Search results for: microarray data analysis

Authors: Zarita Zainuddin, Ong Pauline

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Wavelet neural networks (WNNs) have emerged as a vital alternative to the vastly studied multilayer perceptrons (MLPs) since its first implementation. In this paper, we applied various clustering algorithms, namely, K-means (KM), Fuzzy C-means (FCM), symmetry-based K-means (SBKM), symmetry-based Fuzzy C-means (SBFCM) and modified point symmetry-based K-means (MPKM) clustering algorithms in choosing the translation parameter of a WNN. These modified WNNs are further applied to the heterogeneous cancer classification using benchmark microarray data and were compared against the conventional WNN with random initialization method. Experimental results showed that a WNN classifier with the MPKM algorithm is more precise than the conventional WNN as well as the WNNs with other clustering algorithms.

Keywords: Clustering, microarray, symmetry, wavelet neural networks.

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Authors: Liping Jing, Michael K. Ng, Tieyong Zeng

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Microarray data profiles gene expression on a whole genome scale, therefore, it provides a good way to study associations between gene expression and occurrence or progression of cancer. More and more researchers realized that microarray data is helpful to predict cancer sample. However, the high dimension of gene expressions is much larger than the sample size, which makes this task very difficult. Therefore, how to identify the significant genes causing cancer becomes emergency and also a hot and hard research topic. Many feature selection algorithms have been proposed in the past focusing on improving cancer predictive accuracy at the expense of ignoring the correlations between the features. In this work, a novel framework (named by SGS) is presented for stable gene selection and efficient cancer prediction . The proposed framework first performs clustering algorithm to find the gene groups where genes in each group have higher correlation coefficient, and then selects the significant genes in each group with Bayesian Lasso and important gene groups with group Lasso, and finally builds prediction model based on the shrinkage gene space with efficient classification algorithm (such as, SVM, 1NN, Regression and etc.). Experiment results on real world data show that the proposed framework often outperforms the existing feature selection and prediction methods, say SAM, IG and Lasso-type prediction model.

Keywords: Gene Selection, Cancer Prediction, Lasso, Clustering, Classification.

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Authors: Khlopova N.S., Glazko V.I., Glazko T.T.

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Using DNA microarrays the comparative analysis of a gene expression profiles is carried out in a liver and kidneys of pigs. The hypothesis of a cross hybridization of one probe with different cDNA sites of the same gene or different genes is checked up, and it is shown, that cross hybridization can be a source of essential errors at revealing of a key genes in organ-specific transcriptome. It is reveald that distinctions in profiles of a gene expression are well coordinated with function, morphology, biochemistry and histology of these organs.

Keywords: Microarray, gene expression profiles, key genes.

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Authors: M. Marjaneh, M. Y. Narazah, H. Shahrul

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Array-based gene expression analysis is a powerful tool to profile expression of genes and to generate information on therapeutic effects of new anti-cancer compounds. Anti-apoptotic effect of thymoquinone was studied in MCF7 breast cancer cell line using gene expression profiling with cDNA microarray. The purity and yield of RNA samples were determined using RNeasyPlus Mini kit. The Agilent RNA 6000 NanoLabChip kit evaluated the quantity of the RNA samples. AffinityScript RT oligo-dT promoter primer was used to generate cDNA strands. T7 RNA polymerase was used to convert cDNA to cRNA. The cRNA samples and human universal reference RNA were labelled with Cy-3-CTP and Cy-5-CTP, respectively. Feature Extraction and GeneSpring softwares analysed the data. The single experiment analysis revealed involvement of 64 pathways with up-regulated genes and 78 pathways with downregulated genes. The MAPK and p38-MAPK pathways were inhibited due to the up-regulation of PTPRR gene. The inhibition of p38-MAPK suggested up-regulation of TGF-ß pathway. Inhibition of p38-MAPK caused up-regulation of TP53 and down-regulation of Bcl2 genes indicating involvement of intrinsic apoptotic pathway. Down-regulation of CARD16 gene as an adaptor molecule regulated CASP1 and suggested necrosis-like programmed cell death and involvement of caspase in apoptosis. Furthermore, down-regulation of GPCR, EGF-EGFR signalling pathways suggested reduction of ER. Involvement of AhR pathway which control cytochrome P450 and glucuronidation pathways showed metabolism of Thymoquinone. The findings showed differential expression of several genes in apoptosis pathways with thymoquinone treatment in estrogen receptor-positive breast cancer cells.

