Clustering Algorithms: Their Application to Gene Expression Data

Gene expression data hide vital information required to understand the biological process that takes place in a particular organism in relation to its environment. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks and the volume of genes present increase the challenges of comprehending and interpretation of the resulting mass of data, which consists of millions of measurements; these data also inhibit vagueness, imprecision, and noise. Therefore, the use of clustering techniques is a first step toward addressing these challenges, which is essential in the data mining process to reveal natural structures and iden-tify interesting patterns in the underlying data. The clustering of gene expression data has been proven to be useful in making known the natural structure inherent in gene expression data, understanding gene functions, cellular processes, and subtypes of cells, mining useful information from noisy data, and understanding gene regulation. The other benefit of clustering gene expression data is the identification of homology, which is very important in vaccine design. This review examines the various clustering algorithms applicable to the gene expression data in order to discover and provide useful knowledge of the appropriate clustering technique that will guarantee stability and high degree of accuracy in its analysis procedure

ONLINE APPROXIMATION ASSISTED MULTIOBJECTIVE OPTIMIZATION WITH HEAT EXCHANGER DESIGN APPLICATIONS

Computer simulations can be intensive as is the case in Computational Fluid Dynamics (CFD) and Finite Element Analysis (FEA). The computational cost can become prohibitive when using these simulations with multiobjective design optimization. One way to address this issue is to replace a computationally intensive simulation by an approximation which allows for a quick evaluation of a large number of design alternatives as needed by an optimizer. This dissertation proposes an approach for multiobjective design optimization when combined with computationally expensive simulations for heat exchanger design problems. The research is performed along four research directions. These are: (1) a new Online Approximation Assisted Multiobjective Optimization (OAAMO) approach with a focus on the expected optimum region, (2) a new approximation assisted multiobjective optimization with global and local metamodeling that always produces feasible solutions, (3) a framework that integrates OAAMO with multiscale simulations (OAAMOMS) for design of heat exchangers at the segment and heat exchanger levels, and (4) applications of OAAMO combined with CFD for shape design of a header for a new generation of heat exchangers using Non-Uniform Rational B-Splines (NURBS). The approaches developed in this thesis are also applied to optimize a coldplate used in electronic cooling devices and different types of plate heat exchangers. In addition many numerical test problems are solved by the proposed methods. The results of these studies show that the proposed online approximation assisted multiobjective optimization is an efficient approach that can be used to predict optimum solutions for a wide class of problems including heat exchanger design problems while reducing significantly the computational cost when compared with existing methods

On Proportionate and Truthful International Alliance Contributions: An Analysis of Incentive Compatible Cost Sharing Mechanisms to Burden Sharing

Burden sharing within an international alliance is a contentious topic, especially in the current geopolitical environment, that in practice is generally imposed by a central authority\u27s perception of its members\u27 abilities to contribute. Instead, we propose a cost sharing mechanism such that burden shares are allocated to nations based on their honest declarations of the alliance\u27s worth. Specifically, we develop a set of multiobjective nonlinear optimization problem formulations that respectively impose Bayesian Incentive Compatible (BIC), Strategyproof (SP), and Group Strategyproof (GSP) mechanisms based on probabilistic inspection efforts and deception penalties that are budget balanced and in the core. Any feasible solution to these problems corresponds to a single stage Bayesian stochastic game wherein a collectively honest declaration is a Bayes-Nash equilibrium, a Nash Equilibrium in dominant strategies, or a collusion resistant Nash equilibrium, respectively, but the optimal solution considers the alliance\u27s central authority preferences. Each formulation is shown to be a nonconvex optimization problem. The solution quality and computational effort required for three heuristic algorithms as well as the BARON global solver are analyzed to determine the superlative solution methodology for each problem. The Pareto fronts associated with each multiobjective optimization problem are examined to determine the tradeoff between inspection frequency and penalty severity required to obtain truthfulness under stronger assumptions. Memory limitations are examined to ascertain the size of alliances for which the proposed methodology can be utilized. Finally, a full block design experiment considering the clustering of available alliance valuations and the member nations\u27 probability distributions therein is executed on an intermediate-sized alliance motivated by the South American alliance UNASUR

Innovative Applications of Genetic Algorithms to Problems in Accelerator Physics

The genetic algorithm (GA) is a powerful technique that implements the principles nature uses in biological evolution to optimize a multidimensional nonlinear problem. The GA works especially well for problems with a large number of local extrema, where traditional methods (such as conjugate gradient, steepest descent, and others) fail or, at best, underperform. The field of accelerator physics, among others, abounds with problems which lend themselves to optimization via GAs. In this paper, we report on the successful application of GAs in several problems related to the existing Continuous Electron Beam Accelerator Facility nuclear physics machine, the proposed Medium-energy Electron-Ion Collider at Jefferson Lab, and a radio frequency gun-based injector. These encouraging results are a step forward in optimizing accelerator design and provide an impetus for application of GAs to other problems in the field. To that end, we discuss the details of the GAs used, include a newly devised enhancement which leads to improved convergence to the optimum, and make recommendations for future GA developments and accelerator applications

