Identification of disease-causing genes using microarray data mining and gene ontology

Background: One of the best and most accurate methods for identifying disease-causing genes is monitoring gene expression values in different samples using microarray technology. One of the shortcomings of microarray data is that they provide a small quantity of samples with respect to the number of genes. This problem reduces the classification accuracy of the methods, so gene selection is essential to improve the predictive accuracy and to identify potential marker genes for a disease. Among numerous existing methods for gene selection, support vector machine-based recursive feature elimination (SVMRFE) has become one of the leading methods, but its performance can be reduced because of the small sample size, noisy data and the fact that the method does not remove redundant genes. Methods: We propose a novel framework for gene selection which uses the advantageous features of conventional methods and addresses their weaknesses. In fact, we have combined the Fisher method and SVMRFE to utilize the advantages of a filtering method as well as an embedded method. Furthermore, we have added a redundancy reduction stage to address the weakness of the Fisher method and SVMRFE. In addition to gene expression values, the proposed method uses Gene Ontology which is a reliable source of information on genes. The use of Gene Ontology can compensate, in part, for the limitations of microarrays, such as having a small number of samples and erroneous measurement results. Results: The proposed method has been applied to colon, Diffuse Large B-Cell Lymphoma (DLBCL) and prostate cancer datasets. The empirical results show that our method has improved classification performance in terms of accuracy, sensitivity and specificity. In addition, the study of the molecular function of selected genes strengthened the hypothesis that these genes are involved in the process of cancer growth. Conclusions: The proposed method addresses the weakness of conventional methods by adding a redundancy reduction stage and utilizing Gene Ontology information. It predicts marker genes for colon, DLBCL and prostate cancer with a high accuracy. The predictions made in this study can serve as a list of candidates for subsequent wet-lab verification and might help in the search for a cure for cancers

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

A Comprehensive Survey on Particle Swarm Optimization Algorithm and Its Applications

Particle swarm optimization (PSO) is a heuristic global optimization method, proposed originally by Kennedy and Eberhart in 1995. It is now one of the most commonly used optimization techniques. This survey presented a comprehensive investigation of PSO. On one hand, we provided advances with PSO, including its modifications (including quantum-behaved PSO, bare-bones PSO, chaotic PSO, and fuzzy PSO), population topology (as fully connected, von Neumann, ring, star, random, etc.), hybridization (with genetic algorithm, simulated annealing, Tabu search, artificial immune system, ant colony algorithm, artificial bee colony, differential evolution, harmonic search, and biogeography-based optimization), extensions (to multiobjective, constrained, discrete, and binary optimization), theoretical analysis (parameter selection and tuning, and convergence analysis), and parallel implementation (in multicore, multiprocessor, GPU, and cloud computing forms). On the other hand, we offered a survey on applications of PSO to the following eight fields: electrical and electronic engineering, automation control systems, communication theory, operations research, mechanical engineering, fuel and energy, medicine, chemistry, and biology. It is hoped that this survey would be beneficial for the researchers studying PSO algorithms

A Survey of Feature Selection Strategies for DNA Microarray Classification

Classification tasks are difficult and challenging in the bioinformatics field, that used to predict or diagnose patients at an early stage of disease by utilizing DNA microarray technology. However, crucial characteristics of DNA microarray technology are a large number of features and small sample sizes, which means the technology confronts a "dimensional curse" in its classification tasks because of the high computational execution needed and the discovery of biomarkers difficult. To reduce the dimensionality of features to find the significant features that can employ feature selection algorithms and not affect the performance of classification tasks. Feature selection helps decrease computational time by removing irrelevant and redundant features from the data. The study aims to briefly survey popular feature selection methods for classifying DNA microarray technology, such as filters, wrappers, embedded, and hybrid approaches. Furthermore, this study describes the steps of the feature selection process used to accomplish classification tasks and their relationships to other components such as datasets, cross-validation, and classifier algorithms. In the case study, we chose four different methods of feature selection on two-DNA microarray datasets to evaluate and discuss their performances, namely classification accuracy, stability, and the subset size of selected features. Keywords: Brief survey; DNA microarray data; feature selection; filter methods; wrapper methods; embedded methods; and hybrid methods. DOI: 10.7176/CEIS/14-2-01 Publication date:March 31st 202

Parallel Exchange of Randomized SubGraphs for Optimization of Network Alignment: PERSONA

The aim of Network Alignment in Protein-Protein Interaction Networks is discovering functionally similar regions between compared organisms. One major compromise for solving a network alignment problem is the trade-off among multiple similarity objectives while applying an alignment strategy. An alignment may lose its biological relevance while favoring certain objectives upon others due to the actual relevance of unfavored objectives. One possible solution for solving this issue may be blending the stronger aspects of various alignment strategies until achieving mature solutions. This study proposes a parallel approach called PERSONA that allows aligners to share their partial solutions continuously while they progress. All these aligners pursue their particular heuristics as part of a particle swarm that searches for multi-objective solutions of the same alignment problem in a reactive actor environment. The actors use the stronger portion of a solution as a subgraph that they receive from leading or other actors and send their own stronger subgraphs back upon evaluation of those partial solutions. Moreover, the individual heuristics of each actor takes randomized parameter values at each cycle of parallel execution so that the problem search space can thoroughly be investigated. The results achieved with PERSONA are remarkably optimized and balanced for both topological and node similarity objectives

