Using bayesian networks to construct gene regulatory networks from microarray data

In this research, Bayesian network is proposed as the model to construct gene regulatory networks from Saccharomyces cerevisiae cell-cycle gene expression dataset and Escherichia coli dataset due to its capability of handling microarray datasets with missing values. The goal of this research is to study and to understand the framework of the Bayesian networks, and then to construct gene regulatory networks from Saccharomyces cerevisiae cell-cycle gene expression dataset and Escherichia coli dataset by developing Bayesian networks using hill-climbing algorithm and Efron’s bootstrap approach and then the performance of the constructed gene networks of Saccharomyces cerevisiae are evaluated and are compared with the previously constructed sub-networks by Dejori [14]. At the end of this research, the gene networks constructed for Saccharomyces cerevisiae not only have achieved high True Positive Rate (more than 90%), but the networks constructed also have discovered more potential interactions between genes. Therefore, it can be concluded that the performance of the gene regulatory networks constructed using Bayesian networks in this research is proved to be better because it can reveal more gene relationships

Specific Tuning Parameter for Directed Random Walk Algorithm Cancer Classification

Accuracy of cancerous gene classification is a central challenge in clinical cancer research. Microarray-based gene biomarkers have proved the performance and its ability over traditional clinical parameters. However, gene biomarkers of an individual are less robustness due to litter reproducibility between different cohorts of patients. Several methods incorporating pathway information such as directed random walk have been proposed to infer the pathway activity. This paper discusses the implementation of group specific tuning parameter in directed random walk algorithm. In this experiment, gene expression data and pathway data are used as input data. Throughout this experiment, more significant pathway activities can be identified which increases the accuracy of cancer classification. The lung cancer gene is used as the experimental dataset, with which, the sDRW is used in determining significant pathways. More risk-active pathways are identified throughout this experiment

An Improved Algorithm for Optimising the Production of Biochemical Systems

This chapter presents an improved method for constrained optimisation of biochemical systems production. The aim of the proposed method is to maximise its production and, at the same time, to minimise the total amount of chemical concentrations involved in producing the best production. The proposed method models biochemical systems with ordinary differential equations. The optimisation process became complex for the large size of biochemical systems that contain many chemicals. In addition, several constraints as the steady-state constraint and the constraint of chemical concentrations also contributed to the computational complexity and difficulty in the optimisation process. This chapter considers the biochemical systems as a nonlinear equations system. To solve the nonlinear equations system, the Newton method was applied. Then, both genetic algorithm and cooperative co-evolutionary algorithm were applied to fine-tune the components in the biochemical systems to maximise the production and minimise the total amount of chemical concentrations involved. Two biochemical systems were used, namely the ethanol production in the Saccharomyces cerevisiae pathway and the tryptophan production in the Escherichia coli pathway. In evaluating the performance of the proposed method, several comparisons with other works were performed, and the proposed method demonstrated its effectiveness in maximising the production and minimising the total amount of chemical concentrations involved

An improved hybrid of SVM and SCAD for pathway analysis

Pathway analysis has lead to a new era in genomic research by providing further biological process information compared to traditional single gene analysis. Beside the advantage, pathway analysis provides some challenges to the researchers, one of which is the quality of pathway data itself. The pathway data usually defined from biological context free, when it comes to a specific biological context (e.g. lung cancer disease), typically only several genes within pathways are responsible for the corresponding cellular process. It also can be that some pathways may be included with uninformative genes or perhaps informative genes were excluded. Moreover, many algorithms in pathway analysis neglect these limitations by treating all the genes within pathways as significant. In previous study, a hybrid of support vector machines and smoothly clipped absolute deviation with groups-specific tuning parameters (gSVM-SCAD) was proposed in order to identify and select the informative genes before the pathway evaluation process. However, gSVM-SCAD had showed a limitation in terms of the performance of classification accuracy. In order to deal with this limitation, we made an enhancement to the tuning parameter method for gSVM-SCAD by applying the B-Type generalized approximate cross validation (BGACV). Experimental analyses using one simulated data and two gene expression data have shown that the proposed method obtains significant results in identifying biologically significant genes and pathways, and in classification accuracy

