Parameter Identification of a Fed-Batch Cultivation of S. Cerevisiae using Genetic Algorithms

Fermentation processes as objects of modelling and high-quality control are characterized with interdependence and time-varying of process variables that lead to non-linear models with a very complex structure. This is why the conventional optimization methods cannot lead to a satisfied solution. As an alternative, genetic algorithms, like the stochastic global optimization method, can be applied to overcome these limitations. The application of genetic algorithms is a precondition for robustness and reaching of a global minimum that makes them eligible and more workable for parameter identification of fermentation models. Different types of genetic algorithms, namely simple, modified and multi-population ones, have been applied and compared for estimation of nonlinear dynamic model parameters of fed-batch cultivation of S. cerevisiae.

Optimization of adaptive traffic signal control with transit signal priority at isolated intersections using parallel genetic algorithms

Optimization of adaptive traffic signal timing is one of the most complex problems in traffic control systems. This dissertation presents a new method that applies the parallel genetic algorithm (PGA) to optimize adaptive traffic signal control in the presence of transit signal priority (TSP). The method can optimize the phase plan, cycle length, and green splits at isolated intersections with consideration for the performance of both the transit and the general vehicles. Unlike the simple genetic algorithm (GA), PGA can provide better and faster solutions needed for real-time optimization of adaptive traffic signal control. ^ An important component in the proposed method involves the development of a microscopic delay estimation model that was designed specifically to optimize adaptive traffic signal with TSP. Macroscopic delay models such as the Highway Capacity Manual (HCM) delay model are unable to accurately consider the effect of phase combination and phase sequence in delay calculations. In addition, because the number of phases and the phase sequence of adaptive traffic signal may vary from cycle to cycle, the phase splits cannot be optimized when the phase sequence is also a decision variable. A "flex-phase" concept was introduced in the proposed microscopic delay estimation model to overcome these limitations. ^ The performance of PGA was first evaluated against the simple GA. The results show that PGA achieved both faster convergence and lower delay for both under- or over-saturated traffic conditions. A VISSIM simulation testbed was then developed to evaluate the performance of the proposed PGA-based adaptive traffic signal control with TSP. The simulation results show that the PGA-based optimizer for adaptive TSP outperformed the fully actuated NEMA control in all test cases. The results also show that the PGA-based optimizer was able to produce TSP timing plans that benefit the transit vehicles while minimizing the impact of TSP on the general vehicles. The VISSIM testbed developed in this research provides a powerful tool to design and evaluate different TSP strategies under both actuated and adaptive signal control. ^

Comparison of three algorithms for nonlinear metal cutting problems

This paper compares three alternative numerical algorithms applied to a nonlinear metal cutting problem. One algorithm is based on an explicit method and the other two are implicit. Domain decomposition (DD) is used to break the original domain into subdomains, each containing a properly connected, well-formulated and continuous subproblem. The serial version of the explicit algorithm is implemented in FORTRAN and its parallel version uses MPI (Message Passing Interface) calls. One implicit algorithm is implemented by coupling the state-of-the-art PETSc (Portable, Extensible Toolkit for Scientific Computation) software with in-house software in order to solve the subproblems. The second implicit algorithm is implemented completely within PETSc. PETSc uses MPI as the underlying communication library. Finally, a 2D example is used to test the algorithms and various comparisons are made.

Efficient algorithms to solve scheduling problems with a variety of optimization criteria

La programmation par contraintes est une technique puissante pour résoudre, entre autres, des problèmes d’ordonnancement de grande envergure. L’ordonnancement vise à allouer dans le temps des tâches à des ressources. Lors de son exécution, une tâche consomme une ressource à un taux constant. Généralement, on cherche à optimiser une fonction objectif telle la durée totale d’un ordonnancement. Résoudre un problème d’ordonnancement signifie trouver quand chaque tâche doit débuter et quelle ressource doit l’exécuter. La plupart des problèmes d’ordonnancement sont NP-Difficiles. Conséquemment, il n’existe aucun algorithme connu capable de les résoudre en temps polynomial. Cependant, il existe des spécialisations aux problèmes d’ordonnancement qui ne sont pas NP-Complet. Ces problèmes peuvent être résolus en temps polynomial en utilisant des algorithmes qui leur sont propres. Notre objectif est d’explorer ces algorithmes d’ordonnancement dans plusieurs contextes variés. Les techniques de filtrage ont beaucoup évolué dans les dernières années en ordonnancement basé sur les contraintes. La proéminence des algorithmes de filtrage repose sur leur habilité à réduire l’arbre de recherche en excluant les valeurs des domaines qui ne participent pas à des solutions au problème. Nous proposons des améliorations et présentons des algorithmes de filtrage plus efficaces pour résoudre des problèmes classiques d’ordonnancement. De plus, nous présentons des adaptations de techniques de filtrage pour le cas où les tâches peuvent être retardées. Nous considérons aussi différentes propriétés de problèmes industriels et résolvons plus efficacement des problèmes où le critère d’optimisation n’est pas nécessairement le moment où la dernière tâche se termine. Par exemple, nous présentons des algorithmes à temps polynomial pour le cas où la quantité de ressources fluctue dans le temps, ou quand le coût d’exécuter une tâche au temps t dépend de t.

