Modeling SELEX for regulatory regions using Royal Road and Royal Staircase fitness functions.

The field of evolutionary algorithms (EAs) emerged in the area of computer science due to transfer of ideas from biology and developed independently for several decades, enriched with techniques from probability theory, complexity theory and optimization methods. In this paper, we consider some recent results form the EAs theory transferred back into biology. The well-known biotechnological procedure SELEX (Systematic Evolution of Ligands by EXponential enrichment) is viewed as an experimental implementation of an evolutionary algorithm.

On Proportions of Fit Individuals in Population of Mutation-Based Evolutionary Algorithm with Tournament Selection.

In this article, we consider a fitness-level model of a non-elitist mutation-only evolutionary algorithm (EA) with tournament selection. The model provides upper and lower bounds for the expected proportion of the individuals with fitness above given thresholds. In the case of so-called monotone mutation, the obtained bounds imply that increasing the tournament size improves the EA performance.

On complexity of optimal recombination for binary representations of solutions.

We consider the optimization problem of finding the best possible offspring as a result of a recombination operator in an evolutionary algorithm, given two parent solutions. The optimal recombination is studied in the case where a vector of binary variables is used as a solution encoding. By means of efficient reductions of the optimal recombination problems (ORPs) we show the polynomial solvability of the ORPs for the maximum weight set packing problem, the minimum weight set partition problem, and for linear Boolean programming problems with at most two variables per inequality, and some other problems.