Evolutionary computation is becoming common in the solution of difficult, realworld problems in industry, medicine, and defense. This paper reviews some of the practical advantages to using evolutionary algorithms as compared with classic methods of optimization or artificial intelligence. Specific advantages include the flexibility of the procedures, as well as the ability to self-adapt the search for optimum solutions on the fly. As desktop computers increase in speed, the application of evolutionary algorithms will become routine. 1 Introduction Darwinian evolution is intrinsically a robust search and optimization mechanism. Evolved biota demonstrate optimized complex behavior at every level: the cell, the organ, the individual, and the population. The problems that biological species have solved are typified by chaos, chance, temporality, and nonlinear interactivities. These are also characteristics of problems that have proved to be especially intractable to classic methods of o...

Abstract not found

: Local Search (LS) has proven to be an efficient optimisation technique in clustering applications and in the minimisation of

This article reviews machine learning methods for bioinformatics. It presents modelling methods, such as supervised classification, clustering and probabilistic graphical models for knowledge discovery, as well as deterministic and stochastic heuristics for optimization. Applications in genomics, proteomics, systems biology, evolution and text mining are also shown.

The methods to detect gene-gene interactions between variants in genome-wide association study (GWAS) datasets have not been well developed thus far. PLATO, the Platform for the Analysis, Translation and Organization of large-scale data, is a filter-based method bringing together many analytical methods simultaneously in an effort to solve this problem. PLATO filters a large, genomic dataset down to a subset of genetic variants, which may be useful for interaction analysis. As a precursor to the use of PLATO for the detection of gene-gene interactions, the implementation of a variety of single locus filters was completed and evaluated as a proof of concept. To streamline PLATO for efficient epistasis analysis, we determined which of 24 analytical filters produced redundant results. Using a kappa score to identify agreement between filters, we grouped the analytical filters into 4 filter classes; thus all further analyses employed four filters. We then tested the MAX statistic put forth by Sladek et al. 1 in simulated data exploring a number of genetic models of modest effect size. To find the MAX statistic, the four filters were run on each SNP in each dataset and the smallest p-value among the four results was taken as the final result. Permutation testing was performed to empirically determine the p-value. The power of the MAX statistic to detect each of the simulated effects was determined in addition to the Type 1 error and false positive rates. The results of this simulation study demonstrates that PLATO using the four filters incorporating the MAX statistic has higher power on average to find multiple types of effects and a lower false positive rate than any of the individual filters alone. In the future we will extend PLATO with the MAX statistic to interaction analyses for large-scale genomic datasets.