EADock: docking of small molecules into protein active sites with a multiobjective evolutionary optimization.

In recent years, protein-ligand docking has become a powerful tool for drug development. Although several approaches suitable for high throughput screening are available, there is a need for methods able to identify binding modes with high accuracy. This accuracy is essential to reliably compute the binding free energy of the ligand. Such methods are needed when the binding mode of lead compounds is not determined experimentally but is needed for structure-based lead optimization. We present here a new docking software, called EADock, that aims at this goal. It uses an hybrid evolutionary algorithm with two fitness functions, in combination with a sophisticated management of the diversity. EADock is interfaced with the CHARMM package for energy calculations and coordinate handling. A validation was carried out on 37 crystallized protein-ligand complexes featuring 11 different proteins. The search space was defined as a sphere of 15 A around the center of mass of the ligand position in the crystal structure, and on the contrary to other benchmarks, our algorithm was fed with optimized ligand positions up to 10 A root mean square deviation (RMSD) from the crystal structure, excluding the latter. This validation illustrates the efficiency of our sampling strategy, as correct binding modes, defined by a RMSD to the crystal structure lower than 2 A, were identified and ranked first for 68% of the complexes. The success rate increases to 78% when considering the five best ranked clusters, and 92% when all clusters present in the last generation are taken into account. Most failures could be explained by the presence of crystal contacts in the experimental structure. Finally, the ability of EADock to accurately predict binding modes on a real application was illustrated by the successful docking of the RGD cyclic pentapeptide on the alphaVbeta3 integrin, starting far away from the binding pocket.

Continuous GRASP with a local active-set method for bound-constrained global optimization

Global optimization seeks a minimum or maximum of a multimodal function over a discrete or continuous domain. In this paper, we propose a hybrid heuristic-based on the CGRASP and GENCAN methods-for finding approximate solutions for continuous global optimization problems subject to box constraints. Experimental results illustrate the relative effectiveness of CGRASP-GENCAN on a set of benchmark multimodal test functions.

A novel approach for solving constrained nonlinear optimization problems using neurofuzzy systems

A neural network model for solving constrained nonlinear optimization problems with bounded variables is presented in this paper. More specifically, a modified Hopfield network is developed and its internal parameters are completed using the valid-subspace technique. These parameters guarantee the convergence of the network to the equilibrium points. The network is shown to be completely stable and globally convergent to the solutions of constrained nonlinear optimization problems. A fuzzy logic controller is incorporated in the network to minimize convergence time. Simulation results are presented to validate the proposed approach.

A barrier method for constrained nonlinear optimization using a modified Hopfield network

The ability of neural networks to realize some complex nonlinear function makes them attractive for system identification. This paper describes a novel barrier method using artificial neural networks to solve robust parameter estimation problems for nonlinear model with unknown-but-bounded errors and uncertainties. This problem can be represented by a typical constrained optimization problem. More specifically, a modified Hopfield network is developed and its internal parameters are computed using the valid-subspace technique. These parameters guarantee the network convergence to the equilibrium points. A solution for the robust estimation problem with unknown-but-bounded error corresponds to an equilibrium point of the network. Simulation results are presented as an illustration of the proposed approach.

Bound constrained smooth optimization for solving variational inequalities and related problems

Variational inequalities and related problems may be solved via smooth bound constrained optimization. A comprehensive discussion of the important features involved with this strategy is presented. Complementarity problems and mathematical programming problems with equilibrium constraints are included in this report. Numerical experiments are commented. Conclusions and directions of future research are indicated.

Evolutionary optimization applied for fine-tuning parameter estimation in optical flow-based environments

Optical flow methods are accurate algorithms for estimating the displacement and velocity fields of objects in a wide variety of applications, being their performance dependent on the configuration of a set of parameters. Since there is a lack of research that aims to automatically tune such parameters, in this work we have proposed an evolutionary-based framework for such task, thus introducing three techniques for such purpose: Particle Swarm Optimization, Harmony Search and Social-Spider Optimization. The proposed framework has been compared against with the well-known Large Displacement Optical Flow approach, obtaining the best results in three out eight image sequences provided by a public dataset. Additionally, the proposed framework can be used with any other optimization technique.

On uncertainty and robustness in evolutionary optimization-based multicriterio decision-making

Programa de Doctorado: Sistemas Inteligentes y Aplicaciones Numéricas en Ingeniería

Duality in Constrained DC-Optimization via Toland’s Duality Approach

2000 Mathematics Subject Classification: 90C48, 49N15, 90C25

Multi Objective Evolutionary Algorithm Applied to the Optimal Power Flow Problem

This work presents the application of a multiobjective evolutionary algorithm (MOEA) for optimal power flow (OPF) solution. The OPF is modeled as a constrained nonlinear optimization problem, non-convex of large-scale, with continuous and discrete variables. The violated inequality constraints are treated as objective function of the problem. This strategy allows attending the physical and operational restrictions without compromise the quality of the found solutions. The developed MOEA is based on the theory of Pareto and employs a diversity-preserving mechanism to overcome the premature convergence of algorithm and local optimal solutions. Fuzzy set theory is employed to extract the best compromises of the Pareto set. Results for the IEEE-30, RTS-96 and IEEE-354 test systems are presents to validate the efficiency of proposed model and solution technique.