Hybridization of Biologically Inspired Algorithms for Discrete Optimisation Problems

In the field of Optimization Algorithms, despite the popularity of hybrid designs, not enough consideration has been given to hybridization strategies. This paper aims to raise awareness of the benefits that such a study can bring. It does this by conducting a systematic review of popular algorithms used for optimization, within the context of Combinatorial Optimization Problems. Then, a comparative analysis is performed between Hybrid and Base versions of the algorithms to demonstrate an increase in optimization performance when hybridization is employed

An academic review: applications of data mining techniques in finance industry

With the development of Internet techniques, data volumes are doubling every two years, faster than predicted by Moore’s Law. Big Data Analytics becomes particularly important for enterprise business. Modern computational technologies will provide effective tools to help understand hugely accumulated data and leverage this information to get insights into the finance industry. In order to get actionable insights into the business, data has become most valuable asset of financial organisations, as there are no physical products in finance industry to manufacture. This is where data mining techniques come to their rescue by allowing access to the right information at the right time. These techniques are used by the finance industry in various areas such as fraud detection, intelligent forecasting, credit rating, loan management, customer profiling, money laundering, marketing and prediction of price movements to name a few. This work aims to survey the research on data mining techniques applied to the finance industry from 2010 to 2015.The review finds that Stock prediction and Credit rating have received most attention of researchers, compared to Loan prediction, Money Laundering and Time Series prediction. Due to the dynamics, uncertainty and variety of data, nonlinear mapping techniques have been deeply studied than linear techniques. Also it has been proved that hybrid methods are more accurate in prediction, closely followed by Neural Network technique. This survey could provide a clue of applications of data mining techniques for finance industry, and a summary of methodologies for researchers in this area. Especially, it could provide a good vision of Data Mining Techniques in computational finance for beginners who want to work in the field of computational finance

Hybrid of ant colony optimization and flux variability analysis for improving metabolites production

Metabolic engineering has been successfully used for the production of a variety of useful compounds such as L-phenylalanine and biohydrogen that received high demand on food, pharmaceutical, fossil fuels, and energy industries. Reaction deletion is one of the strategies of in silico metabolic engineering that can alter the metabolism of microbial cells with the objective to get the desired phenotypes. However, due to the size and complexity of metabolic networks, it is difficult to determine the near-optimal set of reactions to be knocked out. The complexity of the metabolic network is also caused by the presence of competing pathway that may interrupt the high production of a desireable metabolite. Consequently, this factor leads to low Biomass-Product Coupled Yield (BPCY), production rate and growth rate. Other than that, inefficiency of existing algorithms in modelling high growth rate and production rate is another problem that should be handled and solved. Therefore, this research proposed a hybrid algorithm comprising Ant Colony Optimization and Flux Variability Analysis (ACOFVA) to identify the best reaction combination to be knocked out to improve the production of desired metabolites in microorganisms. Based on the experimental results, ACOFVA shows an increase in terms of BPCY and production rate of L-Phenylalanine in Yeast and biohydrogen in Cyanobacteria, while maintaining the optimal growth rate for the target organism. Besides, suggested reactions to be knocked out for improving the production yield of L-Phenylalanine and biohydrogen have been identified and validated through the biological database. The algorithm also shows a good performance with better production rate and BPCY of L-Phenylalanine and biohydrogen than existing results

A multi-domain VNE algorithm based on load balancing in the IoT networks

The coordinated development of big data, Internet of Things, cloud computing and other technologies has led to an exponential growth in Internet business. However, the traditional Internet architecture gradually shows a rigid phenomenon due to the binding of the network structure and the hardware. In a high-traffic environment, it has been insufficient to meet people’s increasing service quality requirements. Network virtualization is considered to be an effective method to solve the rigidity of the Internet. Among them, virtual network embedding is one of the key problems of network virtualization. Since virtual network mapping is an NP-hard problem, a large number of research has focused on the evolutionary algorithm’s masterpiece genetic algorithm. However, the parameter setting in the traditional method is too dependent on experience, and its low flexibility makes it unable to adapt to increasingly complex network environments. In addition, link-mapping strategies that do not consider load balancing can easily cause link blocking in high-traffic environments. In the IoT environment involving medical, disaster relief, life support and other equipment, network performance and stability are particularly important. Therefore, how to provide a more flexible virtual network mapping service in a heterogeneous network environment with large traffic is an urgent problem. Aiming at this problem, a virtual network mapping strategy based on hybrid genetic algorithm is proposed. This strategy uses a dynamically calculated cross-probability and pheromone based mutation gene selection strategy to improve the flexibility of the algorithm. In addition, a weight update mechanism based on load balancing is introduced to reduce the probability of mapping failure while balancing the load. Simulation results show that the proposed method performs well in a number of performance metrics including mapping average quotation, link load balancing, mapping cost-benefit ratio, acceptance rate and running time.Peer ReviewedPostprint (published version