On the Easiest and Hardest Fitness Functions

The hardness of fitness functions is an important research topic in the field of evolutionary computation. In theory, the study can help understanding the ability of evolutionary algorithms. In practice, the study may provide a guideline to the design of benchmarks. The aim of this paper is to answer the following research questions: Given a fitness function class, which functions are the easiest with respect to an evolutionary algorithm? Which are the hardest? How are these functions constructed? The paper provides theoretical answers to these questions. The easiest and hardest fitness functions are constructed for an elitist (1+1) evolutionary algorithm to maximise a class of fitness functions with the same optima. It is demonstrated that the unimodal functions are the easiest and deceptive functions are the hardest in terms of the time-fitness landscape. The paper also reveals that the easiest fitness function to one algorithm may become the hardest to another algorithm, and vice versa

Parametric Alignment of Drosophila Genomes

The classic algorithms of Needleman--Wunsch and Smith--Waterman find a maximum a posteriori probability alignment for a pair hidden Markov model (PHMM). In order to process large genomes that have undergone complex genome rearrangements, almost all existing whole genome alignment methods apply fast heuristics to divide genomes into small pieces which are suitable for Needleman--Wunsch alignment. In these alignment methods, it is standard practice to fix the parameters and to produce a single alignment for subsequent analysis by biologists. Our main result is the construction of a whole genome parametric alignment of Drosophila melanogaster and Drosophila pseudoobscura. Parametric alignment resolves the issue of robustness to changes in parameters by finding all optimal alignments for all possible parameters in a PHMM. Our alignment draws on existing heuristics for dividing whole genomes into small pieces for alignment, and it relies on advances we have made in computing convex polytopes that allow us to parametrically align non-coding regions using biologically realistic models. We demonstrate the utility of our parametric alignment for biological inference by showing that cis-regulatory elements are more conserved between Drosophila melanogaster and Drosophila pseudoobscura than previously thought. We also show how whole genome parametric alignment can be used to quantitatively assess the dependence of branch length estimates on alignment parameters. The alignment polytopes, software, and supplementary material can be downloaded at http://bio.math.berkeley.edu/parametric/.Comment: 19 pages, 3 figure