SOP: Parallel surrogate global optimization with Pareto center selection for computationally expensive single objective problems

This paper presents a parallel surrogate-based global optimization method for computationally expensive objective functions that is more effective for larger numbers of processors. To reach this goal, we integrated concepts from multi-objective optimization and tabu search into, single objective, surrogate optimization. Our proposed derivative-free algorithm, called SOP, uses non-dominated sorting of points for which the expensive function has been previously evaluated. The two objectives are the expensive function value of the point and the minimum distance of the point to previously evaluated points. Based on the results of non-dominated sorting, P points from the sorted fronts are selected as centers from which many candidate points are generated by random perturbations. Based on surrogate approximation, the best candidate point is subsequently selected for expensive evaluation for each of the P centers, with simultaneous computation on P processors. Centers that previously did not generate good solutions are tabu with a given tenure. We show almost sure convergence of this algorithm under some conditions. The performance of SOP is compared with two RBF based methods. The test results show that SOP is an efficient method that can reduce time required to find a good near optimal solution. In a number of cases the efficiency of SOP is so good that SOP with 8 processors found an accurate answer in less wall-clock time than the other algorithms did with 32 processors.

New algorithms for automated phylogenetic reconstruction using artificial intelligence and data mining techniques

Academic and industrial research in the late 90s have brought about an exponential explosion of DNA sequence data. Automated expert systems are being created to help biologists to extract patterns, trends and links from this ever-deepening ocean of information. Two such systems aimed on retrieving and subsequently utilizing phylogenetically relevant information have been developed in this dissertation, the major objective of which was to automate the often difficult and confusing phylogenetic reconstruction process. ^ Popular phylogenetic reconstruction methods, such as distance-based methods, attempt to find an optimal tree topology (that reflects the relationships among related sequences and their evolutionary history) by searching through the topology space. Various compromises between the fast (but incomplete) and exhaustive (but computationally prohibitive) search heuristics have been suggested. An intelligent compromise algorithm that relies on a flexible “beam” search principle from the Artificial Intelligence domain and uses the pre-computed local topology reliability information to adjust the beam search space continuously is described in the second chapter of this dissertation. ^ However, sometimes even a (virtually) complete distance-based method is inferior to the significantly more elaborate (and computationally expensive) maximum likelihood (ML) method. In fact, depending on the nature of the sequence data in question either method might prove to be superior. Therefore, it is difficult (even for an expert) to tell a priori which phylogenetic reconstruction method—distance-based, ML or maybe maximum parsimony (MP)—should be chosen for any particular data set. ^ A number of factors, often hidden, influence the performance of a method. For example, it is generally understood that for a phylogenetically “difficult” data set more sophisticated methods (e.g., ML) tend to be more effective and thus should be chosen. However, it is the interplay of many factors that one needs to consider in order to avoid choosing an inferior method (potentially a costly mistake, both in terms of computational expenses and in terms of reconstruction accuracy.) ^ Chapter III of this dissertation details a phylogenetic reconstruction expert system that selects a superior proper method automatically. It uses a classifier (a Decision Tree-inducing algorithm) to map a new data set to the proper phylogenetic reconstruction method. ^

Design and Optimization of Power Delivery and Distribution Systems Using Evolutionary Computation Techniques

