On the role of metaheuristic optimization in bioinformatics

Metaheuristic algorithms are employed to solve complex and large-scale optimization problems in many different fields, from transportation and smart cities to finance. This paper discusses how metaheuristic algorithms are being applied to solve different optimization problems in the area of bioinformatics. While the text provides references to many optimization problems in the area, it focuses on those that have attracted more interest from the optimization community. Among the problems analyzed, the paper discusses in more detail the molecular docking problem, the protein structure prediction, phylogenetic inference, and different string problems. In addition, references to other relevant optimization problems are also given, including those related to medical imaging or gene selection for classification. From the previous analysis, the paper generates insights on research opportunities for the Operations Research and Computer Science communities in the field of bioinformatics

Portfolio Optimization Using Evolutionary Algorithms

Dissertation presented as the partial requirement for obtaining a Master's degree in Data Science and Advanced AnalyticsPortfolio optimization is a widely studied field in modern finance. It involves finding the optimal balance between two contradictory objectives, the risk and the return. As the number of assets rises, the complexity in portfolios increases considerably, making it a computational challenge. This report explores the application of the Multi-Objective Evolutionary Algorithm based on Decomposition (MOEA/D) and Genetic Algorithm (GA) in the field of portfolio optimization. MOEA/D and GA have proven to be effective at finding portfolios. However, it remains unclear how they perform when compared to traditional approaches used in finance. To achieve this, a framework for portfolio optimization is proposed, using MOEA/D, and GA separately as optimization algorithms and Capital Asset Pricing Model (CAPM) and Mean-Variance Model as methods to evaluate portfolios. The proposed framework is able to produce weighted portfolios successfully. These generated portfolios were evaluated using a simulation with subsequent (unseen) prices of the assets included in the portfolio. The simulation was compared with well known portfolios in the same market and other market benchmarks (Security Market Line and Market Portfolio). The results obtained in this investigation exceeded expectation by creating portfolios that perform better than the market. CAPM and Mean-Variance Model, although they fail to model all the variables that affect the stock market, provide a simple valuation for assets and portfolios. MOEA/D using Differential Evolution operators and the CAPM model produced the best portfolios in this research. Work can still be done to accommodate more variables that can affect markets and portfolios, such as taxes, investment horizon and costs for transactions

Stochastic Fractal Based Multiobjective Fruit Fly Optimization

The fruit fly optimization algorithm (FOA) is a global optimization algorithm inspired by the foraging behavior of a fruit fly swarm. In this study, a novel stochastic fractal model based fruit fly optimization algorithm is proposed for multiobjective optimization. A food source generating method based on a stochastic fractal with an adaptive parameter updating strategy is introduced to improve the convergence performance of the fruit fly optimization algorithm. To deal with multiobjective optimization problems, the Pareto domination concept is integrated into the selection process of fruit fly optimization and a novel multiobjective fruit fly optimization algorithm is then developed. Similarly to most of other multiobjective evolutionary algorithms (MOEAs), an external elitist archive is utilized to preserve the nondominated solutions found so far during the evolution, and a normalized nearest neighbor distance based density estimation strategy is adopted to keep the diversity of the external elitist archive. Eighteen benchmarks are used to test the performance of the stochastic fractal based multiobjective fruit fly optimization algorithm (SFMOFOA). Numerical results show that the SFMOFOA is able to well converge to the Pareto fronts of the test benchmarks with good distributions. Compared with four state-of-the-art methods, namely, the non-dominated sorting generic algorithm (NSGA-II), the strength Pareto evolutionary algorithm (SPEA2), multi-objective particle swarm optimization (MOPSO), and multiobjective self-adaptive differential evolution (MOSADE), the proposed SFMOFOA has better or competitive multiobjective optimization performance

Digital Filter Design Using Improved Teaching-Learning-Based Optimization

Digital filters are an important part of digital signal processing systems. Digital filters are divided into finite impulse response (FIR) digital filters and infinite impulse response (IIR) digital filters according to the length of their impulse responses. An FIR digital filter is easier to implement than an IIR digital filter because of its linear phase and stability properties. In terms of the stability of an IIR digital filter, the poles generated in the denominator are subject to stability constraints. In addition, a digital filter can be categorized as one-dimensional or multi-dimensional digital filters according to the dimensions of the signal to be processed. However, for the design of IIR digital filters, traditional design methods have the disadvantages of easy to fall into a local optimum and slow convergence. The Teaching-Learning-Based optimization (TLBO) algorithm has been proven beneficial in a wide range of engineering applications. To this end, this dissertation focusses on using TLBO and its improved algorithms to design five types of digital filters, which include linear phase FIR digital filters, multiobjective general FIR digital filters, multiobjective IIR digital filters, two-dimensional (2-D) linear phase FIR digital filters, and 2-D nonlinear phase FIR digital filters. Among them, linear phase FIR digital filters, 2-D linear phase FIR digital filters, and 2-D nonlinear phase FIR digital filters use single-objective type of TLBO algorithms to optimize; multiobjective general FIR digital filters use multiobjective non-dominated TLBO (MOTLBO) algorithm to optimize; and multiobjective IIR digital filters use MOTLBO with Euclidean distance to optimize. The design results of the five types of filter designs are compared to those obtained by other state-of-the-art design methods. In this dissertation, two major improvements are proposed to enhance the performance of the standard TLBO algorithm. The first improvement is to apply a gradient-based learning to replace the TLBO learner phase to reduce approximation error(s) and CPU time without sacrificing design accuracy for linear phase FIR digital filter design. The second improvement is to incorporate Manhattan distance to simplify the procedure of the multiobjective non-dominated TLBO (MOTLBO) algorithm for general FIR digital filter design. The design results obtained by the two improvements have demonstrated their efficiency and effectiveness