Keywords: CARD16, CASP10, cDNA microarray, PTPRR, Thymoquinone.

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Authors: Adel Dalilottojari, Bahman Delalat, Frances J. Harding, Michaelia P. Cockshell, Claudine S. Bonder, Nicolas H. Voelcker

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Endothelial Progenitor Cell (EPC) based therapies continue to be of interest to treat ischemic events based on their proven role to promote blood vessel formation and thus tissue re-vascularisation. Current strategies for the production of clinical-grade EPCs requires the in vitro isolation of EPCs from peripheral blood followed by cell expansion to provide sufficient quantities EPCs for cell therapy. This study aims to examine the use of different biomolecules to significantly improve the current strategy of EPC capture and expansion on collagen type I (Col I). In this study, four different biomolecules were immobilised on a surface and then investigated for their capacity to support EPC capture and proliferation. First, a cell microarray platform was fabricated by coating a glass surface with epoxy functional allyl glycidyl ether plasma polymer (AGEpp) to mediate biomolecule binding. The four candidate biomolecules tested were Col I, collagen type II (Col II), collagen type IV (Col IV) and vascular endothelial growth factor A (VEGF-A), which were arrayed on the epoxy-functionalised surface using a non-contact printer. The surrounding area between the printed biomolecules was passivated with polyethylene glycol-bisamine (A-PEG) to prevent non-specific cell attachment. EPCs were seeded onto the microarray platform and cell numbers quantified after 1 h (to determine capture) and 72 h (to determine proliferation). All of the extracellular matrix (ECM) biomolecules printed demonstrated an ability to capture EPCs within 1 h of cell seeding with Col II exhibiting the highest level of attachment when compared to the other biomolecules. Interestingly, Col IV exhibited the highest increase in EPC expansion after 72 h when compared to Col I, Col II and VEGF-A. These results provide information for significant improvement in the capture and expansion of human EPC for further application.

Keywords: Cardiovascular disease, cell microarray platform, cell therapy, endothelial progenitor cells, high throughput screening.

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Authors: A. Gruzdz, A. Ihnatowicz, J. Siddiqi, B. Akhgar

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MATCH project [1] entitle the development of an automatic diagnosis system that aims to support treatment of colon cancer diseases by discovering mutations that occurs to tumour suppressor genes (TSGs) and contributes to the development of cancerous tumours. The constitution of the system is based on a) colon cancer clinical data and b) biological information that will be derived by data mining techniques from genomic and proteomic sources The core mining module will consist of the popular, well tested hybrid feature extraction methods, and new combined algorithms, designed especially for the project. Elements of rough sets, evolutionary computing, cluster analysis, self-organization maps and association rules will be used to discover the annotations between genes, and their influence on tumours [2]-[11]. The methods used to process the data have to address their high complexity, potential inconsistency and problems of dealing with the missing values. They must integrate all the useful information necessary to solve the expert's question. For this purpose, the system has to learn from data, or be able to interactively specify by a domain specialist, the part of the knowledge structure it needs to answer a given query. The program should also take into account the importance/rank of the particular parts of data it analyses, and adjusts the used algorithms accordingly.

Keywords: Bioinformatics, gene expression, ontology, selforganizingmaps.

