A review of estimation of distribution algorithms in bioinformatics

Evolutionary search algorithms have become an essential asset in the algorithmic toolbox for solving high-dimensional optimization problems in across a broad range of bioinformatics problems. Genetic algorithms, the most well-known and representative evolutionary search technique, have been the subject of the major part of such applications. Estimation of distribution algorithms (EDAs) offer a novel evolutionary paradigm that constitutes a natural and attractive alternative to genetic algorithms. They make use of a probabilistic model, learnt from the promising solutions, to guide the search process. In this paper, we set out a basic taxonomy of EDA techniques, underlining the nature and complexity of the probabilistic model of each EDA variant. We review a set of innovative works that make use of EDA techniques to solve challenging bioinformatics problems, emphasizing the EDA paradigm's potential for further research in this domain

On the choice of the update strength in estimation-of-distribution algorithms and ant colony optimization

Probabilistic model-building Genetic Algorithms (PMBGAs) are a class of metaheuristics that evolve probability distributions favoring optimal solutions in the underlying search space by repeatedly sampling from the distribution and updating it according to promising samples. We provide a rigorous runtime analysis concerning the update strength, a vital parameter in PMBGAs such as the step size 1 / K in the so-called compact Genetic Algorithm (cGA) and the evaporation factor ρ in ant colony optimizers (ACO). While a large update strength is desirable for exploitation, there is a general trade-off: too strong updates can lead to unstable behavior and possibly poor performance. We demonstrate this trade-off for the cGA and a simple ACO algorithm on the well-known OneMax function. More precisely, we obtain lower bounds on the expected runtime of Ω(Kn−−√+nlogn) and Ω(n−−√/ρ+nlogn), respectively, suggesting that the update strength should be limited to 1/K,ρ=O(1/(n−−√logn)). In fact, choosing 1/K,ρ∼1/(n−−√logn) both algorithms efficiently optimize OneMax in expected time Θ(nlogn). Our analyses provide new insights into the stochastic behavior of PMBGAs and propose new guidelines for setting the update strength in global optimization

Compact Optimization Algorithms with Re-sampled Inheritance

The file attached to this record is the author's final peer reviewed version.Compact optimization algorithms are a class of Estimation of Distribution Algorithms (EDAs) characterized by extremely limited memory requirements (hence they are called \compact"). As all EDAs, compact algorithms build and update a probabilistic model of the distribution of solutions within the search space, as opposed to population-based algorithms that instead make use of an explicit population of solutions. In addition to that, to keep their memory consumption low, compact algorithms purposely employ simple probabilistic models that can be described with a small number of parameters. Despite their simplicity, compact algorithms have shown good performances on a broad range of benchmark functions and real-world problems. However, compact algorithms also come with some drawbacks, i.e. they tend to premature convergence and show poorer performance on non-separable problems. To overcome these limitations, here we investigate a possible algorithmic scheme obtained by combining compact algorithms with a non-disruptive restart mechanism taken from the literature, named Re-Sampled Inheritance (RI). The resulting compact algorithms with RI are tested on the CEC 2014 benchmark functions. The numerical results show on the one hand that the use of RI consistently enhances the performances of compact algorithms, still keeping a limited usage of memory. On the other hand, our experiments show that among the tested algorithms, the best performance is obtained by compact Differential Evolution with RI

Genetic Ancestry-Smoking Interactions and Lung Function in African Americans: A Cohort Study

Background: Smoking tobacco reduces lung function. African Americans have both lower lung function and decreased metabolism of tobacco smoke compared to European Americans. African ancestry is also associated with lower pulmonary function in African Americans. We aimed to determine whether African ancestry modifies the association between smoking and lung function and its rate of decline in African Americans. Methodology/Principal Findings: We evaluated a prospective ongoing cohort of 1,281 African Americans participating in the Health, Aging, and Body Composition (Health ABC) Study initiated in 1997. We also examined an ongoing prospective cohort initiated in 1985 of 1,223 African Americans in the Coronary Artery Disease in Young Adults (CARDIA) Study. Pulmonary function and tobacco smoking exposure were measured at baseline and repeatedly over the follow-up period. Individual genetic ancestry proportions were estimated using ancestry informative markers selected to distinguish European and West African ancestry. African Americans with a high proportion of African ancestry had lower baseline forced expiratory volume in one second (FEV1) per pack-year of smoking (-5.7 ml FEV1/ smoking pack-year) compared with smokers with lower African ancestry (-4.6 ml in FEV1/ smoking pack-year) (interaction P value = 0.17). Longitudinal analyses revealed a suggestive interaction between smoking, and African ancestry on the rate of FEV1 decline in Health ABC and independently replicated in CARDIA. Conclusions/Significance: African American individuals with a high proportion of African ancestry are at greater risk for losing lung function while smoking. © 2012 Aldrich et al

A Framework for Knowledge Integrated Evolutionary Algorithms

One of the main reasons for the success of Evolutionary Algorithms (EAs) is their general-purposeness, i.e. the fact that they can be applied in a straight forward manner to a broad range of optimization problems, without any specific prior knowledge. On the other hand, it has been shown that incorporating a priori knowledge, such as expert knowledge or empirical findings, can significantly improve the performance of an EA. However, integrating knowledge in EAs poses numerous challenges. It is often the case that the features of the search space are unknown, hence any knowledge associated with the search space properties can be hardly used. In addition, a priori knowledge is typically problem-specific and hard to generalize. In this paper, we propose a framework, called Knowledge Integrated Evolutionary Algorithm (KIEA), which facilitates the integration of existing knowledge into EAs. Notably, the KIEA framework is EA-agnostic, i.e. it works with any evolutionary algorithm, problem-independent, i.e. it is not dedicated to a specific type of problems and expandable, i.e. its knowledge base can grow over time. Furthermore, the framework integrates knowledge while the EA is running, thus optimizing the consumption of computational power. In the preliminary experiments shown here, we observe that the KIEA framework produces in the worst case an 80% improvement on the converge time, w.r.t. the corresponding “knowledge-free” EA counterpart