Digital Filter Design Using Improved Artificial Bee Colony Algorithms

Digital filters are often used in digital signal processing applications. The design objective of a digital filter is to find the optimal set of filter coefficients, which satisfies the desired specifications of magnitude and group delay responses. Evolutionary algorithms are population-based meta-heuristic algorithms inspired by the biological behaviors of species. Compared to gradient-based optimization algorithms such as steepest descent and Newton’s like methods, these bio-inspired algorithms have the advantages of not getting stuck at local optima and being independent of the starting point in the solution space. The limitations of evolutionary algorithms include the presence of control parameters, problem specific tuning procedure, premature convergence and slower convergence rate. The artificial bee colony (ABC) algorithm is a swarm-based search meta-heuristic algorithm inspired by the foraging behaviors of honey bee colonies, with the benefit of a relatively fewer control parameters. In its original form, the ABC algorithm has certain limitations such as low convergence rate, and insufficient balance between exploration and exploitation in the search equations. In this dissertation, an ABC-AMR algorithm is proposed by incorporating an adaptive modification rate (AMR) into the original ABC algorithm to increase convergence rate by adjusting the balance between exploration and exploitation in the search equations through an adaptive determination of the number of parameters to be updated in every iteration. A constrained ABC-AMR algorithm is also developed for solving constrained optimization problems.There are many real-world problems requiring simultaneous optimizations of more than one conflicting objectives. Multiobjective (MO) optimization produces a set of feasible solutions called the Pareto front instead of a single optimum solution. For multiobjective optimization, if a decision maker’s preferences can be incorporated during the optimization process, the search process can be confined to the region of interest instead of searching the entire region. In this dissertation, two algorithms are developed for such incorporation. The first one is a reference-point-based MOABC algorithm in which a decision maker’s preferences are included in the optimization process as the reference point. The second one is a physical-programming-based MOABC algorithm in which physical programming is used for setting the region of interest of a decision maker. In this dissertation, the four developed algorithms are applied to solve digital filter design problems. The ABC-AMR algorithm is used to design Types 3 and 4 linear phase FIR differentiators, and the results are compared to those obtained by the original ABC algorithm, three improved ABC algorithms, and the Parks-McClellan algorithm. The constrained ABC-AMR algorithm is applied to the design of sparse Type 1 linear phase FIR filters of filter orders 60, 70 and 80, and the results are compared to three state-of-the-art design methods. The reference-point-based multiobjective ABC algorithm is used to design of asymmetric lowpass, highpass, bandpass and bandstop FIR filters, and the results are compared to those obtained by the preference-based multiobjective differential evolution algorithm. The physical-programming-based multiobjective ABC algorithm is used to design IIR lowpass, highpass and bandpass filters, and the results are compared to three state-of-the-art design methods. Based on the obtained design results, the four design algorithms are shown to be competitive as compared to the state-of-the-art design methods

A cognitive approach for the multi-objective optimization of RC structural problems

This paper proposes a cognitive approach for analyzing and reducing the Pareto optimal set for multi-objective optimization (MOO) of structural problems by means of jointly incorporating subjective and objective aspects. The approach provides improved knowledge on the decision-making process and makes it possible for the actors involved in the resolution process and its integrated systems to learn from the experience. The methodology consists of four steps: (i) the construction of the Pareto set using MOO models; (ii) the filtering of the Pareto set by compromise programming methods; (iii) the selection of the preferred solutions, utilizing the relative importance of criteria and the Analytic Hierarchy Process (AHP); (iv) the extraction of the relevant knowledge derived from the resolution process. A case study on the reinforced concrete (RC) I-beam has been included to illustrate the methodology. The compromise solutions are obtained through the objectives of economic feasibility, structural safety, and environmental sustainability criteria. The approach further identifies the patterns of behavior and critical points of the resolution process which reflect the relevant knowledge derived from the cognitive perspective. Results indicated that the solutions selected increased the number of years of service life. The procedure produced durable and ecological structures without price trade-offs.The Spanish Ministry of Science and Innovation.Yepes, V.; García Segura, T.; Moreno-Jiménez, J. (2015). A cognitive approach for the multi-objective optimization of RC structural problems. Archives of Civil and Mechanical Engineering. 15(4):1024-1036. https://doi.org/10.1016/j.acme.2015.05.001S1024103615

Volumetric Techniques for Product Routing and Loading Optimisation in Industry 4.0: A Review

Industry 4.0 has become a crucial part in the majority of processes, components, and related modelling, as well as predictive tools that allow a more efficient, automated and sustainable approach to industry. The availability of large quantities of data, and the advances in IoT, AI, and data-driven frameworks, have led to an enhanced data gathering, assessment, and extraction of actionable information, resulting in a better decision-making process. Product picking and its subsequent packing is an important area, and has drawn increasing attention for the research community. However, depending of the context, some of the related approaches tend to be either highly mathematical, or applied to a specific context. This article aims to provide a survey on the main methods, techniques, and frameworks relevant to product packing and to highlight the main properties and features that should be further investigated to ensure a more efficient and optimised approach

International Conference on Continuous Optimization (ICCOPT) 2019 Conference Book

The Sixth International Conference on Continuous Optimization took place on the campus of the Technical University of Berlin, August 3-8, 2019. The ICCOPT is a flagship conference of the Mathematical Optimization Society (MOS), organized every three years. ICCOPT 2019 was hosted by the Weierstrass Institute for Applied Analysis and Stochastics (WIAS) Berlin. It included a Summer School and a Conference with a series of plenary and semi-plenary talks, organized and contributed sessions, and poster sessions. This book comprises the full conference program. It contains, in particular, the scientific program in survey style as well as with all details, and information on the social program, the venue, special meetings, and more

Applied Metaheuristic Computing

For decades, Applied Metaheuristic Computing (AMC) has been a prevailing optimization technique for tackling perplexing engineering and business problems, such as scheduling, routing, ordering, bin packing, assignment, facility layout planning, among others. This is partly because the classic exact methods are constrained with prior assumptions, and partly due to the heuristics being problem-dependent and lacking generalization. AMC, on the contrary, guides the course of low-level heuristics to search beyond the local optimality, which impairs the capability of traditional computation methods. This topic series has collected quality papers proposing cutting-edge methodology and innovative applications which drive the advances of AMC