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Authors: Hung-Ming Lai, Andreas Albrecht, Kathleen Steinhöfel

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Cancers could normally be marked by a number of differentially expressed genes which show enormous potential as biomarkers for a certain disease. Recent years, cancer classification based on the investigation of gene expression profiles derived by high-throughput microarrays has widely been used. The selection of discriminative genes is, therefore, an essential preprocess step in carcinogenesis studies. In this paper, we have proposed a novel gene selector using information-theoretic measures for biological discovery. This multivariate filter is a four-stage framework through the analyses of feature relevance, feature interdependence, feature redundancy-dependence and subset rankings, and having been examined on the colon cancer data set. Our experimental result show that the proposed method outperformed other information theorem based filters in all aspect of classification errors and classification performance.

Keywords: Colon cancer, feature interdependence, feature subset selection, gene selection, microarray data analysis.

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Authors: Reza Nadimi, Fariborz Jolai

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This article combines two techniques: data envelopment analysis (DEA) and Factor analysis (FA) to data reduction in decision making units (DMU). Data envelopment analysis (DEA), a popular linear programming technique is useful to rate comparatively operational efficiency of decision making units (DMU) based on their deterministic (not necessarily stochastic) input–output data and factor analysis techniques, have been proposed as data reduction and classification technique, which can be applied in data envelopment analysis (DEA) technique for reduction input – output data. Numerical results reveal that the new approach shows a good consistency in ranking with DEA.

Keywords: Effectiveness, Decision Making, Data EnvelopmentAnalysis, Factor Analysis

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Authors: Cristina G. Dascâlu, Corina Dima Cozma, Elena Carmen Cotrutz

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The medical data statistical analysis often requires the using of some special techniques, because of the particularities of these data. The principal components analysis and the data clustering are two statistical methods for data mining very useful in the medical field, the first one as a method to decrease the number of studied parameters, and the second one as a method to analyze the connections between diagnosis and the data about the patient-s condition. In this paper we investigate the implications obtained from a specific data analysis technique: the data clustering preceded by a selection of the most relevant parameters, made using the principal components analysis. Our assumption was that, using the principal components analysis before data clustering - in order to select and to classify only the most relevant parameters – the accuracy of clustering is improved, but the practical results showed the opposite fact: the clustering accuracy decreases, with a percentage approximately equal with the percentage of information loss reported by the principal components analysis.

Keywords: Data clustering, medical data, principal components analysis.

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Authors: Khin May Win, Nan Sai Moon Kham

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Identification of cancer genes that might anticipate the clinical behaviors from different types of cancer disease is challenging due to the huge number of genes and small number of patients samples. The new method is being proposed based on supervised learning of classification like support vector machines (SVMs).A new solution is described by the introduction of the Maximized Margin (MM) in the subset criterion, which permits to get near the least generalization error rate. In class prediction problem, gene selection is essential to improve the accuracy and to identify genes for cancer disease. The performance of the new method was evaluated with real-world data experiment. It can give the better accuracy for classification.

Keywords: Microarray data, feature selection, recursive featureelimination, support vector machines.

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Authors: Liang Zhao, Jili Zhang, Chongquan Zhong

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Energy consumption data, in particular those involving public buildings, are impacted by many factors: the building structure, climate/environmental parameters, construction, system operating condition, and user behavior patterns. Traditional methods for data analysis are insufficient. This paper delves into the data mining technology to determine its application in the analysis of building energy consumption data including energy consumption prediction, fault diagnosis, and optimal operation. Recent literature are reviewed and summarized, the problems faced by data mining technology in the area of energy consumption data analysis are enumerated, and research points for future studies are given.

Keywords: Data mining, data analysis, prediction, optimization, building operational performance.

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Authors: Billel Kenidra, Mohamed Benmohammed

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Data mining technique used in the field of clustering is a subject of active research and assists in biological pattern recognition and extraction of new knowledge from raw data. Clustering means the act of partitioning an unlabeled dataset into groups of similar objects. Each group, called a cluster, consists of objects that are similar between themselves and dissimilar to objects of other groups. Several clustering methods are based on partitional clustering. This category attempts to directly decompose the dataset into a set of disjoint clusters leading to an integer number of clusters that optimizes a given criterion function. The criterion function may emphasize a local or a global structure of the data, and its optimization is an iterative relocation procedure. The K-Means algorithm is one of the most widely used partitional clustering techniques. Since K-Means is extremely sensitive to the initial choice of centers and a poor choice of centers may lead to a local optimum that is quite inferior to the global optimum, we propose a strategy to initiate K-Means centers. The improved K-Means algorithm is compared with the original K-Means, and the results prove how the efficiency has been significantly improved.

