Chaperonin-facilitated protein folding: optimization of rate and yield by an iterative annealing mechanism.

We develop a heuristic model for chaperonin-facilitated protein folding, the iterative annealing mechanism, based on theoretical descriptions of "rugged" conformational free energy landscapes for protein folding, and on experimental evidence that (i) folding proceeds by a nucleation mechanism whereby correct and incorrect nucleation lead to fast and slow folding kinetics, respectively, and (ii) chaperonins optimize the rate and yield of protein folding by an active ATP-dependent process. The chaperonins GroEL and GroES catalyze the folding of ribulose bisphosphate carboxylase at a rate proportional to the GroEL concentration. Kinetically trapped folding-incompetent conformers of ribulose bisphosphate carboxylase are converted to the native state in a reaction involving multiple rounds of quantized ATP hydrolysis by GroEL. We propose that chaperonins optimize protein folding by an iterative annealing mechanism; they repeatedly bind kinetically trapped conformers, randomly disrupt their structure, and release them in less folded states, allowing substrate proteins multiple opportunities to find pathways leading to the most thermodynamically stable state. By this mechanism, chaperonins greatly expand the range of environmental conditions in which folding to the native state is possible. We suggest that the development of this device for optimizing protein folding was an early and significant evolutionary event.

An evolutionary approach to the delineation of functional areas based on travel-to-work flows

This paper presents a new approach to the delineation of local labor markets based on evolutionary computation. The aim of the exercise is the division of a given territory into functional regions based on travel-to-work flows. Such regions are defined so that a high degree of inter-regional separation and of intra-regional integration in both cases in terms of commuting flows is guaranteed. Additional requirements include the absence of overlap between delineated regions and the exhaustive coverage of the whole territory. The procedure is based on the maximization of a fitness function that measures aggregate intra-region interaction under constraints of inter-region separation and minimum size. In the experimentation stage, two variations of the fitness function are used, and the process is also applied as a final stage for the optimization of the results from one of the most successful existing methods, which are used by the British authorities for the delineation of travel-to-work areas (TTWAs). The empirical exercise is conducted using real data for a sufficiently large territory that is considered to be representative given the density and variety of travel-to-work patterns that it embraces. The paper includes the quantitative comparison with alternative traditional methods, the assessment of the performance of the set of operators which has been specifically designed to handle the regionalization problem and the evaluation of the convergence process. The robustness of the solutions, something crucial in a research and policy-making context, is also discussed in the paper.

Multi-objective adaptive evolutionary strategy for tuning compilations

Tuning compilations is the process of adjusting the values of a compiler options to improve some features of the final application. In this paper, a strategy based on the use of a genetic algorithm and a multi-objective scheme is proposed to deal with this task. Unlike previous works, we try to take advantage of the knowledge of this domain to provide a problem-specific genetic operation that improves both the speed of convergence and the quality of the results. The evaluation of the strategy is carried out by means of a case of study aimed to improve the performance of the well-known web server Apache. Experimental results show that a 7.5% of overall improvement can be achieved. Furthermore, the adaptive approach has shown an ability to markedly speed-up the convergence of the original strategy.

Tuning compilations by multi-objective optimization: Application to Apache web server

Modern compilers present a great and ever increasing number of options which can modify the features and behavior of a compiled program. Many of these options are often wasted due to the required comprehensive knowledge about both the underlying architecture and the internal processes of the compiler. In this context, it is usual, not having a single design goal but a more complex set of objectives. In addition, the dependencies between different goals are difficult to be a priori inferred. This paper proposes a strategy for tuning the compilation of any given application. This is accomplished by using an automatic variation of the compilation options by means of multi-objective optimization and evolutionary computation commanded by the NSGA-II algorithm. This allows finding compilation options that simultaneously optimize different objectives. The advantages of our proposal are illustrated by means of a case study based on the well-known Apache web server. Our strategy has demonstrated an ability to find improvements up to 7.5% and up to 27% in context switches and L2 cache misses, respectively, and also discovers the most important bottlenecks involved in the application performance.

Population-based continuous optimization, probabilistic modelling and mean shift

Evolutionary algorithms perform optimization using a population of sample solution points. An interesting development has been to view population-based optimization as the process of evolving an explicit, probabilistic model of the search space. This paper investigates a formal basis for continuous, population-based optimization in terms of a stochastic gradient descent on the Kullback-Leibler divergence between the model probability density and the objective function, represented as an unknown density of assumed form. This leads to an update rule that is related and compared with previous theoretical work, a continuous version of the population-based incremental learning algorithm, and the generalized mean shift clustering framework. Experimental results are presented that demonstrate the dynamics of the new algorithm on a set of simple test problems.

