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

Gravity Inversion of Talwani Model using Very Fast Simulated Annealing

Global approaches for estimating geophysical model parameters have been proposed by several authors, including their application for gravity interpretation, which is currently limited to simple and fixed geometrical problems. This paper proposes implementation of Very Fast Simulated Annealing (VFSA) in two-dimensional gravity interpretation problems, which are still rarely addressed. The modeling domain was divided into smaller sub-domains and gravity anomaly calculation was carried out based on the Talwani formulation.  To improve the uniqueness of the solution of under-determined problems, specific constraints were added in addition to the assumed known symmetry axes. The inversion of VFSA was tested on synthetic data generated by simple models and on previously published real data to evaluate the applicability of the proposed approach to the interpretation of field data

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

Coverage Protocols for Wireless Sensor Networks: Review and Future Directions

The coverage problem in wireless sensor networks (WSNs) can be generally defined as a measure of how effectively a network field is monitored by its sensor nodes. This problem has attracted a lot of interest over the years and as a result, many coverage protocols were proposed. In this survey, we first propose a taxonomy for classifying coverage protocols in WSNs. Then, we classify the coverage protocols into three categories (i.e. coverage aware deployment protocols, sleep scheduling protocols for flat networks, and cluster-based sleep scheduling protocols) based on the network stage where the coverage is optimized. For each category, relevant protocols are thoroughly reviewed and classified based on the adopted coverage techniques. Finally, we discuss open issues (and recommend future directions to resolve them) associated with the design of realistic coverage protocols. Issues such as realistic sensing models, realistic energy consumption models, realistic connectivity models and sensor localization are covered

Community Detection in Networks using Bio-inspired Optimization: Latest Developments, New Results and Perspectives with a Selection of Recent Meta-Heuristics

Detecting groups within a set of interconnected nodes is a widely addressed prob- lem that can model a diversity of applications. Unfortunately, detecting the opti- mal partition of a network is a computationally demanding task, usually conducted by means of optimization methods. Among them, randomized search heuristics have been proven to be efficient approaches. This manuscript is devoted to pro- viding an overview of community detection problems from the perspective of bio-inspired computation. To this end, we first review the recent history of this research area, placing emphasis on milestone studies contributed in the last five years. Next, we present an extensive experimental study to assess the performance of a selection of modern heuristics over weighted directed network instances. Specifically, we combine seven global search heuristics based on two different similarity metrics and eight heterogeneous search operators designed ad-hoc. We compare our methods with six different community detection techniques over a benchmark of 17 Lancichinetti-Fortunato-Radicchi network instances. Ranking statistics of the tested algorithms reveal that the proposed methods perform com- petitively, but the high variability of the rankings leads to the main conclusion: no clear winner can be declared. This finding aligns with community detection tools available in the literature that hinge on a sequential application of different algorithms in search for the best performing counterpart. We end our research by sharing our envisioned status of this area, for which we identify challenges and opportunities which should stimulate research efforts in years to come

Surrogate Model Optimisation for PWR Fuel Management

Pressurised Water Reactor (PWR) fuel management is an operational problem for nuclear operators, requiring solutions on a regular basis throughout the life of the plant. A variety of conflicting factors and changing goals mean that fuel loading pattern design problems are multiobjective and, by design, have many input variables. This causes a combinatorial explosion, known as the ‘curse of dimensionality’, which makes these complex problems difficult to investigate. In this thesis, the method of surrogate model optimisation is adapted to PWR loading pattern generation. Surrogate models are developed based around three approaches: deep learning methods (convolutional neural networks and multi-layer perceptrons), the fission matrix and simulated quantum annealing. The models are used to predict core parameters of reactors in simplified optimisation scenarios for a microcore, a small modular reactor, and a ‘standard’ PWR. The experiments with deep learning models show that competitive results can be obtained for training sets using a much lower number of simulations than direct optimisation. Fission matrix experiments demonstrate the method to predict core parameters for the first time, with interesting preliminary results. Novel experiments using simulated quantum annealing demonstrate the technique is able to generate loading patterns by following heuristic rules and is suitable for application to custom optimisation hardware. The principal contribution of this work is to show that surrogate model optimisation can be used to augment fuel loading pattern optimisation, generating competitive results and providing enormous computational cost reduction and thus permitting more investigation within a given computational budget. These methods can also make use of new computational hardware such as neural chips and quantum annealers. The promising methods developed in this thesis thus provide candidate implementations that can bring the benefits of these innovations to the sphere of nuclear engineering