Keywords: Microarray data mining, biological pattern recognition, partitional clustering, k-means algorithm, centroid initialization.

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Authors: Michael Netzer, Michael Seger, Mahesh Visvanathan, Bernhard Pfeifer, Gerald H. Lushington, Christian Baumgartner

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Lung cancer accounts for the most cancer related deaths for men as well as for women. The identification of cancer associated genes and the related pathways are essential to provide an important possibility in the prevention of many types of cancer. In this work two filter approaches, namely the information gain and the biomarker identifier (BMI) are used for the identification of different types of small-cell and non-small-cell lung cancer. A new method to determine the BMI thresholds is proposed to prioritize genes (i.e., primary, secondary and tertiary) using a k-means clustering approach. Sets of key genes were identified that can be found in several pathways. It turned out that the modified BMI is well suited for microarray data and therefore BMI is proposed as a powerful tool for the search for new and so far undiscovered genes related to cancer.

Keywords: lung cancer, micro arrays, data mining, feature selection.

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Authors: M. Klimavicius

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This paper proposes a modeling methodology for the development of data analysis solution. The Author introduce the approach to address data warehousing issues at the at enterprise level. The methodology covers the process of the requirements eliciting and analysis stage as well as initial design of data warehouse. The paper reviews extended business process model, which satisfy the needs of data warehouse development. The Author considers that the use of business process models is necessary, as it reflects both enterprise information systems and business functions, which are important for data analysis. The Described approach divides development into three steps with different detailed elaboration of models. The Described approach gives possibility to gather requirements and display them to business users in easy manner.

Keywords: Data warehouse, data analysis, business processmanagement.

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Authors: Jihyun Song, Kyeongjoo Kim, Minsoo Lee

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Due to the development of information technology and wireless Internet technology, various data are being generated in various fields. These data are advantageous in that they provide real-time information to the users themselves. However, when the data are accumulated and analyzed, more various information can be extracted. In addition, development and dissemination of boards such as Arduino and Raspberry Pie have made it possible to easily test various sensors, and it is possible to collect sensor data directly by using database application tools such as MySQL. These directly collected data can be used for various research and can be useful as data for data mining. However, there are many difficulties in using the board to collect data, and there are many difficulties in using it when the user is not a computer programmer, or when using it for the first time. Even if data are collected, lack of expert knowledge or experience may cause difficulties in data analysis and visualization. In this paper, we aim to construct a library for sensor data collection and analysis to overcome these problems.

Keywords: Clustering, data mining, DBSCAN, k-means, k-medoids, sensor data.

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Authors: Fahd Sabry Esmail, M. Badr Senousy, Mohamed Ragaie

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In recent years, there has been an explosion in the rate of using technology that help discovering the diseases. For example, DNA microarrays allow us for the first time to obtain a "global" view of the cell. It has great potential to provide accurate medical diagnosis, to help in finding the right treatment and cure for many diseases. Various classification algorithms can be applied on such micro-array datasets to devise methods that can predict the occurrence of Leukemia disease. In this study, we compared the classification accuracy and response time among eleven decision tree methods and six rule classifier methods using five performance criteria. The experiment results show that the performance of Random Tree is producing better result. Also it takes lowest time to build model in tree classifier. The classification rules algorithms such as nearest- neighbor-like algorithm (NNge) is the best algorithm due to the high accuracy and it takes lowest time to build model in classification.

Keywords: Data mining, classification techniques, decision tree, classification rule, leukemia diseases, microarray data.

