision support system for a routing problem in waste collection

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Algorithms and tools for in silico design of cell factories

PhD thesis in Bioengineering

Development of an intelligent earthwork optimization system

Tese de Doutoramento em Engenharia Civil.

Line search multilevel optimization as computational methods for dense optical flow

We evaluate the performance of different optimization techniques developed in the context of optical flowcomputation with different variational models. In particular, based on truncated Newton methods (TN) that have been an effective approach for large-scale unconstrained optimization, we develop the use of efficient multilevel schemes for computing the optical flow. More precisely, we evaluate the performance of a standard unidirectional multilevel algorithm - called multiresolution optimization (MR/OPT), to a bidrectional multilevel algorithm - called full multigrid optimization (FMG/OPT). The FMG/OPT algorithm treats the coarse grid correction as an optimization search direction and eventually scales it using a line search. Experimental results on different image sequences using four models of optical flow computation show that the FMG/OPT algorithm outperforms both the TN and MR/OPT algorithms in terms of the computational work and the quality of the optical flow estimation.

A convex optimization framework for global tractography

In this article we present a novel approach for diffusion MRI global tractography. Our formulation models the signal in each voxel as a linear combination of fiber-tract basis func- tions, which consist of a comprehensive set of plausible fiber tracts that are locally compatible with the measured MR signal. This large dictionary of candidate fibers is directly estimated from the data and, subsequently, efficient convex optimization techniques are used for recovering the smallest subset globally best fitting the measured signal. Experimen- tal results conducted on a realistic phantom demonstrate that our approach significantly reduces the computational cost of global tractography while still attaining a reconstruction quality at least as good as the state-of-the-art global methods.

Line search multilevel optimization as computational methods for dense optical flow

We evaluate the performance of different optimization techniques developed in the context of optical flow computation with different variational models. In particular, based on truncated Newton methods (TN) that have been an effective approach for large-scale unconstrained optimization, we de- velop the use of efficient multilevel schemes for computing the optical flow. More precisely, we evaluate the performance of a standard unidirectional mul- tilevel algorithm - called multiresolution optimization (MR/OPT), to a bidrec- tional multilevel algorithm - called full multigrid optimization (FMG/OPT). The FMG/OPT algorithm treats the coarse grid correction as an optimiza- tion search direction and eventually scales it using a line search. Experimental results on different image sequences using four models of optical flow com- putation show that the FMG/OPT algorithm outperforms both the TN and MR/OPT algorithms in terms of the computational work and the quality of the optical flow estimation.

Quantitative integration of high-resolution hydrogeophysical data through Monte-Carlo-type conditional simulations

Geophysical techniques can help to bridge the inherent gap with regard to spatial resolution and the range of coverage that plagues classical hydrological methods. This has lead to the emergence of the new and rapidly growing field of hydrogeophysics. Given the differing sensitivities of various geophysical techniques to hydrologically relevant parameters and their inherent trade-off between resolution and range the fundamental usefulness of multi-method hydrogeophysical surveys for reducing uncertainties in data analysis and interpretation is widely accepted. A major challenge arising from such endeavors is the quantitative integration of the resulting vast and diverse database in order to obtain a unified model of the probed subsurface region that is internally consistent with all available data. To address this problem, we have developed a strategy towards hydrogeophysical data integration based on Monte-Carlo-type conditional stochastic simulation that we consider to be particularly suitable for local-scale studies characterized by high-resolution and high-quality datasets. Monte-Carlo-based optimization techniques are flexible and versatile, allow for accounting for a wide variety of data and constraints of differing resolution and hardness and thus have the potential of providing, in a geostatistical sense, highly detailed and realistic models of the pertinent target parameter distributions. Compared to more conventional approaches of this kind, our approach provides significant advancements in the way that the larger-scale deterministic information resolved by the hydrogeophysical data can be accounted for, which represents an inherently problematic, and as of yet unresolved, aspect of Monte-Carlo-type conditional simulation techniques. We present the results of applying our algorithm to the integration of porosity log and tomographic crosshole georadar data to generate stochastic realizations of the local-scale porosity structure. Our procedure is first tested on pertinent synthetic data and then applied to corresponding field data collected at the Boise Hydrogeophysical Research Site near Boise, Idaho, USA.