Comparative analysis of strut-and-tie models using Smooth Evolutionary Structural Optimization

The strut-and-tie models are widely used in certain types of structural elements in reinforced concrete and in regions with complexity of the stress state, called regions D, where the distribution of deformations in the cross section is not linear. This paper introduces a numerical technique to determine the strut-and-tie models using a variant of the classical Evolutionary Structural Optimization, which is called Smooth Evolutionary Structural Optimization. The basic idea of this technique is to identify the numerical flow of stresses generated in the structure, setting out in more technical and rational members of strut-and-tie, and to quantify their value for future structural design. This paper presents an index performance based on the evolutionary topology optimization method for automatically generating optimal strut-and-tie models in reinforced concrete structures with stress constraints. In the proposed approach, the element with the lowest Von Mises stress is calculated for element removal, while a performance index is used to monitor the evolutionary optimization process. Thus, a comparative analysis of the strut-and-tie models for beams is proposed with the presentation of examples from the literature that demonstrates the efficiency of this formulation. © 2013 Elsevier Ltd.

A comparison about evolutionary algorithms for optimum-path forest clustering optimization

In this paper we deal with the problem of boosting the Optimum-Path Forest (OPF) clustering approach using evolutionary-based optimization techniques. As the OPF classifier performs an exhaustive search to find out the size of sample's neighborhood that allows it to reach the minimum graph cut as a quality measure, we compared several optimization techniques that can obtain close graph cut values to the ones obtained by brute force. Experiments in two public datasets in the context of unsupervised network intrusion detection have showed the evolutionary optimization techniques can find suitable values for the neighborhood faster than the exhaustive search. Additionally, we have showed that it is not necessary to employ many agents for such task, since the neighborhood size is defined by discrete values, with constrain the set of possible solution to a few ones.

l-stable Functions and Constrained Optimization

Иван Гинчев - Класът на ℓ-устойчивите в точка функции, дефиниран в [2] и разширяващ класа на C1,1 функциите, се обобщава от скаларни за векторни функции. Доказани са някои свойства на ℓ-устойчивите векторни функции. Показано е, че векторни оптимизационни задачи с ограничения допускат условия от втори ред изразени чрез посочни производни, което обобщава резултати от [2] и [5].

Improvement of a filters method in a derivative free optimization

Constraints nonlinear optimization problems can be solved using penalty or barrier functions. This strategy, based on solving the problems without constraints obtained from the original problem, have shown to be e ective, particularly when used with direct search methods. An alternative to solve the previous problems is the lters method. The lters method introduced by Fletcher and Ley er in 2002, , has been widely used to solve problems of the type mentioned above. These methods use a strategy di erent from the barrier or penalty functions. The previous functions de ne a new one that combine the objective function and the constraints, while the lters method treat optimization problems as a bi-objective problems that minimize the objective function and a function that aggregates the constraints. Motivated by the work of Audet and Dennis in 2004, using lters method with derivative-free algorithms, the authors developed works where other direct search meth- ods were used, combining their potential with the lters method. More recently. In a new variant of these methods was presented, where it some alternative aggregation restrictions for the construction of lters were proposed. This paper presents a variant of the lters method, more robust than the previous ones, that has been implemented with a safeguard procedure where values of the function and constraints are interlinked and not treated completely independently.

Filters method in direct search optimization, new measures to admissibility

Constrained nonlinear optimization problems are usually solved using penalty or barrier methods combined with unconstrained optimization methods. Another alternative used to solve constrained nonlinear optimization problems is the lters method. Filters method, introduced by Fletcher and Ley er in 2002, have been widely used in several areas of constrained nonlinear optimization. These methods treat optimization problem as bi-objective attempts to minimize the objective function and a continuous function that aggregates the constraint violation functions. Audet and Dennis have presented the rst lters method for derivative-free nonlinear programming, based on pattern search methods. Motivated by this work we have de- veloped a new direct search method, based on simplex methods, for general constrained optimization, that combines the features of the simplex method and lters method. This work presents a new variant of these methods which combines the lters method with other direct search methods and are proposed some alternatives to aggregate the constraint violation functions.

Evolutionary Testing of Autonomous Software Agents

A system built in terms of autonomous agents may require even greater correctness assurance than one which is merely reacting to the immediate control of its users. Agents make substantial decisions for themselves, so thorough testing is an important consideration. However, autonomy also makes testing harder; by their nature, autonomous agents may react in different ways to the same inputs over time, because, for instance they have changeable goals and knowledge. For this reason, we argue that testing of autonomous agents requires a procedure that caters for a wide range of test case contexts, and that can search for the most demanding of these test cases, even when they are not apparent to the agents’ developers. In this paper, we address this problem, introducing and evaluating an approach to testing autonomous agents that uses evolutionary optimization to generate demanding test cases.