Nowadays computing platforms consist of a very large number of components that require to be supplied with diferent voltage levels and power requirements. Even a very small platform, like a handheld computer, may contain more than twenty diferent loads and voltage regulators. The power delivery designers of these systems are required to provide, in a very short time, the right power architecture that optimizes the performance, meets electrical specifications plus cost and size targets. The appropriate selection of the architecture and converters directly defines the performance of a given solution. Therefore, the designer needs to be able to evaluate a significant number of options in order to know with good certainty whether the selected solutions meet the size, energy eficiency and cost targets. The design dificulties of selecting the right solution arise due to the wide range of power conversion products provided by diferent manufacturers. These products range from discrete components (to build converters) to complete power conversion modules that employ diferent manufacturing technologies. Consequently, in most cases it is not possible to analyze all the alternatives (combinations of power architectures and converters) that can be built. The designer has to select a limited number of converters in order to simplify the analysis. In this thesis, in order to overcome the mentioned dificulties, a new design methodology for power supply systems is proposed. This methodology integrates evolutionary computation techniques in order to make possible analyzing a large number of possibilities. This exhaustive analysis helps the designer to quickly define a set of feasible solutions and select the best trade-off in performance according to each application. The proposed approach consists of two key steps, one for the automatic generation of architectures and other for the optimized selection of components. In this thesis are detailed the implementation of these two steps. The usefulness of the methodology is corroborated by contrasting the results using real problems and experiments designed to test the limits of the algorithms.

An improved bit parallel exact maximum clique algorithm

This paper describes new improvements for BB-MaxClique (San Segundo et al. in Comput Oper Resour 38(2):571–581, 2011 ), a leading maximum clique algorithm which uses bit strings to efficiently compute basic operations during search by bit masking. Improvements include a recently described recoloring strategy in Tomita et al. (Proceedings of the 4th International Workshop on Algorithms and Computation. Lecture Notes in Computer Science, vol 5942. Springer, Berlin, pp 191–203, 2010 ), which is now integrated in the bit string framework, as well as different optimization strategies for fast bit scanning. Reported results over DIMACS and random graphs show that the new variants improve over previous BB-MaxClique for a vast majority of cases. It is also established that recoloring is mainly useful for graphs with high densities.

Projector Model for Efficient List-Mode Reconstruction in PET Scanners with Parallel Planar Detectors

We have developed a new projector model specifically tailored for fast list-mode tomographic reconstructions in Positron emission tomography (PET) scanners with parallel planar detectors. The model provides an accurate estimation of the probability distribution of coincidence events defined by pairs of scintillating crystals. This distribution is parameterized with 2D elliptical Gaussian functions defined in planes perpendicular to the main axis of the tube of response (TOR). The parameters of these Gaussian functions have been obtained by fitting Monte Carlo simulations that include positron range, acolinearity of gamma rays, as well as detector attenuation and scatter effects. The proposed model has been applied efficiently to list-mode reconstruction algorithms. Evaluation with Monte Carlo simulations over a rotating high resolution PET scanner indicates that this model allows to obtain better recovery to noise ratio in OSEM (ordered-subsets, expectation-maximization) reconstruction, if compared to list-mode reconstruction with symmetric circular Gaussian TOR model, and histogram-based OSEM with precalculated system matrix using Monte Carlo simulated models and symmetries.

Particle methods parallel implementations by GP-GPU strategies

This paper outlines the problems found in the parallelization of SPH (Smoothed Particle Hydrodynamics) algorithms using Graphics Processing Units. Different results of some parallel GPU implementations in terms of the speed-up and the scalability compared to the CPU sequential codes are shown. The most problematic stage in the GPU-SPH algorithms is the one responsible for locating neighboring particles and building the vectors where this information is stored, since these specific algorithms raise many dificulties for a data-level parallelization. Because of the fact that the neighbor location using linked lists does not show enough data-level parallelism, two new approaches have been pro- posed to minimize bank conflicts in the writing and subsequent reading of the neighbor lists. The first strategy proposes an efficient coordination between CPU-GPU, using GPU algorithms for those stages that allow a straight forward parallelization, and sequential CPU algorithms for those instructions that involve some kind of vector reduction. This coordination provides a relatively orderly reading of the neighbor lists in the interactions stage, achieving a speed-up factor of x47 in this stage. However, since the construction of the neighbor lists is quite expensive, it is achieved an overall speed-up of x41. The second strategy seeks to maximize the use of the GPU in the neighbor's location process by executing a specific vector sorting algorithm that allows some data-level parallelism. Al- though this strategy has succeeded in improving the speed-up on the stage of neighboring location, the global speed-up on the interactions stage falls, due to inefficient reading of the neighbor vectors. Some changes to these strategies are proposed, aimed at maximizing the computational load of the GPU and using the GPU texture-units, in order to reach the maximum speed-up for such codes. Different practical applications have been added to the mentioned GPU codes. First, the classical dam-break problem is studied. Second, the wave impact of the sloshing fluid contained in LNG vessel tanks is also simulated as a practical example of particle methods