Conflict-based Method for Conceptual Process Synthesis

The changing business environment demands that chemical industrial processes be designed such that they enable the attainment of multi-objective requirements and the enhancement of innovativedesign activities. The requirements and key issues for conceptual process synthesis have changed and are no longer those of conventional process design; there is an increased emphasis on innovative research to develop new concepts, novel techniques and processes. A central issue, how to enhance the creativity of the design process, requires further research into methodologies. The thesis presentsa conflict-based methodology for conceptual process synthesis. The motivation of the work is to support decision-making in design and synthesis and to enhance the creativity of design activities. It deals with the multi-objective requirements and combinatorially complex nature of process synthesis. The work is carriedout based on a new concept and design paradigm adapted from Theory of InventiveProblem Solving methodology (TRIZ). TRIZ is claimed to be a `systematic creativity' framework thanks to its knowledge based and evolutionary-directed nature. The conflict concept, when applied to process synthesis, throws new lights on design problems and activities. The conflict model is proposed as a way of describing design problems and handling design information. The design tasks are represented as groups of conflicts and conflict table is built as the design tool. The general design paradigm is formulated to handle conflicts in both the early and detailed design stages. The methodology developed reflects the conflict nature of process design and synthesis. The method is implemented and verified through case studies of distillation system design, reactor/separator network design and waste minimization. Handling the various levels of conflicts evolve possible design alternatives in a systematic procedure which consists of establishing an efficient and compact solution space for the detailed design stage. The approach also provides the information to bridge the gap between the application of qualitative knowledge in the early stage and quantitative techniques in the detailed design stage. Enhancement of creativity is realized through the better understanding of the design problems gained from the conflict concept and in the improvement in engineering design practice via the systematic nature of the approach.

Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models

Background: Design of newly engineered microbial strains for biotechnological purposes would greatly benefit from the development of realistic mathematical models for the processes to be optimized. Such models can then be analyzed and, with the development and application of appropriate optimization techniques, one could identify the modifications that need to be made to the organism in order to achieve the desired biotechnological goal. As appropriate models to perform such an analysis are necessarily non-linear and typically non-convex, finding their global optimum is a challenging task. Canonical modeling techniques, such as Generalized Mass Action (GMA) models based on the power-law formalism, offer a possible solution to this problem because they have a mathematical structure that enables the development of specific algorithms for global optimization. Results: Based on the GMA canonical representation, we have developed in previous works a highly efficient optimization algorithm and a set of related strategies for understanding the evolution of adaptive responses in cellular metabolism. Here, we explore the possibility of recasting kinetic non-linear models into an equivalent GMA model, so that global optimization on the recast GMA model can be performed. With this technique, optimization is greatly facilitated and the results are transposable to the original non-linear problem. This procedure is straightforward for a particular class of non-linear models known as Saturable and Cooperative (SC) models that extend the power-law formalism to deal with saturation and cooperativity. Conclusions: Our results show that recasting non-linear kinetic models into GMA models is indeed an appropriate strategy that helps overcoming some of the numerical difficulties that arise during the global optimization task.

An efficient total variation algorithm for super-resolution in fetal brain MRI with adaptive regularization.

Although fetal anatomy can be adequately viewed in new multi-slice MR images, many critical limitations remain for quantitative data analysis. To this end, several research groups have recently developed advanced image processing methods, often denoted by super-resolution (SR) techniques, to reconstruct from a set of clinical low-resolution (LR) images, a high-resolution (HR) motion-free volume. It is usually modeled as an inverse problem where the regularization term plays a central role in the reconstruction quality. Literature has been quite attracted by Total Variation energies because of their ability in edge preserving but only standard explicit steepest gradient techniques have been applied for optimization. In a preliminary work, it has been shown that novel fast convex optimization techniques could be successfully applied to design an efficient Total Variation optimization algorithm for the super-resolution problem. In this work, two major contributions are presented. Firstly, we will briefly review the Bayesian and Variational dual formulations of current state-of-the-art methods dedicated to fetal MRI reconstruction. Secondly, we present an extensive quantitative evaluation of our SR algorithm previously introduced on both simulated fetal and real clinical data (with both normal and pathological subjects). Specifically, we study the robustness of regularization terms in front of residual registration errors and we also present a novel strategy for automatically select the weight of the regularization as regards the data fidelity term. Our results show that our TV implementation is highly robust in front of motion artifacts and that it offers the best trade-off between speed and accuracy for fetal MRI recovery as in comparison with state-of-the art methods.

