Optimization strategies for fast detection of positive selection on phylogenetic trees.

MOTIVATION: The detection of positive selection is widely used to study gene and genome evolution, but its application remains limited by the high computational cost of existing implementations. We present a series of computational optimizations for more efficient estimation of the likelihood function on large-scale phylogenetic problems. We illustrate our approach using the branch-site model of codon evolution. RESULTS: We introduce novel optimization techniques that substantially outperform both CodeML from the PAML package and our previously optimized sequential version SlimCodeML. These techniques can also be applied to other likelihood-based phylogeny software. Our implementation scales well for large numbers of codons and/or species. It can therefore analyse substantially larger datasets than CodeML. We evaluated FastCodeML on different platforms and measured average sequential speedups of FastCodeML (single-threaded) versus CodeML of up to 5.8, average speedups of FastCodeML (multi-threaded) versus CodeML on a single node (shared memory) of up to 36.9 for 12 CPU cores, and average speedups of the distributed FastCodeML versus CodeML of up to 170.9 on eight nodes (96 CPU cores in total).Availability and implementation: ftp://ftp.vital-it.ch/tools/FastCodeML/. CONTACT: selectome@unil.ch or nicolas.salamin@unil.ch.

Identifying the preferred subset of enzymatic profiles in nonlinear kinetic metabolic models via multiobjective global optimization and pareto filters

Optimization models in metabolic engineering and systems biology focus typically on optimizing a unique criterion, usually the synthesis rate of a metabolite of interest or the rate of growth. Connectivity and non-linear regulatory effects, however, make it necessary to consider multiple objectives in order to identify useful strategies that balance out different metabolic issues. This is a fundamental aspect, as optimization of maximum yield in a given condition may involve unrealistic values in other key processes. Due to the difficulties associated with detailed non-linear models, analysis using stoichiometric descriptions and linear optimization methods have become rather popular in systems biology. However, despite being useful, these approaches fail in capturing the intrinsic nonlinear nature of the underlying metabolic systems and the regulatory signals involved. Targeting more complex biological systems requires the application of global optimization methods to non-linear representations. In this work we address the multi-objective global optimization of metabolic networks that are described by a special class of models based on the power-law formalism: the generalized mass action (GMA) representation. Our goal is to develop global optimization methods capable of efficiently dealing with several biological criteria simultaneously. In order to overcome the numerical difficulties of dealing with multiple criteria in the optimization, we propose a heuristic approach based on the epsilon constraint method that reduces the computational burden of generating a set of Pareto optimal alternatives, each achieving a unique combination of objectives values. To facilitate the post-optimal analysis of these solutions and narrow down their number prior to being tested in the laboratory, we explore the use of Pareto filters that identify the preferred subset of enzymatic profiles. We demonstrate the usefulness of our approach by means of a case study that optimizes the ethanol production in the fermentation of Saccharomyces cerevisiae.

Generating Aesthetically Pleasing Images in a Virtual Environment using Particle Swarm Optimization

This research focuses on generating aesthetically pleasing images in virtual environments using the particle swarm optimization (PSO) algorithm. The PSO is a stochastic population based search algorithm that is inspired by the flocking behavior of birds. In this research, we implement swarms of cameras flying through a virtual world in search of an image that is aesthetically pleasing. Virtual world exploration using particle swarm optimization is considered to be a new research area and is of interest to both the scientific and artistic communities. Aesthetic rules such as rule of thirds, subject matter, colour similarity and horizon line are all analyzed together as a multi-objective problem to analyze and solve with rendered images. A new multi-objective PSO algorithm, the sum of ranks PSO, is introduced. It is empirically compared to other single-objective and multi-objective swarm algorithms. An advantage of the sum of ranks PSO is that it is useful for solving high-dimensional problems within the context of this research. Throughout many experiments, we show that our approach is capable of automatically producing images satisfying a variety of supplied aesthetic criteria.