Visual Servoing for the Robotenis System: a Strategy for a 3 DOF Parallel Robot to Hit a Ping-Pong Ball

This article describes a new visual servo control and strategies that are used to carry out dynamic tasks by the Robotenis platform. This platform is basically a parallel robot that is equipped with an acquisition and processing system of visual information, its main feature is that it has a completely open architecture control, and planned in order to design, implement, test and compare control strategies and algorithms (visual and actuated joint controllers). Following sections describe a new visual control strategy specially designed to track and intercept objects in 3D space. The results are compared with a controller shown in previous woks, where the end effector of the robot keeps a constant distance from the tracked object. In this work, the controller is specially designed in order to allow changes in the tracking reference. Changes in the tracking reference can be used to grip an object that is under movement, or as in this case, hitting a hanging Ping-Pong ball. Lyapunov stability is taken into account in the controller design.

High Performance Algorithms and Implementations Using Sparse and Parallelization Techniques on MBS

In this paper we will see how the efficiency of the MBS simulations can be improved in two different ways, by considering both an explicit and implicit semi-recursive formulation. The explicit method is based on a double velocity transformation that involves the solution of a redundant but compatible system of equations. The high computational cost of this operation has been drastically reduced by taking into account the sparsity pattern of the system. Regarding this, the goal of this method is the introduction of MA48, a high performance mathematical library provided by Harwell Subroutine Library. The second method proposed in this paper has the particularity that, depending on the case, between 70 and 85% of the computation time is devoted to the evaluation of forces derivatives with respect to the relative position and velocity vectors. Keeping in mind that evaluating these derivatives can be decomposed into concurrent tasks, the main goal of this paper lies on a successful and straightforward parallel implementation that have led to a substantial improvement with a speedup of 3.2 by keeping all the cores busy in a quad-core processor and distributing the workload between them, achieving on this way a huge time reduction by doing an ideal CPU usage

A review of estimation of distribution algorithms in bioinformatics

Evolutionary search algorithms have become an essential asset in the algorithmic toolbox for solving high-dimensional optimization problems in across a broad range of bioinformatics problems. Genetic algorithms, the most well-known and representative evolutionary search technique, have been the subject of the major part of such applications. Estimation of distribution algorithms (EDAs) offer a novel evolutionary paradigm that constitutes a natural and attractive alternative to genetic algorithms. They make use of a probabilistic model, learnt from the promising solutions, to guide the search process. In this paper, we set out a basic taxonomy of EDA techniques, underlining the nature and complexity of the probabilistic model of each EDA variant. We review a set of innovative works that make use of EDA techniques to solve challenging bioinformatics problems, emphasizing the EDA paradigm's potential for further research in this domain.

Annotation algorithms for unrestricted independent and-parallelism in logic programs

We present two new algorithms which perform automatic parallelization via source-to-source transformations. The objective is to exploit goal-level, unrestricted independent and-parallelism. The proposed algorithms use as targets new parallel execution primitives which are simpler and more flexible than the well-known &/2 parallel operator. This makes it possible to genérate better parallel expressions by exposing more potential parallelism among the literals of a clause than is possible with &/2. The difference between the two algorithms stems from whether the order of the solutions obtained is preserved or not. We also report on a preliminary evaluation of an implementation of our approach. We compare the performance obtained to that of previous annotation algorithms and show that relevant improvements can be obtained.