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Authors: M. Amir Abas, M. Dahlui

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This paper presents the development of analysis tools for Home Agriculture project. The tools are required for monitoring the condition of greenhouse which involves two components: measurement hardware and data analysis engine. Measurement hardware is functioned to measure environment parameters such as temperature, humidity, air quality, dust and etc while analysis tool is used to analyse and interpret the integrated data against the condition of weather, quality of health, irradiance, quality of soil and etc. The current development of the tools is completed for off-line data recorded technique. The data is saved in MMC and transferred via ZigBee to Environment Data Manager (EDM) for data analysis. EDM converts the raw data and plot three combination graphs. It has been applied in monitoring three months data measurement for irradiance, temperature and humidity of the greenhouse..

Keywords: Monitoring, Environment, Greenhouse, Analysis tools

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Authors: M. Pandi, K. Premalatha

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The DNA microarray technology concurrently monitors the expression levels of thousands of genes during significant biological processes and across the related samples. The better understanding of functional genomics is obtained by extracting the patterns hidden in gene expression data. It is handled by clustering which reveals natural structures and identify interesting patterns in the underlying data. In the proposed work clustering gene expression data is done through an Advanced Nelder Mead (ANM) algorithm. Nelder Mead (NM) method is a method designed for optimization process. In Nelder Mead method, the vertices of a triangle are considered as the solutions. Many operations are performed on this triangle to obtain a better result. In the proposed work, the operations like reflection and expansion is eliminated and a new operation called spread-out is introduced. The spread-out operation will increase the global search area and thus provides a better result on optimization. The spread-out operation will give three points and the best among these three points will be used to replace the worst point. The experiment results are analyzed with optimization benchmark test functions and gene expression benchmark datasets. The results show that ANM outperforms NM in both benchmarks.

Keywords: Spread out, simplex, multi-minima, fitness function, optimization, search area, monocyte, solution, genomes.

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Authors: Ameur Abdelkader, Abed Bouarfa Hafida

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Since its inception, predictive analysis has revolutionized the IT industry through its robustness and decision-making facilities. It involves the application of a set of data processing techniques and algorithms in order to create predictive models. Its principle is based on finding relationships between explanatory variables and the predicted variables. Past occurrences are exploited to predict and to derive the unknown outcome. With the advent of big data, many studies have suggested the use of predictive analytics in order to process and analyze big data. Nevertheless, they have been curbed by the limits of classical methods of predictive analysis in case of a large amount of data. In fact, because of their volumes, their nature (semi or unstructured) and their variety, it is impossible to analyze efficiently big data via classical methods of predictive analysis. The authors attribute this weakness to the fact that predictive analysis algorithms do not allow the parallelization and distribution of calculation. In this paper, we propose to extend the predictive analysis algorithm, Classification And Regression Trees (CART), in order to adapt it for big data analysis. The major changes of this algorithm are presented and then a version of the extended algorithm is defined in order to make it applicable for a huge quantity of data.

Keywords: Predictive analysis, big data, predictive analysis algorithms. CART algorithm.

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Authors: M. Anidha, K. Premalatha

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Feature Selection is significant in order to perform constructive classification in the area of cancer diagnosis. However, a large number of features compared to the number of samples makes the task of classification computationally very hard and prone to errors in microarray gene expression datasets. In this paper, we present an innovative method for selecting highly informative gene subsets of gene expression data that effectively classifies the cancer data into tumorous and non-tumorous. The hybrid gene selection technique comprises of combined Mutual Information and Fisher score to select informative genes. The gene selection is validated by classification using Support Vector Machine (SVM) which is a supervised learning algorithm capable of solving complex classification problems. The results obtained from improved Mutual Information and F-Score with SVM as a classifier has produced efficient results.

Keywords: Gene selection, mutual information, Fisher score, classification, SVM.

