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C. FERREIRA, 2002 (Terms of Use) ISBN: 9729589054

Gene Expression Programming: Mathematical Modeling by an Artificial Intelligence

The entities of gene expression programming
 

In this chapter:


In contrast to its analogous cellular gene expression, GEP gene expression is rather simple. The main players in GEP are only two: the chromosomes and the expression trees, the latter consisting of the expression of the genetic information encoded in the former. The process of information decoding (from the chromosomes to the expression trees) is called translation. And this translation implies obviously a kind of code and a set of rules. The genetic code is very simple: a one-to-one relationship between the symbols of the chromosome and the functions or terminals they represent. The rules are also quite simple: they determine the spatial organization of the functions and terminals in the expression trees and the type of interaction between sub-expression trees in multigenic systems.

Therefore, there are two languages in GEP: the language of the genes and the language of the expression trees, and we will see that the sequence or structure of one of these languages is more than sufficient to infer exactly the other. In nature, although the inference of the sequence of proteins given the sequence of genes and vice versa is possible, very little is known about the rules that determine the folding of the protein. And the expression of a protein gene is not complete before the folding of the protein, that is, strings of amino acids only become proteins when they are correctly folded into their native three-dimensional structure. The only thing we know for sure about protein folding is that the sequence of the amino acids determines the folding. However, the rules that orchestrate the folding are still unknown. But, in GEP, thanks to the simple rules that determine the structure of expression trees and their interactions, it is possible to infer immediately the phenotype (the final structure, which is equivalent to the folded protein molecule) given the sequence of a gene, and vice versa. This bilingual and unequivocal system is called Karva language. The details of this language are explored in this chapter.

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