Relating goal scheduling, precedence, and memory management in and-parallel execution of logic programs

The interactions among three important issues involved in the implementation of logic programs in parallel (goal scheduling, precedence, and memory management) are discussed. A simplified, parallel memory management model and an efficient, load-balancing goal scheduling strategy are presented. It is shown how, for systems which support "don't know" non-determinism, special care has to be taken during goal scheduling if the space recovery characteristics of sequential systems are to be preserved. A solution based on selecting only "newer" goals for execution is described, and an algorithm is proposed for efficiently maintaining and determining precedence relationships and variable ages across parallel goals. It is argued that the proposed schemes and algorithms make it possible to extend the storage performance of sequential systems to parallel execution without the considerable overhead previously associated with it. The results are applicable to a wide class of parallel and coroutining systems, and they represent an efficient alternative to "all heap" or "spaghetti stack" allocation models.

B-LOG: A branch and bound methodology for the parallel execution of logic programs

We propose a computational methodology -"B-LOG"-, which offers the potential for an effective implementation of Logic Programming in a parallel computer. We also propose a weighting scheme to guide the search process through the graph and we apply the concepts of parallel "branch and bound" algorithms in order to perform a "best-first" search using an information theoretic bound. The concept of "session" is used to speed up the search process in a succession of similar queries. Within a session, we strongly modify the bounds in a local database, while bounds kept in a global database are weakly modified to provide a better initial condition for other sessions. We also propose an implementation scheme based on a database machine using "semantic paging", and the "B-LOG processor" based on a scoreboard driven controller.

Design equations for reinforced concrete members strengthened in shear with external FRP reinforcement formulated in an evolutionary multi-objective framework

Methods for predicting the shear capacity of FRP shear strengthened RC beams assume the traditional approach of superimposing the contribution of the FRP reinforcing to the contributions from the reinforcing steel and the concrete. These methods become the basis for most guides for the design of externally bonded FRP systems for strengthening concrete structures. The variations among them come from the way they account for the effect of basic shear design parameters on shear capacity. This paper presents a simple method for defining improved equations to calculate the shear capacity of reinforced concrete beams externally shear strengthened with FRP. For the first time, the equations are obtained in a multiobjective optimization framework solved by using genetic algorithms, resulting from considering simultaneously the experimental results of beams with and without FRP external reinforcement. The performance of the new proposed equations is compared to the predictions with some of the current shear design guidelines for strengthening concrete structures using FRPs. The proposed procedure is also reformulated as a constrained optimization problem to provide more conservative shear predictions.

Modeling, simulation and application of bacterial transduction in genetic algorithms

At present, all methods in Evolutionary Computation are bioinspired by the fundamental principles of neo-Darwinism, as well as by a vertical gene transfer. Virus transduction is one of the key mechanisms of horizontal gene propagation in microorganisms (e.g. bacteria). In the present paper, we model and simulate a transduction operator, exploring the possible role and usefulness of transduction in a genetic algorithm. The genetic algorithm including transduction has been named PETRI (abbreviation of Promoting Evolution Through Reiterated Infection). Our results showed how PETRI approaches higher fitness values as transduction probability comes close to 100%. The conclusion is that transduction improves the performance of a genetic algorithm, assuming a population divided among several sub-populations or ?bacterial colonies?.

Orthogonal MCMC algorithms

Monte Carlo (MC) methods are widely used in signal processing, machine learning and stochastic optimization. A well-known class of MC methods are Markov Chain Monte Carlo (MCMC) algorithms. In this work, we introduce a novel parallel interacting MCMC scheme, where the parallel chains share information using another MCMC technique working on the entire population of current states. These parallel ?vertical? chains are led by random-walk proposals, whereas the ?horizontal? MCMC uses a independent proposal, which can be easily adapted by making use of all the generated samples. Numerical results show the advantages of the proposed sampling scheme in terms of mean absolute error, as well as robustness w.r.t. to initial values and parameter choice.