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Authors: Shohei Maruyama, Yasuo Matsuyama, Sachiyo Aburatani

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Development of a method to estimate gene functions is an important task in bioinformatics. One of the approaches for the annotation is the identification of the metabolic pathway that genes are involved in. Since gene expression data reflect various intracellular phenomena, those data are considered to be related with genes’ functions. However, it has been difficult to estimate the gene function with high accuracy. It is considered that the low accuracy of the estimation is caused by the difficulty of accurately measuring a gene expression. Even though they are measured under the same condition, the gene expressions will vary usually. In this study, we proposed a feature extraction method focusing on the variability of gene expressions to estimate the genes' metabolic pathway accurately. First, we estimated the distribution of each gene expression from replicate data. Next, we calculated the similarity between all gene pairs by KL divergence, which is a method for calculating the similarity between distributions. Finally, we utilized the similarity vectors as feature vectors and trained the multiclass SVM for identifying the genes' metabolic pathway. To evaluate our developed method, we applied the method to budding yeast and trained the multiclass SVM for identifying the seven metabolic pathways. As a result, the accuracy that calculated by our developed method was higher than the one that calculated from the raw gene expression data. Thus, our developed method combined with KL divergence is useful for identifying the genes' metabolic pathway.

Keywords: Metabolic pathways, gene expression data, microarray, Kullback–Leibler divergence, KL divergence, support vector machines, SVM, machine learning.

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Authors: Anamika Gupta, Naveen Kumar, Vasudha Bhatnagar

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This paper focuses on analyzing medical diagnostic data using classification rules in data mining and context reduction in formal concept analysis. It helps in finding redundancies among the various medical examination tests used in diagnosis of a disease. Classification rules have been derived from positive and negative association rules using the Concept lattice structure of the Formal Concept Analysis. Context reduction technique given in Formal Concept Analysis along with classification rules has been used to find redundancies among the various medical examination tests. Also it finds out whether expensive medical tests can be replaced by some cheaper tests.

Keywords: Data Mining, Formal Concept Analysis, Medical Data, Negative Classification Rules.

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Authors: S. Vidhya, S. Sarumathi, N. Shanthi

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Over the past era, there have been a lot of efforts and studies are carried out in growing proficient tools for performing various tasks in big data. Recently big data have gotten a lot of publicity for their good reasons. Due to the large and complex collection of datasets it is difficult to process on traditional data processing applications. This concern turns to be further mandatory for producing various tools in big data. Moreover, the main aim of big data analytics is to utilize the advanced analytic techniques besides very huge, different datasets which contain diverse sizes from terabytes to zettabytes and diverse types such as structured or unstructured and batch or streaming. Big data is useful for data sets where their size or type is away from the capability of traditional relational databases for capturing, managing and processing the data with low-latency. Thus the out coming challenges tend to the occurrence of powerful big data tools. In this survey, a various collection of big data tools are illustrated and also compared with the salient features.

Keywords: Big data, Big data analytics, Business analytics, Data analysis, Data visualization, Data discovery.

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Authors: Takahiro Nishigaki, Katsumi Nitta, Takashi Onoda

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In this paper, we present a method of applying Independent Topic Analysis (ITA) to increasing the number of document data. The number of document data has been increasing since the spread of the Internet. ITA was presented as one method to analyze the document data. ITA is a method for extracting the independent topics from the document data by using the Independent Component Analysis (ICA). ICA is a technique in the signal processing; however, it is difficult to apply the ITA to increasing number of document data. Because ITA must use the all document data so temporal and spatial cost is very high. Therefore, we present Incremental ITA which extracts the independent topics from increasing number of document data. Incremental ITA is a method of updating the independent topics when the document data is added after extracted the independent topics from a just previous the data. In addition, Incremental ITA updates the independent topics when the document data is added. And we show the result applied Incremental ITA to benchmark datasets.

Keywords: Text mining, topic extraction, independent, incremental, independent component analysis.