Combination of Evolutionary Algorithms with Experimental Design, Traditional Optimization and Machine Learning

Evolutionary algorithms alone cannot solve optimization problems very efficiently since there are many random (not very rational) decisions in these algorithms. Combination of evolutionary algorithms and other techniques have been proven to be an efficient optimization methodology. In this talk, I will explain the basic ideas of our three algorithms along this line (1): Orthogonal genetic algorithm which treats crossover/mutation as an experimental design problem, (2) Multiobjective evolutionary algorithm based on decomposition (MOEA/D) which uses decomposition techniques from traditional mathematical programming in multiobjective optimization evolutionary algorithm, and (3) Regular model based multiobjective estimation of distribution algorithms (RM-MEDA) which uses the regular property and machine learning methods for improving multiobjective evolutionary algorithms.

I. Quantal effects in biochemical cooperativity and a proposed mechanism for the differentiation of calcium signaling in synaptic plasticity. II. Evolutionary algorithms for the optimization of methods in computational chemistry

In Part 1 of this thesis, we propose that biochemical cooperativity is a fundamentally non-ideal process. We show quantal effects underlying biochemical cooperativity and highlight apparent ergodic breaking at small volumes. The apparent ergodic breaking manifests itself in a divergence of deterministic and stochastic models. We further predict that this divergence of deterministic and stochastic results is a failure of the deterministic methods rather than an issue of stochastic simulations.

Ergodic breaking at small volumes may allow these molecular complexes to function as switches to a greater degree than has previously been shown. We propose that this ergodic breaking is a phenomenon that the synapse might exploit to differentiate Ca$^{2+}$ signaling that would lead to either the strengthening or weakening of a synapse. Techniques such as lattice-based statistics and rule-based modeling are tools that allow us to directly confront this non-ideality. A natural next step to understanding the chemical physics that underlies these processes is to consider \textit{in silico} specifically atomistic simulation methods that might augment our modeling efforts.

In the second part of this thesis, we use evolutionary algorithms to optimize \textit{in silico} methods that might be used to describe biochemical processes at the subcellular and molecular levels. While we have applied evolutionary algorithms to several methods, this thesis will focus on the optimization of charge equilibration methods. Accurate charges are essential to understanding the electrostatic interactions that are involved in ligand binding, as frequently discussed in the first part of this thesis.

Optimization of Pattern Matching Algorithms for Multi- and Many-Core Platforms

Image and video compression play a major role in the world today, allowing the storage and transmission of large multimedia content volumes. However, the processing of this information requires high computational resources, hence the improvement of the computational performance of these compression algorithms is very important. The Multidimensional Multiscale Parser (MMP) is a pattern-matching-based compression algorithm for multimedia contents, namely images, achieving high compression ratios, maintaining good image quality, Rodrigues et al. [2008]. However, in comparison with other existing algorithms, this algorithm takes some time to execute. Therefore, two parallel implementations for GPUs were proposed by Ribeiro [2016] and Silva [2015] in CUDA and OpenCL-GPU, respectively. In this dissertation, to complement the referred work, we propose two parallel versions that run the MMP algorithm in CPU: one resorting to OpenMP and another that converts the existing OpenCL-GPU into OpenCL-CPU. The proposed solutions are able to improve the computational performance of MMP by 3 and 2:7 , respectively. The High Efficiency Video Coding (HEVC/H.265) is the most recent standard for compression of image and video. Its impressive compression performance, makes it a target for many adaptations, particularly for holoscopic image/video processing (or light field). Some of the proposed modifications to encode this new multimedia content are based on geometry-based disparity compensations (SS), developed by Conti et al. [2014], and a Geometric Transformations (GT) module, proposed by Monteiro et al. [2015]. These compression algorithms for holoscopic images based on HEVC present an implementation of specific search for similar micro-images that is more efficient than the one performed by HEVC, but its implementation is considerably slower than HEVC. In order to enable better execution times, we choose to use the OpenCL API as the GPU enabling language in order to increase the module performance. With its most costly setting, we are able to reduce the GT module execution time from 6.9 days to less then 4 hours, effectively attaining a speedup of 45 .