Analysis and Optimization of Machining Process Using Evolutionary Algorithms

To ensure quality of machined products at minimum machining costs and maximum machining effectiveness, it is very important to select optimum parameters when metal cutting machine tools are employed. Traditionally, the experience of the operator plays a major role in the selection of optimum metal cutting conditions. However, attaining optimum values each time by even a skilled operator is difficult. The non-linear nature of the machining process has compelled engineers to search for more effective methods to attain optimization. The design objective preceding most engineering design activities is simply to minimize the cost of production or to maximize the production efficiency. The main aim of research work reported here is to build robust optimization algorithms by exploiting ideas that nature has to offer from its backyard and using it to solve real world optimization problems in manufacturing processes.In this thesis, after conducting an exhaustive literature review, several optimization techniques used in various manufacturing processes have been identified. The selection of optimal cutting parameters, like depth of cut, feed and speed is a very important issue for every machining process. Experiments have been designed using Taguchi technique and dry turning of SS420 has been performed on Kirlosker turn master 35 lathe. Analysis using S/N and ANOVA were performed to find the optimum level and percentage of contribution of each parameter. By using S/N analysis the optimum machining parameters from the experimentation is obtained.Optimization algorithms begin with one or more design solutions supplied by the user and then iteratively check new design solutions, relative search spaces in order to achieve the true optimum solution. A mathematical model has been developed using response surface analysis for surface roughness and the model was validated using published results from literature.Methodologies in optimization such as Simulated annealing (SA), Particle Swarm Optimization (PSO), Conventional Genetic Algorithm (CGA) and Improved Genetic Algorithm (IGA) are applied to optimize machining parameters while dry turning of SS420 material. All the above algorithms were tested for their efficiency, robustness and accuracy and observe how they often outperform conventional optimization method applied to difficult real world problems. The SA, PSO, CGA and IGA codes were developed using MATLAB. For each evolutionary algorithmic method, optimum cutting conditions are provided to achieve better surface finish.The computational results using SA clearly demonstrated that the proposed solution procedure is quite capable in solving such complicated problems effectively and efficiently. Particle Swarm Optimization (PSO) is a relatively recent heuristic search method whose mechanics are inspired by the swarming or collaborative behavior of biological populations. From the results it has been observed that PSO provides better results and also more computationally efficient.Based on the results obtained using CGA and IGA for the optimization of machining process, the proposed IGA provides better results than the conventional GA. The improved genetic algorithm incorporating a stochastic crossover technique and an artificial initial population scheme is developed to provide a faster search mechanism. Finally, a comparison among these algorithms were made for the specific example of dry turning of SS 420 material and arriving at optimum machining parameters of feed, cutting speed, depth of cut and tool nose radius for minimum surface roughness as the criterion. To summarize, the research work fills in conspicuous gaps between research prototypes and industry requirements, by simulating evolutionary procedures seen in nature that optimize its own systems.

Assessment of virtual design and manufacturing techniques for fibre reinforced composite materials

Virtual tools are commonly used nowadays to optimize product design and manufacturing process of fibre reinforced composite materials. The present work focuses on two areas of interest to forecast the part performance and the production process particularities. The first part proposes a multi-physical optimization tool to support the concept stage of a composite part. The strategy is based on the strategic handling of information and, through a single control parameter, is able to evaluate the effects of design variations throughout all these steps in parallel. The second part targets the resin infusion process and the impact of thermal effects. The numerical and experimental approach allowed the identificationof improvement opportunities regarding the implementation of algorithms in commercially available simulation software.

Modeling small-scale dairy farms in central Mexico using multi-criteria programming

Milk supply from Mexican dairy farms does not meet demand and small-scale farms can contribute toward closing the gap. Two multi-criteria programming techniques, goal programming and compromise programming, were used in a study of small-scale dairy farms in central Mexico. To build the goal and compromise programming models, 4 ordinary linear programming models were also developed, which had objective functions to maximize metabolizable energy for milk production, to maximize margin of income over feed costs, to maximize metabolizable protein for milk production, and to minimize purchased feedstuffs. Neither multicriteria approach was significantly better than the other; however, by applying both models it was possible to perform a more comprehensive analysis of these small-scale dairy systems. The multi-criteria programming models affirm findings from previous work and suggest that a forage strategy based on alfalfa, rye-grass, and corn silage would meet nutrient requirements of the herd. Both models suggested that there is an economic advantage in rescheduling the calving season to the second and third calendar quarters to better synchronize higher demand for nutrients with the period of high forage availability.

