A tutorial for competent memetic algorithms: Model, taxonomy and design issues

The combination of evolutionary algorithms with local search was named "memetic algorithms" (MAs) (Moscato, 1989). These methods are inspired by models of natural systems that combine the evolutionary adaptation of a population with individual learning within the lifetimes of its members. Additionally, MAs are inspired by Richard Dawkin's concept of a meme, which represents a unit of cultural evolution that can exhibit local refinement (Dawkins, 1976). In the case of MA's, "memes" refer to the strategies (e.g., local refinement, perturbation, or constructive methods, etc.) that are employed to improve individuals. In this paper, we review some works on the application of MAs to well-known combinatorial optimization problems, and place them in a framework defined by a general syntactic model. This model provides us with a classification scheme based on a computable index D, which facilitates algorithmic comparisons and suggests areas for future research. Also, by having an abstract model for this class of metaheuristics, it is possible to explore their design space and better understand their behavior from a theoretical standpoint. We illustrate the theoretical and practical relevance of this model and taxonomy for MAs in the context of a discussion of important design issues that must be addressed to produce effective and efficient MAs

A self-adaptive multimeme memetic algorithm co-evolving utility scores to control genetic operators and their parameter settings

Memetic algorithms are a class of well-studied metaheuristics which combine evolutionary algorithms and local search techniques. A meme represents contagious piece of information in an adaptive information sharing system. The canonical memetic algorithm uses a fixed meme, denoting a hill climbing operator, to improve each solution in a population during the evolutionary search process. Given global parameters and multiple parametrised operators, adaptation often becomes a crucial constituent in the design of MAs. In this study, a self-adaptive self-configuring steady-state multimeme memetic algorithm (SSMMA) variant is proposed. Along with the individuals (solutions), SSMMA co-evolves memes, encoding the utility score for each algorithmic component choice and relevant parameter setting option. An individual uses tournament selection to decide which operator and parameter setting to employ at a given step. The performance of the proposed algorithm is evaluated on six combinatorial optimisation problems from a cross-domain heuristic search benchmark. The results indicate the success of SSMMA when compared to the static Mas as well as widely used self-adaptive Multimeme Memetic Algorithm from the scientific literature

Estimating meme fitness in adaptive memetic algorithms for combinatorial problems

Among the most promising and active research areas in heuristic optimisation is the field of adaptive memetic algorithms (AMAs). These gain much of their reported robustness by adapting the probability with which each of a set of local improvement operators is applied, according to an estimate of their current value to the search process. This paper addresses the issue of how the current value should be estimated. Assuming the estimate occurs over several applications of a meme, we consider whether the extreme or mean improvements should be used, and whether this aggregation should be global, or local to some part of the solution space. To investigate these issues, we use the well-established COMA framework that coevolves the specification of a population of memes (representing different local search algorithms) alongside a population of candidate solutions to the problem at hand. Two very different memetic algorithms are considered: the first using adaptive operator pursuit to adjust the probabilities of applying a fixed set of memes, and a second which applies genetic operators to dynamically adapt and create memes and their functional definitions. For the latter, especially on combinatorial problems, credit assignment mechanisms based on historical records, or on notions of landscape locality, will have limited application, and it is necessary to estimate the value of a meme via some form of sampling. The results on a set of binary encoded combinatorial problems show that both methods are very effective, and that for some problems it is necessary to use thousands of variables in order to tease apart the differences between different reward schemes. However, for both memetic algorithms, a significant pattern emerges that reward based on mean improvement is better than that based on extreme improvement. This contradicts recent findings from adapting the parameters of operators involved in global evolutionary search. The results also show that local reward schemes outperform global reward schemes in combinatorial spaces, unlike in continuous spaces. An analysis of evolving meme behaviour is used to explain these findings. © 2012 by the Massachusetts Institute of Technology