Temperature management for heterogeneous multi-core FPGAs using adaptive evolutionary multi-objective approaches

Heterogeneous multi-core FPGAs contain different types of cores, which can improve efficiency when used with an effective online task scheduler. However, it is not easy to find the right cores for tasks when there are multiple objectives or dozens of cores. Inappropriate scheduling may cause hot spots which decrease the reliability of the chip. Given that, our research builds a simulating platform to evaluate all kinds of scheduling algorithms on a variety of architectures. On this platform, we provide an online scheduler which uses multi-objective evolutionary algorithm (EA). Comparing the EA and current algorithms such as Predictive Dynamic Thermal Management (PDTM) and Adaptive Temperature Threshold Dynamic Thermal Management (ATDTM), we find some drawbacks in previous work. First, current algorithms are overly dependent on manually set constant parameters. Second, those algorithms neglect optimization for heterogeneous architectures. Third, they use single-objective methods, or use linear weighting method to convert a multi-objective optimization into a single-objective optimization. Unlike other algorithms, the EA is adaptive and does not require resetting parameters when workloads switch from one to another. EAs also improve performance when used on heterogeneous architecture. A efficient Pareto front can be obtained with EAs for the purpose of multiple objectives.

Operation sequencing optimization for five-axis prismatic parts using a particle swarm optimization approach

Operation sequencing is one of the crucial tasks in process planning. However, it is an intractable process to identify an optimized operation sequence with minimal machining cost in a vast search space constrained by manufacturing conditions. Also, the information represented by current process plan models for three-axis machining is not sufficient for five-axis machining owing to the two extra degrees of freedom and the difficulty of set-up planning. In this paper, a representation of process plans for five-axis machining is proposed, and the complicated operation sequencing process is modelled as a combinatorial optimization problem. A modern evolutionary algorithm, i.e. the particle swarm optimization (PSO) algorithm, has been employed and modified to solve it effectively. Initial process plan solutions are formed and encoded into particles of the PSO algorithm. The particles 'fly' intelligently in the search space to achieve the best sequence according to the optimization strategies of the PSO algorithm. Meanwhile, to explore the search space comprehensively and to avoid being trapped into local optima, several new operators have been developed to improve the particle movements to form a modified PSO algorithm. A case study used to verify the performance of the modified PSO algorithm shows that the developed PSO can generate satisfactory results in optimizing the process planning problem. © IMechE 2009.

Optimization of pavement maintenance and rehabilitation programming using shuffled complex evolution algorithm

The major barrier to practical optimization of pavement preservation programming has always been that for formulations where the identity of individual projects is preserved, the solution space grows exponentially with the problem size to an extent where it can become unmanageable by the traditional analytical optimization techniques within reasonable limit. This has been attributed to the problem of combinatorial explosion that is, exponential growth of the number of combinations. The relatively large number of constraints often presents in a real-life pavement preservation programming problems and the trade-off considerations required between preventive maintenance, rehabilitation and reconstruction, present yet another factor that contributes to the solution complexity. In this research study, a new integrated multi-year optimization procedure was developed to solve network level pavement preservation programming problems, through cost-effectiveness based evolutionary programming analysis, using the Shuffled Complex Evolution (SCE) algorithm.^ A case study problem was analyzed to illustrate the robustness and consistency of the SCE technique in solving network level pavement preservation problems. The output from this program is a list of maintenance and rehabilitation treatment (M&R) strategies for each identified segment of the network in each programming year, and the impact on the overall performance of the network, in terms of the performance levels of the recommended optimal M&R strategy. ^ The results show that the SCE is very efficient and consistent in the simultaneous consideration of the trade-off between various pavement preservation strategies, while preserving the identity of the individual network segments. The flexibility of the technique is also demonstrated, in the sense that, by suitably coding the problem parameters, it can be used to solve several forms of pavement management programming problems. It is recommended that for large networks, some sort of decomposition technique should be applied to aggregate sections, which exhibit similar performance characteristics into links, such that whatever M&R alternative is recommended for a link can be applied to all the sections connected to it. In this way the problem size, and hence the solution time, can be greatly reduced to a more manageable solution space. ^ The study concludes that the robust search characteristics of SCE are well suited for solving the combinatorial problems in long-term network level pavement M&R programming and provides a rich area for future research. ^

Hybrid multi-objective optimization and hybridized self-organizing response surface method