Optimization as a method of search engine marketing

This study is dedicated to search engine marketing (SEM). It aims for developing a business model of SEM firms and to provide explicit research of trustworthy practices of virtual marketing companies. Optimization is a general term that represents a variety of techniques and methods of the web pages promotion. The research addresses optimization as a business activity, and it explains its role for the online marketing. Additionally, it highlights issues of unethical techniques utilization by marketers which created relatively negative attitude to them on the Internet environment. Literature insight combines in the one place both technical and economical scientific findings in order to highlight technological and business attributes incorporated in SEM activities. Empirical data regarding search marketers was collected via e-mail questionnaires. 4 representatives of SEM companies were engaged in this study to accomplish the business model design. Additionally, the fifth respondent was a representative of the search engine portal, who provided insight on relations between search engines and marketers. Obtained information of the respondents was processed qualitatively. Movement of commercial organizations to the online market increases demand on promotional programs. SEM is the largest part of online marketing, and it is a prerogative of search engines portals. However, skilled users, or marketers, are able to implement long-term marketing programs by utilizing web page optimization techniques, key word consultancy or content optimization to increase web site visibility to search engines and, therefore, user’s attention to the customer pages. SEM firms are related to small knowledge-intensive businesses. On the basis of data analysis the business model was constructed. The SEM model includes generalized constructs, although they represent a wider amount of operational aspects. Constructing blocks of the model includes fundamental parts of SEM commercial activity: value creation, customer, infrastructure and financial segments. Also, approaches were provided on company’s differentiation and competitive advantages evaluation. It is assumed that search marketers should apply further attempts to differentiate own business out of the large number of similar service providing companies. Findings indicate that SEM companies are interested in the increasing their trustworthiness and the reputation building. Future of the search marketing is directly depending on search engines development.

Evolution of architectural floor plans

Layout planning is a process of sizing and placing rooms (e.g. in a house) while a t t empt ing to optimize various criteria. Often the r e are conflicting c r i t e r i a such as construction cost, minimizing the distance between r e l a t ed activities, and meeting the area requirements for these activities. The process of layout planning ha s mostly been done by hand, wi th a handful of a t t empt s to automa t e the process. Thi s thesis explores some of these pa s t a t t empt s and describes several new techniques for automa t ing the layout planning process using evolutionary computation. These techniques a r e inspired by the existing methods, while adding some of the i r own innovations. Additional experimenLs are done to t e s t the possibility of allowing polygonal exteriors wi th rectilinear interior walls. Several multi-objective approaches are used to evaluate and compare fitness. The evolutionary r epr e s ent a t ion and requirements specification used provide great flexibility in problem scope and depth and is worthy of considering in future layout and design a t t empt s . The system outlined in thi s thesis is capable of evolving a variety of floor plans conforming to functional and geometric specifications. Many of the resulting plans look reasonable even when compared to a professional floor plan. Additionally polygonal and multi-floor buildings were also generated.

Genetic Programming for Non-Photorealistic Rendering

This thesis focuses on developing an evolutionary art system using genetic programming. The main goal is to produce new forms of evolutionary art that filter existing images into new non-photorealistic (NPR) styles, by obtaining images that look like traditional media such as watercolor or pencil, as well as brand new effects. The approach permits GP to generate creative forms of NPR results. The GP language is extended with different techniques and methods inspired from NPR research such as colour mixing expressions, image processing filters and painting algorithm. Colour mixing is a major new contribution, as it enables many familiar and innovative NPR effects to arise. Another major innovation is that many GP functions process the canvas (rendered image), while is dynamically changing. Automatic fitness scoring uses aesthetic evaluation models and statistical analysis, and multi-objective fitness evaluation is used. Results showed a variety of NPR effects, as well as new, creative possibilities.

Solution Methods for Service Network Design with Resource Management Consideration

