Networks in Natural Computing and Precision Medicine

Abstract

The nodes in both of these main subcategories are mathematical constructions performing data operations inspired by the natural mechanisms governing the modification and restructuring of DNA sequences.In the Networks of Evolutionary Processors (NEP), the mathematical calculations in the nodes emulate the computational counterpart of one of the point mutations in DNA sequences (insertion, deletion or substitution of a single pair) through the application of evolutionary rules of the same kind. Abstracting to a natural point of view, the processors can be thought of as cells holding genetic data encoded in DNA sequences which are subjected to local evolutionary mutations in natural evolution.In a Network of Splicing Processors, each processor performs a formal operation called splicing which is designed after the breaking and recombination process of DNA controlled by restriction enzymes and ligases [162]. This natural event is taken advantage of in genetic engineering with the aim of allowing simple organisms to produce different useful compounds (hormones, hydrocarbon fuels, etc.), strengthening plant resistance, obtaining better adapted organisms, etc. The role of restriction enzymes is to cut the DNA sequences at some recognition sites, yielding two DNA sequences having the so-called "sticky ends" while ligases reconnect the produced sequences.Under this framework, strings encode DNA molecules over some alphabet and each of its characters represent a nucleotide or a larger DNA segment such as a gene. A pair of strings is cut according to the restrictions set by rules, called splicing rules, composed by quadruples of strings specifying the cutting points for both strings. Then, the fragments generated by this same splicing rule are rejoined to acquire new strings. Figure 1.1 illustrates a schematic view of the splicing operation.The paper [166] introduces a language-theoretic computational model, called splicing system, generating sets of strings by means of the operation described above.Since then, different types of splicing systems as language generating devices have been introduced and analyzed, with their computational power as the main focus of the majority