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

An Evolutionary Approach to Multistage Portfolio Optimization

Portfolio optimization is an important problem in quantitative finance due to its application in asset management and corporate financial decision making. This involves quantitatively selecting the optimal portfolio for an investor given their asset return distribution assumptions, investment objectives and constraints. Analytical portfolio optimization methods suffer from limitations in terms of the problem specification and modelling assumptions that can be used. Therefore, a heuristic approach is taken where Monte Carlo simulations generate the investment scenarios and' a problem specific evolutionary algorithm is used to find the optimal portfolio asset allocations. Asset allocation is known to be the most important determinant of a portfolio's investment performance and also affects its risk/return characteristics. The inclusion of equity options in an equity portfolio should enable an investor to improve their efficient frontier due to options having a nonlinear payoff. Therefore, a research area of significant importance to equity investors, in which little research has been carried out, is the optimal asset allocation in equity options for an equity investor. A purpose of my thesis is to carry out an original analysis of the impact of allowing the purchase of put options and/or sale of call options for an equity investor. An investigation is also carried out into the effect ofchanging the investor's risk measure on the optimal asset allocation. A dynamic investment strategy obtained through multistage portfolio optimization has the potential to result in a superior investment strategy to that obtained from a single period portfolio optimization. Therefore, a novel analysis of the degree of the benefits of a dynamic investment strategy for an equity portfolio is performed. In particular, the ability of a dynamic investment strategy to mimic the effects ofthe inclusion ofequity options in an equity portfolio is investigated. The portfolio optimization problem is solved using evolutionary algorithms, due to their ability incorporate methods from a wide range of heuristic algorithms. Initially, it is shown how the problem specific parts ofmy evolutionary algorithm have been designed to solve my original portfolio optimization problem. Due to developments in evolutionary algorithms and the variety of design structures possible, a purpose of my thesis is to investigate the suitability of alternative algorithm design structures. A comparison is made of the performance of two existing algorithms, firstly the single objective stepping stone island model, where each island represents a different risk aversion parameter, and secondly the multi-objective Non-Dominated Sorting Genetic Algorithm2. Innovative hybrids of these algorithms which also incorporate features from multi-objective evolutionary algorithms, multiple population models and local search heuristics are then proposed. . A novel way is developed for solving the portfolio optimization by dividing my problem solution into two parts and then applying a multi-objective cooperative coevolution evolutionary algorithm. The first solution part consists of the asset allocation weights within the equity portfolio while the second solution part consists 'ofthe asset allocation weights within the equity options and the asset allocation weights between the different asset classes. An original portfolio optimization multiobjective evolutionary algorithm that uses an island model to represent different risk measures is also proposed.Imperial Users onl

Preventing premature convergence and proving the optimality in evolutionary algorithms

http://ea2013.inria.fr//proceedings.pdfInternational audienceEvolutionary Algorithms (EA) usually carry out an efficient exploration of the search-space, but get often trapped in local minima and do not prove the optimality of the solution. Interval-based techniques, on the other hand, yield a numerical proof of optimality of the solution. However, they may fail to converge within a reasonable time due to their inability to quickly compute a good approximation of the global minimum and their exponential complexity. The contribution of this paper is a hybrid algorithm called Charibde in which a particular EA, Differential Evolution, cooperates with a Branch and Bound algorithm endowed with interval propagation techniques. It prevents premature convergence toward local optima and outperforms both deterministic and stochastic existing approaches. We demonstrate its efficiency on a benchmark of highly multimodal problems, for which we provide previously unknown global minima and certification of optimality