National Endowment for the Arts: News Articles (1980): Article 05

<p>The result of two-fitness evaluation concept in case study 2.</p

Social Environment Influence Lifestyle of Youth in Rural Area

This paper aims to discuss the influence of social environment on the lifestyle of youth in the rural area. The social environment refers to the immediate physical and social setting in which youth live or in which something happens or develops. It includes the public amenities provided by the authority to be used by the public. A healthy lifestyle was measured by asking respondents to respond to questions whether social environment facilities provided in the area influence the youth lifestyle. Social environment positively influences the healthy lifestyle of youth. However it differed between areas.Keywords: Social Environment, Lifestyle, YouthISSN: 2398-4287© 2017. The Authors. Published for AMER ABRA by e-International Publishing House, Ltd., UK. This is an open access article under the CC BYNC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Peer–review under responsibility of AMER (Association of Malaysian Environment-Behaviour Researchers), ABRA (Association of Behavioural Researchers on Asians) and cE-Bs (Centre for Environment-Behaviour Studies), Faculty of Architecture, Planning &amp; Surveying, Universiti Teknologi MARA, Malaysia

Review of the machine learning methods in the classification of phishing attack

The development of computer networks today has increased rapidly. This can be seen based on the trend of computer users around the world, whereby they need to connect their computer to the Internet. This shows that the use of Internet networks is very important, whether for work purposes or access to social media accounts. However, in widely using this computer network, the privacy of computer users is in danger, especially for computer users who do not install security systems in their computer. This problem will allow hackers to hack and commit network attacks. This is very dangerous, especially for Internet users because hackers can steal confidential information such as bank login account or social media login account. The attacks that can be made include phishing attacks. The goal of this study is to review the types of phishing attacks and current methods used in preventing them. Based on the literature, the machine learning method is widely used to prevent phishing attacks. There are several algorithms that can be used in the machine learning method to prevent these attacks. This study focused on an algorithm that was thoroughly made and the methods in implementing this algorithm are discussed in detail

Multi-objective Optimization of Biochemical System Production Using an Improve Newton Competitive Differential Evolution Method

In this paper, an improve method of multi-objective optimization for biochemical system production is presented and discussed in detail. The optimization process of biochemical system production become hard and difficult when involved a large biochemical system that contain with many components. In addition, the multi-objective problem also need to be considered. Due to that, this study proposed and improve method that comprises with Newton method, differential evolution algorithm (DE) and competitive co-evolutionary algorithm(ComCA). The aim of the proposed method is to maximize the production and simultaneously minimize the total amount of chemical concentrations involves. The operation of the proposed method starts with Newton method by dealing with biochemical system production as a nonlinear equations system. Then DE and ComCA are used to represent the variables in nonlinear equation system and tune the variables in order to find the best solution. The used of DE is to maximize the production while ComCA is to minimize the total amount of chemical concentrations involves. The effectiveness of the proposed method is evaluated using two benchmark biochemical systems and the experimental results show that the proposed method perform well compared to other works

Solar energy : dilemma and the way forward / Norhafizah Yusop ... [et al.]

Renewable energy plays important roles in supplying energy to the world since it able to reduce the demand of fossil fuels. Natural processes and minerals such as sunlight, wind, tide and geothermal heat describes renewable energy. Nowadays, the world is shifting to renewable energy sources due to several factors such as rising prices of oil and gas and scarcity. Theoretically, solar energy is the energy from the sun. Too expensive for mainstream market was the main factors that make solar technologies occupied on uncomfortable position. As time change, global warming and climate change began to emerge. Essentially, solar power can offer a greener, cheaper path to development.Furthermore, meeting rising energy demand with cost-effective new generation capacity is a critical challenge facing most developing countries. Review of literatures shows that it is a clear signal that something needs to be done about renewable energy to put the world on a better path to avoiding the impacts of climate change.Thus, Just in Time (JIT), one procurement mechanism and support schemes for clean energy such as solar energy seems to lead the charge. This research involved a literature search on the challenges of the solar energy and the way forward based on the frequency of the factors identified by past researchers. As a result, more effort is necessary to boost and further stimulate action towards a better understanding on the positive and negative effects of solar energy, which will result in greener, cheaper and better path of the current and future development