Novel memetic algorithm for protein structure prediction

A novel Memetic Algorithm (MA) is proposed for investigating the complex ab initio protein structure prediction problem. The proposed MA has a new fitness function incorporating domain knowledge in the form of two new measures (H-compliance and P-compliance) to indicate hydrophobic and hydrophilic nature of a residue. It also includes two novel techniques for dynamically preserving best fit schema and for providing a guided search. The algorithm performance is investigated with the aid of commonly studied 2D lattice hydrophobic polar (HP) model for the benchmark as well as non-benchmark sequences. Comparative studies with other search algorithms reveal superior performance of the proposed techniqu

New evolutionary approaches to protein structure prediction

Programa de doctorado en Biotecnología y Tecnología QuímicaThe problem of Protein Structure Prediction (PSP) is one of the principal topics in Bioinformatics. Multiple approaches have been developed in order to predict the protein structure of a protein. Determining the three dimensional structure of proteins is necessary to understand the functions of molecular protein level. An useful, and commonly used, representation for protein 3D structure is the protein contact map, which represents binary proximities (contact or non-contact) between each pair of amino acids of a protein. This thesis work, includes a compilation of the soft computing techniques for the protein structure prediction problem (secondary and tertiary structures). A novel evolutionary secondary structure predictor is also widely described in this work. Results obtained confirm the validity of our proposal. Furthermore, we also propose a multi-objective evolutionary approach for contact map prediction based on physico-chemical properties of amino acids. The evolutionary algorithm produces a set of decision rules that identifies contacts between amino acids. The rules obtained by the algorithm impose a set of conditions based on amino acid properties in order to predict contacts. Results obtained by our approach on four different protein data sets are also presented. Finally, a statistical study was performed to extract valid conclusions from the set of prediction rules generated by our algorithm.Universidad Pablo de Olavide. Centro de Estudios de Postgrad

Algoritmos Meméticos con Propiedades Self-* para la Optimización de Problemas Complejos

Las propiedades self-* de un sistema son aquellas que le permiten controlar de forma autónoma diferentes aspectos de su funcionamiento. En esta tesis doctoral se estudia el diseño y desarrollo de algoritmos meméticos con propiedades self-* a partir de una clase de algoritmo multimemético (MMA) con estructura espacial. En este MMA la población se dispone conforme a una cierta topología que permite restringir las interacciones entre los individuos, y en él los memes se definen como reglas de reescritura. Estos memes están sujetos a un proceso evolutivo propio similar al de la evolución genética mediante el cual pueden variar su estructura y complejidad, auto-optimizando de esta forma el proceso de búsqueda local. En este contexto se estudia la propagación y difusión de los memes a través de la población, proceso en el que la calidad de estos últimos solo se percibe indirectamente por el efecto que producen sobre los genotipos. Considerando el modelo teórico anterior como sustrato se incorporan características adicionales al MMA. Por un lado se crean algoritmos híbridos con el uso de modelos probabilísticos para la generación de la descendencia utilizando algoritmos de estimación de distribuciones (EDAs) y por otro, se consideran MMAs basados en islas. Este último modelo distribuido es objeto de un estudio más detallado, analizándose cómo afecta a su funcionamiento la utilización de diferentes políticas de migración de individuos entre nodos y el impacto que sobre el rendimiento de los mismos tiene la inestabilidad del entorno donde se ejecutan. Para ello se diseñan mecanismos de tolerancia a fallos y se estudia la utilización de redes complejas como topología de interconexión de los nodos. Asimismo, se proporciona al algoritmo la capacidad de escalabilidad automática mediante técnicas de auto-equilibrado de la carga, de forma tal que el propio MMA sea capaz, por sí mismo y sin necesidad de recurrir a un control central, de auto-adaptarse a la volatilidad del entorno. Finalmente se incorporan procedimientos de auto-reparación para compensar el deterioro producido por dicha inestabilidad: (i) auto-muestreo a través de un modelo probabilístico dinámico sobre las poblaciones de los nodos y (ii) auto-adaptación de la topología de interconexión a medida que diferentes nodos de cómputo entran o abandonan el sistema. Los experimentos realizados permiten concluir que la auto-adaptación de los memes contribuye a mejorar el rendimiento del MMA, así como que los modelos híbridos que utilizan EDAs proporcionan resultados notables, preferentemente los basados en distribuciones bivariadas. Con respecto al modelo de islas, las políticas de migración relativas a la selección de los migrantes o la estrategia de reemplazo de estos en la isla receptora son determinantes. Asimismo, las estrategias de gestión de fallos basadas en puntos de restauración mitigan la degradación del rendimiento conforme la red se vuelve más volátil, si bien conllevan sobrecargas computacionales. Como alternativa, la incorporación de propiedades self-* tales como el auto-equilibrado de la carga, el auto-muestreo probabilístico o la auto-adaptación de la topología de la red, tiene un impacto claramente positivo en el sistema, limitando su degradación en escenarios altamente inestables

