In computer programming, genetic representation is a way of presenting solutions/individuals in evolutionary computation methods. The term encompasses both the concrete data structures and data types used to realize the genetic material of the candidate solutions in the form of a genome, and the relationships between search space and problem space. In the simplest case, the search space corresponds to the problem space (direct representation). The choice of problem representation is tied to the choice of genetic operators, both of which have a decisive effect on the efficiency of the optimization. Genetic representation can encode appearance, behavior, physical qualities of individuals. Difference in genetic representations is one of the major criteria drawing a line between known classes of evolutionary computation. Terminology is often analogous with natural genetics. The block of computer memory that represents one candidate solution is called an individual. The data in that block is called a chromosome. Each chromosome consists of genes. The possible values of a particular gene are called alleles. A programmer may represent all the individuals of a population using binary encoding, permutational encoding, encoding by tree, or any one of several other representations.
Representations in some popular evolutionary algorithms Genetic algorithms (GAs) are typically linear representations; these are often, but not always, binary. Holland's original description of GA used arrays of bits. Arrays of other types and structures can be used in essentially the same way. The main property that makes these genetic representations convenient is that their parts are easily aligned due to their fixed size. This facilitates simple crossover operation. Depending on the application, variable-length representations have also been successfully used and tested in evolutionary algorithms (EA) in general and genetic algorithms in particular, although the implementation of crossover is more complex in this case. Evolution strategy uses linear real-valued representations, e.g., an array of real values. It uses mostly gaussian mutation and blending/averaging crossover. Genetic programming (GP) pioneered tree-like representations and developed genetic operators suitable for such representations. Tree-like representations are used in GP to represent and evolve functional programs with desired properties. Human-based genetic algorithm (HBGA) offers a way to avoid solving hard representation problems by outsourcing all genetic operators to outside agents, in this case, humans. The algorithm has no need for knowledge of a particular fixed genetic representation as long as there are enough external agents capable of handling those representations, allowing for free-form and evolving genetic representations.
Common genetic representations binary array integer or real-valued array binary tree natural language parse tree directed graph
Distinction between search space and problem space Analogous to biology, EAs distinguish between problem space (corresponds to phenotype) and search space (corresponds to genotype). The problem space contains concrete solutions to the problem being addressed, while the search space contains the encoded solutions. The mapping from search space to problem space is called genotype-phenotype mapping. The genetic operators are applied to elements of the search space, and for evaluation, elements of the search space are mapped to elements of the problem space via genotype-phenotype mapping.
Relationships between search space and problem space The importance of an appropriate choice of search space for the success of an EA application was recognized early on. The following requirements can be placed on a suitable search space and thus on a suitable genotype-phenotype mapping:
Completeness All possible admissible solutions must be contained in the search space.
Redundancy When more possible genotypes exist than phenotypes, the genetic representation of the EA is called redundant. In nature, this is termed a degenerate genetic code. In the case of a redundant representation, neutral mutations are possible. These are mutations that change the genotype but do not affect the phenotype. Thus, depending on the use of the genetic operators, there may be phenotypically unchanged offspring, which can lead to unnecessary fitness determinations, among other things. Since the evaluation in real-world applications usually accounts for the lion's share of the computation time, it can slow down the optimization process. In addition, this can cause the population to have higher genotypic diversity than phenotypic diversity, which can also hinder evolutionary progress. In biology, the Neutral Theory of Molecular Evolution states that this effect plays a dominant role in natural evolution. This has motivated researchers in the EA community to examine whether neutral mutations can improve EA functioning by giving populations that have converged to a local optimum a way to escape that local optimum through genetic drift. This is discussed controversially and there are no conclusive results on neutrality in EAs. On the other hand, there are other proven measures to handle premature convergence.
Locality The locality of a genetic representation corresponds to the degree to which distances in the search space are preserved in the problem space after genotype-phenotype mapping. That is, a representation has a high locality exactly when neighbors in the search space are also neighbors in the problem space. In order for successful schemata not to be destroyed by genotype-phenotype mapping after a minor mutation, the locality of a representation must be high.
Scaling In genotype-phenotype mapping, the elements of the genotype can be scaled (weighted) differently. The simplest case is uniform scaling: all elements of the genotype are equally weighted in the phenotype. A common scaling is exponential. If integers are binary coded, the individual digits of the resulting binary number have exponentially different weights in representing the phenotype.
… excerpt ends here. Continue reading the full article.