A Comparative Analysis Between Genetic Algorithms and Complex Nonlinear Least Squares on Electrical Impedance Characterization

This paper compares the performance of the complex nonlinear least squares algorithm implemented in the LEVM/LEVMW software with the performance of a genetic algorithm in the characterization of an electrical impedance of known topology. The effect of the number of measured frequency points and of measurement uncertainty on the estimation of circuit parameters is presented. The analysis is performed on the equivalent circuit impedance of a humidity sensor.

Effective procedure for the optimization of the linear controller in an industrial drive for a nonlinear mechanism

Il progetto di tesi è incentrato sull’ottimizzazione del procedimento di taratura dei regolatori lineari degli anelli di controllo di posizione e velocità presenti negli azionamenti usati industrialmente su macchine automatiche, specialmente quando il carico è ad inerzia variabile in dipendenza dalla posizione, dunque non lineare, come ad esempio un quadrilatero articolato. Il lavoro è stato svolto in collaborazione con l’azienda G.D S.p.A. ed il meccanismo di prova è realmente utilizzato nelle macchine automatiche per il packaging di sigarette. L’ottimizzazione si basa sulla simulazione in ambiente Matlab/Simulink dell’intero sistema di controllo, cioè comprensivo del modello Simulink degli anelli di controllo del drive, inclusa la dinamica elettrica del motore, e del modello Simscape del meccanismo, perciò una prima necessaria fase del lavoro è stata la validazione di tali modelli affinché fossero sufficientemente fedeli al comportamento reale. Il secondo passo è stato fornire una prima taratura di tentativo che fungesse da punto di partenza per l’algoritmo di ottimizzazione, abbiamo fatto ciò linearizzando il modello meccanico con l’inerzia minima e utilizzando il metodo delle formule di inversione per determinare i parametri di controllo. Già questa taratura, seppur conservativa, ha portato ad un miglioramento delle performance del sistema rispetto alla taratura empirica comunemente fatta in ambito industriale. Infine, abbiamo lanciato l’algoritmo di ottimizzazione definendo opportunamente la funzione di costo, ed il risultato è stato decisamente positivo, portando ad un miglioramento medio del massimo errore di inseguimento di circa il 25%, ma anche oltre il 30% in alcuni casi.

Adjustable robust optimization with nonlinear recourses

Over the last century, mathematical optimization has become a prominent tool for decision making. Its systematic application in practical fields such as economics, logistics or defense led to the development of algorithmic methods with ever increasing efficiency. Indeed, for a variety of real-world problems, finding an optimal decision among a set of (implicitly or explicitly) predefined alternatives has become conceivable in reasonable time. In the last decades, however, the research community raised more and more attention to the role of uncertainty in the optimization process. In particular, one may question the notion of optimality, and even feasibility, when studying decision problems with unknown or imprecise input parameters. This concern is even more critical in a world becoming more and more complex —by which we intend, interconnected —where each individual variation inside a system inevitably causes other variations in the system itself. In this dissertation, we study a class of optimization problems which suffer from imprecise input data and feature a two-stage decision process, i.e., where decisions are made in a sequential order —called stages —and where unknown parameters are revealed throughout the stages. The applications of such problems are plethora in practical fields such as, e.g., facility location problems with uncertain demands, transportation problems with uncertain costs or scheduling under uncertain processing times. The uncertainty is dealt with a robust optimization (RO) viewpoint (also known as "worst-case perspective") and we present original contributions to the RO literature on both the theoretical and practical side.

Models and algorithms for real-world optimization problems

This thesis deals with efficient solution of optimization problems of practical interest. The first part of the thesis deals with bin packing problems. The bin packing problem (BPP) is one of the oldest and most fundamental combinatorial optimiza- tion problems. The bin packing problem and its generalizations arise often in real-world ap- plications, from manufacturing industry, logistics and transportation of goods, and scheduling. After an introductory chapter, I will present two applications of two of the most natural extensions of the bin packing: Chapter 2 will be dedicated to an application of bin packing in two dimension to a problem of scheduling a set of computational tasks on a computer cluster, while Chapter 3 deals with the generalization of BPP in three dimensions that arise frequently in logistic and transportation, often com- plemented with additional constraints on the placement of items and characteristics of the solution, like, for example, guarantees on the stability of the items, to avoid potential damage to the transported goods, on the distribution of the total weight of the bins, and on compatibility with loading and unloading operations. The second part of the thesis, and in particular Chapter 4 considers the Trans- mission Expansion Problem (TEP), where an electrical transmission grid must be expanded so as to satisfy future energy demand at the minimum cost, while main- taining some guarantees of robustness to potential line failures. These problems are gaining importance in a world where a shift towards renewable energy can impose a significant geographical reallocation of generation capacities, resulting in the ne- cessity of expanding current power transmission grids.

