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Parallel Evolutionary Computation in R
Abstract
Evolutionary Computation (EC) is a branch of Artificial Intelligence which encompasses heuristic optimization methods loosely based on biological evolutionary processes. These methods are efficient in finding optimal or near-optimal solutions in large, complex non-linear search spaces. While evolutionary algorithms (EAs) are comparatively slow in comparison to deterministic or sampling approaches, they are also inherently parallelizable. As technology shifts towards multicore and cloud computing, this overhead becomes less relevant, provided a parallel framework is used. In this chapter the authors discuss how to implement and run parallel evolutionary algorithms in the popular statistical programming language R. R has become the de facto language for statistical programming and it is widely used in biostatistics and bioinformatics due to the availability of thousands of packages to manipulate and analyze data. It is also extremely easy to parallelize routines within R, which makes it a perfect environment for evolutionary algorithms. EC is a large field of research, and many different algorithms have been proposed. While there is no single silver bullet that can handle all classes of problems, an algorithm that is extremely simple, efficient, and with good generalization properties is Differential Evolution (DE). Herein the authors discuss step-by-step how to implement DE in R and how to parallelize it. They then illustrate with a toy genome-wide association study (GWAS) how to identify candidate regions associated with a quantitative trait of interest.
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