La gestion des ressources, équipements, équipes de travail, et autres, devrait être prise en compte lors de la conception de tout plan réalisable pour le problème de conception de réseaux de services. Cependant, les travaux de recherche portant sur la gestion des ressources et la conception de réseaux de services restent limités. La présente thèse a pour objectif de combler cette lacune en faisant l’examen de problèmes de conception de réseaux de services prenant en compte la gestion des ressources. Pour ce faire, cette thèse se décline en trois études portant sur la conception de réseaux. La première étude considère le problème de capacitated multi-commodity fixed cost network design with design-balance constraints(DBCMND). La structure multi-produits avec capacité sur les arcs du DBCMND, de même que ses contraintes design-balance, font qu’il apparaît comme sous-problème dans de nombreux problèmes reliés à la conception de réseaux de services, d’où l’intérêt d’étudier le DBCMND dans le contexte de cette thèse. Nous proposons une nouvelle approche pour résoudre ce problème combinant la recherche tabou, la recomposition de chemin, et une procédure d’intensification de la recherche dans une région particulière de l’espace de solutions. Dans un premier temps la recherche tabou identifie de bonnes solutions réalisables. Ensuite la recomposition de chemin est utilisée pour augmenter le nombre de solutions réalisables. Les solutions trouvées par ces deux méta-heuristiques permettent d’identifier un sous-ensemble d’arcs qui ont de bonnes chances d’avoir un statut ouvert ou fermé dans une solution optimale. Le statut de ces arcs est alors fixé selon la valeur qui prédomine dans les solutions trouvées préalablement. Enfin, nous utilisons la puissance d’un solveur de programmation mixte en nombres entiers pour intensifier la recherche sur le problème restreint par le statut fixé ouvert/fermé de certains arcs. Les tests montrent que cette approche est capable de trouver de bonnes solutions aux problèmes de grandes tailles dans des temps raisonnables. Cette recherche est publiée dans la revue scientifique Journal of heuristics. La deuxième étude introduit la gestion des ressources au niveau de la conception de réseaux de services en prenant en compte explicitement le nombre fini de véhicules utilisés à chaque terminal pour le transport de produits. Une approche de solution faisant appel au slope-scaling, la génération de colonnes et des heuristiques basées sur une formulation en cycles est ainsi proposée. La génération de colonnes résout une relaxation linéaire du problème de conception de réseaux, générant des colonnes qui sont ensuite utilisées par le slope-scaling. Le slope-scaling résout une approximation linéaire du problème de conception de réseaux, d’où l’utilisation d’une heuristique pour convertir les solutions obtenues par le slope-scaling en solutions réalisables pour le problème original. L’algorithme se termine avec une procédure de perturbation qui améliore les solutions réalisables. Les tests montrent que l’algorithme proposé est capable de trouver de bonnes solutions au problème de conception de réseaux de services avec un nombre fixe des ressources à chaque terminal. Les résultats de cette recherche seront publiés dans la revue scientifique Transportation Science. La troisième étude élargie nos considérations sur la gestion des ressources en prenant en compte l’achat ou la location de nouvelles ressources de même que le repositionnement de ressources existantes. Nous faisons les hypothèses suivantes: une unité de ressource est nécessaire pour faire fonctionner un service, chaque ressource doit retourner à son terminal d’origine, il existe un nombre fixe de ressources à chaque terminal, et la longueur du circuit des ressources est limitée. Nous considérons les alternatives suivantes dans la gestion des ressources: 1) repositionnement de ressources entre les terminaux pour tenir compte des changements de la demande, 2) achat et/ou location de nouvelles ressources et leur distribution à différents terminaux, 3) externalisation de certains services. Nous présentons une formulation intégrée combinant les décisions reliées à la gestion des ressources avec les décisions reliées à la conception des réseaux de services. Nous présentons également une méthode de résolution matheuristique combinant le slope-scaling et la génération de colonnes. Nous discutons des performances de cette méthode de résolution, et nous faisons une analyse de l’impact de différentes décisions de gestion des ressources dans le contexte de la conception de réseaux de services. Cette étude sera présentée au XII International Symposium On Locational Decision, en conjonction avec XXI Meeting of EURO Working Group on Locational Analysis, Naples/Capri (Italy), 2014. En résumé, trois études différentes sont considérées dans la présente thèse. La première porte sur une nouvelle méthode de solution pour le "capacitated multi-commodity fixed cost network design with design-balance constraints". Nous y proposons une matheuristique comprenant la recherche tabou, la recomposition de chemin, et l’optimisation exacte. Dans la deuxième étude, nous présentons un nouveau modèle de conception de réseaux de services prenant en compte un nombre fini de ressources à chaque terminal. Nous y proposons une matheuristique avancée basée sur la formulation en cycles comprenant le slope-scaling, la génération de colonnes, des heuristiques et l’optimisation exacte. Enfin, nous étudions l’allocation des ressources dans la conception de réseaux de services en introduisant des formulations qui modèlent le repositionnement, l’acquisition et la location de ressources, et l’externalisation de certains services. À cet égard, un cadre de solution slope-scaling développé à partir d’une formulation en cycles est proposé. Ce dernier comporte la génération de colonnes et une heuristique. Les méthodes proposées dans ces trois études ont montré leur capacité à trouver de bonnes solutions.

Web Service Composition Systems for the Web Service Challenge - A Detailed Review

This report gives a detailed discussion on the system, algorithms, and techniques that we have applied in order to solve the Web Service Challenges (WSC) of the years 2006 and 2007. These international contests are focused on semantic web service composition. In each challenge of the contests, a repository of web services is given. The input and output parameters of the services in the repository are annotated with semantic concepts. A query to a semantic composition engine contains a set of available input concepts and a set of wanted output concepts. In order to employ an offered service for a requested role, the concepts of the input parameters of the offered operations must be more general than requested (contravariance). In contrast, the concepts of the output parameters of the offered service must be more specific than requested (covariance). The engine should respond to a query by providing a valid composition as fast as possible. We discuss three different methods for web service composition: an uninformed search in form of an IDDFS algorithm, a greedy informed search based on heuristic functions, and a multi-objective genetic algorithm.