PARTIAL STABILITY FOR A CLASS OF NONLINEAR SYSTEMS

This paper studies a nonlinear, discrete-time matrix system arising in the stability analysis of Kalman filters. These systems present an internal coupling between the state components that gives rise to complex dynamic behavior. The problem of partial stability, which requires that a specific component of the state of the system converge exponentially, is studied and solved. The convergent state component is strongly linked with the behavior of Kalman filters, since it can be used to provide bounds for the error covariance matrix under uncertainties in the noise measurements. We exploit the special features of the system-mainly the connections with linear systems-to obtain an algebraic test for partial stability. Finally, motivated by applications in which polynomial divergence of the estimates is acceptable, we study and solve a partial semistability problem.

Node-Depth Encoding and Multiobjective Evolutionary Algorithm Applied to Large-Scale Distribution System Reconfiguration

The power loss reduction in distribution systems (DSs) is a nonlinear and multiobjective problem. Service restoration in DSs is even computationally hard since it additionally requires a solution in real-time. Both DS problems are computationally complex. For large-scale networks, the usual problem formulation has thousands of constraint equations. The node-depth encoding (NDE) enables a modeling of DSs problems that eliminates several constraint equations from the usual formulation, making the problem solution simpler. On the other hand, a multiobjective evolutionary algorithm (EA) based on subpopulation tables adequately models several objectives and constraints, enabling a better exploration of the search space. The combination of the multiobjective EA with NDE (MEAN) results in the proposed approach for solving DSs problems for large-scale networks. Simulation results have shown the MEAN is able to find adequate restoration plans for a real DS with 3860 buses and 632 switches in a running time of 0.68 s. Moreover, the MEAN has shown a sublinear running time in function of the system size. Tests with networks ranging from 632 to 5166 switches indicate that the MEAN can find network configurations corresponding to a power loss reduction of 27.64% for very large networks requiring relatively low running time.

GOOAL: A routine based on Genetic Algorithms to track harmonics in electric power systems

Voltage and current waveforms of a distribution or transmission power system are not pure sinusoids. There are distortions in these waveforms that can be represented as a combination of the fundamental frequency, harmonics and high frequency transients. This paper presents a novel approach to identifying harmonics in power system distorted waveforms. The proposed method is based on Genetic Algorithms, which is an optimization technique inspired by genetics and natural evolution. GOOAL, a specially designed intelligent algorithm for optimization problems, was successfully implemented and tested. Two kinds of representations concerning chromosomes are utilized: binary and real. The results show that the proposed method is more precise than the traditional Fourier Transform, especially considering the real representation of the chromosomes.

Optimization of modal filters based on arrays of piezoelectric sensors

Modal filters may be obtained by a properly designed weighted sum of the output signals of an array of sensors distributed on the host structure. Although several research groups have been interested in techniques for designing and implementing modal filters based on a given array of sensors, the effect of the array topology on the effectiveness of the modal filter has received much less attention. In particular, it is known that some parameters, such as size, shape and location of a sensor, are very important in determining the observability of a vibration mode. Hence, this paper presents a methodology for the topological optimization of an array of sensors in order to maximize the effectiveness of a set of selected modal filters. This is done using a genetic algorithm optimization technique for the selection of 12 piezoceramic sensors from an array of 36 piezoceramic sensors regularly distributed on an aluminum plate, which maximize the filtering performance, over a given frequency range, of a set of modal filters, each one aiming to isolate one of the first vibration modes. The vectors of the weighting coefficients for each modal filter are evaluated using QR decomposition of the complex frequency response function matrix. Results show that the array topology is not very important for lower frequencies but it greatly affects the filter effectiveness for higher frequencies. Therefore, it is possible to improve the effectiveness and frequency range of a set of modal filters by optimizing the topology of an array of sensors. Indeed, using 12 properly located piezoceramic sensors bonded on an aluminum plate it is shown that the frequency range of a set of modal filters may be enlarged by 25-50%.