Automated Alphabet Reduction for Protein Datasets

<p>Abstract</p> <p>Background</p> <p>We investigate automated and generic alphabet reduction techniques for protein structure prediction datasets. Reducing alphabet cardinality without losing key biochemical information opens the door to potentially faster machine learning, data mining and optimization applications in structural bioinformatics. Furthermore, reduced but informative alphabets often result in, e.g., more compact and human-friendly classification/clustering rules. In this paper we propose a robust and sophisticated alphabet reduction protocol based on mutual information and state-of-the-art optimization techniques.</p> <p>Results</p> <p>We applied this protocol to the prediction of two protein structural features: contact number and relative solvent accessibility. For both features we generated alphabets of two, three, four and five letters. The five-letter alphabets gave prediction accuracies statistically similar to that obtained using the full amino acid alphabet. Moreover, the automatically designed alphabets were compared against other reduced alphabets taken from the literature or human-designed, outperforming them. The differences between our alphabets and the alphabets taken from the literature were quantitatively analyzed. All the above process had been performed using a primary sequence representation of proteins. As a final experiment, we extrapolated the obtained five-letter alphabet to reduce a, much richer, protein representation based on evolutionary information for the prediction of the same two features. Again, the performance gap between the full representation and the reduced representation was small, showing that the results of our automated alphabet reduction protocol, even if they were obtained using a simple representation, are also able to capture the crucial information needed for state-of-the-art protein representations.</p> <p>Conclusion</p> <p>Our automated alphabet reduction protocol generates competent reduced alphabets tailored specifically for a variety of protein datasets. This process is done without any domain knowledge, using information theory metrics instead. The reduced alphabets contain some unexpected (but sound) groups of amino acids, thus suggesting new ways of interpreting the data.</p

Soft Computing Techiniques for the Protein Folding Problem on High Performance Computing Architectures

The protein-folding problem has been extensively studied during the last fifty years. The understanding of the dynamics of global shape of a protein and the influence on its biological function can help us to discover new and more effective drugs to deal with diseases of pharmacological relevance. Different computational approaches have been developed by different researchers in order to foresee the threedimensional arrangement of atoms of proteins from their sequences. However, the computational complexity of this problem makes mandatory the search for new models, novel algorithmic strategies and hardware platforms that provide solutions in a reasonable time frame. We present in this revision work the past and last tendencies regarding protein folding simulations from both perspectives; hardware and software. Of particular interest to us are both the use of inexact solutions to this computationally hard problem as well as which hardware platforms have been used for running this kind of Soft Computing techniques.This work is jointly supported by the FundaciónSéneca (Agencia Regional de Ciencia y Tecnología, Región de Murcia) under grants 15290/PI/2010 and 18946/JLI/13, by the Spanish MEC and European Commission FEDER under grant with reference TEC2012-37945-C02-02 and TIN2012-31345, by the Nils Coordinated Mobility under grant 012-ABEL-CM-2014A, in part financed by the European Regional Development Fund (ERDF). We also thank NVIDIA for hardware donation within UCAM GPU educational and research centers.Ingeniería, Industria y Construcció