Enhanced parallel Differential Evolution algorithm for problems in computational systems biology

[Abstract] Many key problems in computational systems biology and bioinformatics can be formulated and solved using a global optimization framework. The complexity of the underlying mathematical models require the use of efficient solvers in order to obtain satisfactory results in reasonable computation times. Metaheuristics are gaining recognition in this context, with Differential Evolution (DE) as one of the most popular methods. However, for most realistic applications, like those considering parameter estimation in dynamic models, DE still requires excessive computation times. Here we consider this latter class of problems and present several enhancements to DE based on the introduction of additional algorithmic steps and the exploitation of parallelism. In particular, we propose an asynchronous parallel implementation of DE which has been extended with improved heuristics to exploit the specific structure of parameter estimation problems in computational systems biology. The proposed method is evaluated with different types of benchmarks problems: (i) black-box global optimization problems and (ii) calibration of non-linear dynamic models of biological systems, obtaining excellent results both in terms of quality of the solution and regarding speedup and scalability.Ministerio de Economía y Competitividad; DPI2011-28112-C04-03Consejo Superior de Investigaciones Científicas; PIE-201170E018Ministerio de Ciencia e Innovación; TIN2013-42148-PGalicia. Consellería de Cultura, Educación e Ordenación Universitaria; GRC2013/05

Multi-objective power quality optimization of smart grid based on improved differential evolution

In the modern generation, Electric Power has become one of the fundamental needs for humans to survive. This is due to the dependence of continuous availability of power. However, for electric power to be available to the society, it has to pass through a number of complex stages. Through each stage power quality problems are experienced on the grid. Under-voltages and over-voltages are the most common electric problems experienced on the grid, causing industries and business firms losses of Billions of dollars each year. Researchers from different regions are attracted by an idea that will overcome all the electrical issues experienced in the traditional grid using Artificial Intelligence (AI). The idea is said to provide electric power that is sustainable, economical, reliable and efficient to the society based on Evolutionary Algorithms (EAs). The idea is Smart Grid. The research focused on Power Quality Optimization in Smart Grid based on improved Differential Evolution (DE), with the objective functions to minimize voltage swells, counterbalance voltage sags and eliminate voltage surges or spikes, while maximizing the power quality. During Differential Evolution improvement research, elimination of stagnation, better and fast convergence speed were achieved based on modification of DE’s mutation schemes and parameter control selection. DE/Modi/2 and DE/Modi/3 modified mutation schemes proved to be the excellent improvement for DE algorithm by achieving excellent optimization results with regards to convergence speed and elimination of stagnation during simulations. The improved DE was used to optimize Power Quality in smart grid in combination with the reconfigured and modified Dynamic Voltage Restorer (DVR). Excellent convergence results of voltage swells and voltage sags minimization were achieved based on application of multi-objective parallel operation strategy during simulations. MATLAB was used to model the proposed solution and experimental simulations.Electrical and Mining EngineeringM. Tech. (Electrical Engineering

Fast micro-differential evolution for topological active net optimization

This paper studies the optimization problem of topological active net (TAN), which is often seen in image segmentation and shape modeling. A TAN is a topological structure containing many nodes, whose positions must be optimized while a predefined topology needs to be maintained. TAN optimization is often time-consuming and even constructing a single solution is hard to do. Such a problem is usually approached by a ``best improvement local search'' (BILS) algorithm based on deterministic search (DS), which is inefficient because it spends too much efforts in nonpromising probing. In this paper, we propose the use of micro-differential evolution (DE) to replace DS in BILS for improved directional guidance. The resultant algorithm is termed deBILS. Its micro-population efficiently utilizes historical information for potentially promising search directions and hence improves efficiency in probing. Results show that deBILS can probe promising neighborhoods for each node of a TAN. Experimental tests verify that deBILS offers substantially higher search speed and solution quality not only than ordinary BILS, but also the genetic algorithm and scatter search algorithm

Multimodal estimation of distribution algorithms

Taking the advantage of estimation of distribution algorithms (EDAs) in preserving high diversity, this paper proposes a multimodal EDA. Integrated with clustering strategies for crowding and speciation, two versions of this algorithm are developed, which operate at the niche level. Then these two algorithms are equipped with three distinctive techniques: 1) a dynamic cluster sizing strategy; 2) an alternative utilization of Gaussian and Cauchy distributions to generate offspring; and 3) an adaptive local search. The dynamic cluster sizing affords a potential balance between exploration and exploitation and reduces the sensitivity to the cluster size in the niching methods. Taking advantages of Gaussian and Cauchy distributions, we generate the offspring at the niche level through alternatively using these two distributions. Such utilization can also potentially offer a balance between exploration and exploitation. Further, solution accuracy is enhanced through a new local search scheme probabilistically conducted around seeds of niches with probabilities determined self-adaptively according to fitness values of these seeds. Extensive experiments conducted on 20 benchmark multimodal problems confirm that both algorithms can achieve competitive performance compared with several state-of-the-art multimodal algorithms, which is supported by nonparametric tests. Especially, the proposed algorithms are very promising for complex problems with many local optima

Optimization of force-limiting seismic devices connecting structural subsystems

This paper is focused on the optimum design of an original force-limiting floor anchorage system for the seismic protection of reinforced concrete (RC) dual wall-frame buildings. This protection strategy is based on the interposition of elasto-plastic links between two structural subsystems, namely the lateral force resisting system (LFRS) and the gravity load resisting system (GLRS). The most efficient configuration accounting for the optimal position and mechanical characteristics of the nonlinear devices is obtained numerically by means of a modified constrained differential evolution algorithm. A 12-storey prototype RC dual wall-frame building is considered to demonstrate the effectiveness of the seismic protection strategy

Using competitive population evaluation in a differential evolution algorithm for dynamic environments

This paper proposes two adaptations to DynDE, a differential evolution-based algorithm for solving dynamic optimization problems. The first adapted algorithm, Competitive Population Evaluation (CPE), is a multi-population DE algorithm aimed at locating optima faster in the dynamic environment. This adaptation is based on allowing populations to compete for function evaluations based on their performance. The second adapted algorithm, Reinitialization Midpoint Check (RMC), is aimed at improving the technique used by DynDE to maintain populations on different peaks in the search space. A combination of the CPE and RMC adaptations is investigated. The new adaptations are empirically compared to DynDE using various problem sets. The empirical results show that the adaptations constitute an improvement over DynDE and compares favorably to other approaches in the literature. The general applicability of the adaptations is illustrated by incorporating the combination of CPE and RMC into another Differential Evolution-based algorithm, jDE, which is shown to yield improved results.http://www.elsevier.com/locate/ejo