A hybridised evolutionary algorithm for multi-criterion minimum spanning tree problems

A hybridised and Knowledge-based Evolutionary Algorithm (KEA) is applied to the multi-criterion minimum spanning tree problems. Hybridisation is used across its three phases. In the first phase a deterministic single objective optimization algorithm finds the extreme points of the Pareto front. In the second phase a K-best approach finds the first neighbours of the extreme points, which serve as an elitist parent population to an evolutionary algorithm in the third phase. A knowledge-based mutation operator is applied in each generation to reproduce individuals that are at least as good as the unique parent. The advantages of KEA over previous algorithms include its speed (making it applicable to large real-world problems), its scalability to more than two criteria, and its ability to find both the supported and unsupported optimal solutions.

Developing a Communication link between Agents and cross Platform IDE

The main objective of this thesis work is to develop communication link between Runrev Revolution (IDE) and JADE (Multi-Agent System) through Socket programming using TCP/IP layer. These two independent platforms are connected using socket programming technique. Socket programming is considered to be newly emerging technology among these two platforms, the work done in this thesis work is considered to be a prototype.A Graphical simulation model is developed by salixphere (Company in Hedemora) to simulate logistic problems using Runrev Revolution (IDE). The simulation software/program is called “BIOSIM”. The logistic problems are complex, and conventional optimization techniques are unlikely very successful. “BIOSIM” can demonstrate the graphical representation of logistic problems depending upon the problem domains. As this simulation model is developed in revolution programming language (Transcript) which is dynamically typed and English-like language, it is quite slow compared to other high level programming languages. The object of this thesis work is to add intelligent behaviour in graphical objects and develop communication link between Runrev revolution (IDE) and JADE (Multi-Agent System) using TCP/IP layers.The test shows the intelligent behaviour in the graphical objects and successful communication between Runrev Revolution (IDE) and JADE (Multi-Agent System).

A Diagnostic Assessment Of Evolutionary Multiobjective Optimization For Water Resources Systems

This study contributes a rigorous diagnostic assessment of state-of-the-art multiobjective evolutionary algorithms (MOEAs) and highlights key advances that the water resources field can exploit to better discover the critical tradeoffs constraining our systems. This study provides the most comprehensive diagnostic assessment of MOEAs for water resources to date, exploiting more than 100,000 MOEA runs and trillions of design evaluations. The diagnostic assessment measures the effectiveness, efficiency, reliability, and controllability of ten benchmark MOEAs for a representative suite of water resources applications addressing rainfall-runoff calibration, long-term groundwater monitoring (LTM), and risk-based water supply portfolio planning. The suite of problems encompasses a range of challenging problem properties including (1) many-objective formulations with 4 or more objectives, (2) multi-modality (or false optima), (3) nonlinearity, (4) discreteness, (5) severe constraints, (6) stochastic objectives, and (7) non-separability (also called epistasis). The applications are representative of the dominant problem classes that have shaped the history of MOEAs in water resources and that will be dominant foci in the future. Recommendations are provided for which modern MOEAs should serve as tools and benchmarks in the future water resources literature.

Artificial neural networks and clustering techniques applied in the reconfiguration of distribution systems

One objective of the feeder reconfiguration problem in distribution systems is to minimize the power losses for a specific load. For this problem, mathematical modeling is a nonlinear mixed integer problem that is generally hard to solve. This paper proposes an algorithm based on artificial neural network theory. In this context, clustering techniques to determine the best training set for a single neural network with generalization ability are also presented. The proposed methodology was employed for solving two electrical systems and presented good results. Moreover, the methodology can be employed for large-scale systems in real-time environment.

