Measures of Diversity for Populations and Distances Between Individuals with Highly Reorganizable Genomes

In this paper we address the problem of defining a measure of diversity for a population of individuals whose genome can be subjected to major reorganizations during the evolutionary process. To this end, we introduce a measure of diversity for populations of strings of variable length defined on a finite alphabet, and from this measure we derive a semi-metric distance between pairs of strings. The definitions are based on counting the number of substrings of the strings, considered first separately and then collectively. This approach is related to the concept of linguistic complexity, whose definition we generalize from single strings to populations. Using the substring count approach we also define a new kind of Tanimoto distance between strings. We show how to extend the approach to representations that are not based on strings and, in particular, to the tree-based representations used in the field of genetic programming. We describe how suffix trees can allow these measur...

• Type: Journal
• Year: 2004
• Where: Evolutionary Computation
• Authors: Claudio Mattiussi, Markus Waibel, Dario Floreano
• Keywords: Computational Linguistics, Data Complexity, Distance Functions, Diversity, Evolutionary Computation, Nucleotide Polymorphism Positions, String Distance Measures