Numerical optimization is a technique where a computer is used to explore design parameter combinations to find extremes in performance factors. In multi-objective optimization several performance factors can be optimized simultaneously. The solution to multi-objective optimization problems is not a single design, but a family of optimized designs referred to as the Pareto frontier. The Pareto frontier is a trade-off curve in the objective function space composed of solutions where performance in one objective function is traded for performance in others. A Multi-Objective Hybridized Optimizer (MOHO) was created for the purpose of solving multi-objective optimization problems by utilizing a set of constituent optimization algorithms. MOHO tracks the progress of the Pareto frontier approximation development and automatically switches amongst those constituent evolutionary optimization algorithms to speed the formation of an accurate Pareto frontier approximation. Aerodynamic shape optimization is one of the oldest applications of numerical optimization. MOHO was used to perform shape optimization on a 0.5-inch ballistic penetrator traveling at Mach number 2.5. Two objectives were simultaneously optimized: minimize aerodynamic drag and maximize penetrator volume. This problem was solved twice. The first time the problem was solved by using Modified Newton Impact Theory (MNIT) to determine the pressure drag on the penetrator. In the second solution, a Parabolized Navier-Stokes (PNS) solver that includes viscosity was used to evaluate the drag on the penetrator. The studies show the difference in the optimized penetrator shapes when viscosity is absent and present in the optimization. In modern optimization problems, objective function evaluations may require many hours on a computer cluster to perform these types of analysis. One solution is to create a response surface that models the behavior of the objective function. Once enough data about the behavior of the objective function has been collected, a response surface can be used to represent the actual objective function in the optimization process. The Hybrid Self-Organizing Response Surface Method (HYBSORSM) algorithm was developed and used to make response surfaces of objective functions. HYBSORSM was evaluated using a suite of 295 non-linear functions. These functions involve from 2 to 100 variables demonstrating robustness and accuracy of HYBSORSM.

An experimental study of adaptive control for evolutionary algorithms

International audience

A Bayesian optimization algorithm for the nurse scheduling problem

A Bayesian optimization algorithm for the nurse scheduling problem is presented, which involves choosing a suitable scheduling rule from a set for each nurse’s assignment. Unlike our previous work that used GAs to implement implicit learning, the learning in the proposed algorithm is explicit, i.e. eventually, we will be able to identify and mix building blocks directly. The Bayesian optimization algorithm is applied to implement such explicit learning by building a Bayesian network of the joint distribution of solutions. The conditional probability of each variable in the network is computed according to an initial set of promising solutions. Subsequently, each new instance for each variable is generated by using the corresponding conditional probabilities, until all variables have been generated, i.e. in our case, a new rule string has been obtained. Another set of rule strings will be generated in this way, some of which will replace previous strings based on fitness selection. If stopping conditions are not met, the conditional probabilities for all nodes in the Bayesian network are updated again using the current set of promising rule strings. Computational results from 52 real data instances demonstrate the success of this approach. It is also suggested that the learning mechanism in the proposed approach might be suitable for other scheduling problems.

Efficient Hill Climber for Constrained Pseudo-Boolean Optimization Problems

Efficient hill climbers have been recently proposed for single- and multi-objective pseudo-Boolean optimization problems. For $k$-bounded pseudo-Boolean functions where each variable appears in at most a constant number of subfunctions, it has been theoretically proven that the neighborhood of a solution can be explored in constant time. These hill climbers, combined with a high-level exploration strategy, have shown to improve state of the art methods in experimental studies and open the door to the so-called Gray Box Optimization, where part, but not all, of the details of the objective functions are used to better explore the search space. One important limitation of all the previous proposals is that they can only be applied to unconstrained pseudo-Boolean optimization problems. In this work, we address the constrained case for multi-objective $k$-bounded pseudo-Boolean optimization problems. We find that adding constraints to the pseudo-Boolean problem has a linear computational cost in the hill climber.

Multi-objective optimization of material model parameters of an adhesive layer by using SPEA2

The usage of multi material structures in industry, especially in the automotive industry are increasing. To overcome the difficulties in joining these structures, adhesives have several benefits over traditional joining methods. Therefore, accurate simulations of the entire process of fracture including the adhesive layer is crucial. In this paper, material parameters of a previously developed meso mechanical finite element (FE) model of a thin adhesive layer are optimized using the Strength Pareto Evolutionary Algorithm (SPEA2). Objective functions are defined as the error between experimental data and simulation data. The experimental data is provided by previously performed experiments where an adhesive layer was loaded in monotonically increasing peel and shear. Two objective functions are dependent on 9 model parameters (decision variables) in total and are evaluated by running two FEsimulations, one is loading the adhesive layer in peel and the other in shear. The original study converted the two objective functions into one function that resulted in one optimal solution. In this study, however, a Pareto frontis obtained by employing the SPEA2 algorithm. Thus, more insight into the material model, objective functions, optimal solutions and decision space is acquired using the Pareto front. We compare the results and show good agreement with the experimental data.