Una metodología eficiente para manejo de restricciones en algoritmos evolutivos multi-objetivo

This paper presents a new approach for solving constraint optimization problems (COP) based on the philosophy of lexicographical goal programming. A two-phase methodology for solving COP using a multi-objective strategy is used. In the first phase, the objective function is completely disregarded and the entire search effort is directed towards finding a single feasible solution. In the second phase, the problem is treated as a bi-objective optimization problem, turning the constraint optimization into a two-objective optimization. The two resulting objectives are the original objective function and the constraint violation degree. In the first phase a methodology based on progressive hardening of soft constraints is proposed in order to find feasible solutions. The performance of the proposed methodology was tested on 11 well-known benchmark functions.

A mixed-integer LP model for the optimal allocation of voltage regulators and capacitors in radial distribution systems

This paper presents a mixed-integer linear programming model to solve the problem of allocating voltage regulators and fixed or switched capacitors (VRCs) in radial distribution systems. The use of a mixed-integer linear model guarantees convergence to optimality using existing optimization software. In the proposed model, the steady-state operation of the radial distribution system is modeled through linear expressions. The results of one test system and one real distribution system are presented in order to show the accuracy as well as the efficiency of the proposed solution technique. An heuristic to obtain the Pareto front for the multiobjective VRCs allocation problem is also presented. © 2012 Elsevier Ltd. All rights reserved.

Design of laminated piezocomposite shell transducers with arbitrary fiber orientation using topology optimization approach

Sensor and actuator based on laminated piezocomposite shells have shown increasing demand in the field of smart structures. The distribution of piezoelectric material within material layers affects the performance of these structures; therefore, its amount, shape, size, placement, and polarization should be simultaneously considered in an optimization problem. In addition, previous works suggest the concept of laminated piezocomposite structure that includes fiber-reinforced composite layer can increase the performance of these piezoelectric transducers; however, the design optimization of these devices has not been fully explored yet. Thus, this work aims the development of a methodology using topology optimization techniques for static design of laminated piezocomposite shell structures by considering the optimization of piezoelectric material and polarization distributions together with the optimization of the fiber angle of the composite orthotropic layers, which is free to assume different values along the same composite layer. The finite element model is based on the laminated piezoelectric shell theory, using the degenerate three-dimensional solid approach and first-order shell theory kinematics that accounts for the transverse shear deformation and rotary inertia effects. The topology optimization formulation is implemented by combining the piezoelectric material with penalization and polarization model and the discrete material optimization, where the design variables describe the amount of piezoelectric material and polarization sign at each finite element, with the fiber angles, respectively. Three different objective functions are formulated for the design of actuators, sensors, and energy harvesters. Results of laminated piezocomposite shell transducers are presented to illustrate the method. Copyright (C) 2012 John Wiley & Sons, Ltd.

Development of heat sink device by using topology optimization

Small scale fluid flow systems have been studied for various applications, such as chemical reagent dosages and cooling devices of compact electronic components. This work proposes to present the complete cycle development of an optimized heat sink designed by using Topology Optimization Method (TOM) for best performance, including minimization of pressure drop in fluid flow and maximization of heat dissipation effects, aiming small scale applications. The TOM is applied to a domain, to obtain an optimized channel topology, according to a given multi-objective function that combines pressure drop minimization and heat transfer maximization. Stokes flow hypothesis is adopted. Moreover, both conduction and forced convection effects are included in the steady-state heat transfer model. The topology optimization procedure combines the Finite Element Method (to carry out the physical analysis) with Sequential Linear Programming (as the optimization algorithm). Two-dimensional topology optimization results of channel layouts obtained for a heat sink design are presented as example to illustrate the design methodology. 3D computational simulations and prototype manufacturing have been carried out to validate the proposed design methodology.

Application of evolutionary algorithms and the boundary element method in the optimization of noise barrier profiles

[EN]This Ph.D. thesis presents a general, robust methodology that may cover any type of 2D acoustic optimization problem. A procedure involving the coupling of Boundary Elements (BE) and Evolutionary Algorithms is proposed for systematic geometric modifications of road barriers that lead to designs with ever-increasing screening performance. Numerical simulations involving single- and multi-objective optimizations of noise barriers of varied nature are included in this document. results disclosed justify the implementation of this methodology by leading to optimal solutions of previously defined topologies that, in general, greatly outperform the acoustic efficiency of classical, widely used barrier designs normally erected near roads.