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Authors: Femi Elegbeleye, Seani Rananga

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This paper focused on cost effective storage architecture using fog and cloud data storage gateway, and presented the design of the framework for the data privacy model and data analytics framework on a real-time analysis when using machine learning method. The paper began with the system analysis, system architecture and its component design, as well as the overall system operations. Several results obtained from this study on data privacy models show that when two or more data privacy models are integrated via a fog storage gateway, we often have more secure data. Our main focus in the study is to design a framework for the data privacy model, data storage, and real-time analytics. This paper also shows the major system components and their framework specification. And lastly, the overall research system architecture was shown, including its structure, and its interrelationships.

Keywords: IoT, fog storage, cloud storage, data analysis, data privacy.

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Authors: S. Madhavi, S. Abirami, C. Bharathi, B. Ekambaram, T. Krishna Sankar, A. Nattudurai, N. Vijayarangan

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The high utilization rate of Automated Teller Machine (ATM) has inevitably caused the phenomena of waiting for a long time in the queue. This in turn has increased the out of stock situations. The ATM utilization helps to determine the usage level and states the necessity of the ATM based on the utilization of the ATM system. The time in which the ATM used more frequently (peak time) and based on the predicted solution the necessary actions are taken by the bank management. The analysis can be done by using the concept of Data Mining and the major part are analyzed based on the predictive data mining. The results are predicted from the historical data (past data) and track the relevant solution which is required. Weka tool is used for the analysis of data based on predictive data mining.

Keywords: ATM, Bank Management, Data Mining, Historical data, Predictive Data Mining, Weka tool.

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Authors: Masahiro Kuzunishi, Tetsuya Furukawa, Ke Lu

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Classifying data hierarchically is an efficient approach to analyze data. Data is usually classified into multiple categories, or annotated with a set of labels. To analyze multi-labeled data, such data must be specified by giving a set of labels as a semantic range. There are some certain purposes to analyze data. This paper shows which multi-labeled data should be the target to be analyzed for those purposes, and discusses the role of a label against a set of labels by investigating the change when a label is added to the set of labels. These discussions give the methods for the advanced analysis of multi-labeled data, which are based on the role of a label against a semantic range.

Keywords: Classification Hierarchies, Data Analysis, Multilabeled Data, Orders of Sets of Labels

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Authors: N. R. N. Idris, S. Baharom

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A meta-analysis may be performed using aggregate data (AD) or an individual patient data (IPD). In practice, studies may be available at both IPD and AD level. In this situation, both the IPD and AD should be utilised in order to maximize the available information. Statistical advantages of combining the studies from different level have not been fully explored. This study aims to quantify the statistical benefits of including available IPD when conducting a conventional summary-level meta-analysis. Simulated meta-analysis were used to assess the influence of the levels of data on overall meta-analysis estimates based on IPD-only, AD-only and the combination of IPD and AD (mixed data, MD), under different study scenario. The percentage relative bias (PRB), root mean-square-error (RMSE) and coverage probability were used to assess the efficiency of the overall estimates. The results demonstrate that available IPD should always be included in a conventional meta-analysis using summary level data as they would significantly increased the accuracy of the estimates.On the other hand, if more than 80% of the available data are at IPD level, including the AD does not provide significant differences in terms of accuracy of the estimates. Additionally, combining the IPD and AD has moderating effects on the biasness of the estimates of the treatment effects as the IPD tends to overestimate the treatment effects, while the AD has the tendency to produce underestimated effect estimates. These results may provide some guide in deciding if significant benefit is gained by pooling the two levels of data when conducting meta-analysis.

Keywords: Aggregate data, combined-level data, Individual patient data, meta analysis.

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias, Hany T. Alashwal, Rohayanti Hassan, FarhanMohamed

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The most important property of the Gene Ontology is the terms. These control vocabularies are defined to provide consistent descriptions of gene products that are shareable and computationally accessible by humans, software agent, or other machine-readable meta-data. Each term is associated with information such as definition, synonyms, database references, amino acid sequences, and relationships to other terms. This information has made the Gene Ontology broadly applied in microarray and proteomic analysis. However, the process of searching the terms is still carried out using traditional approach which is based on keyword matching. The weaknesses of this approach are: ignoring semantic relationships between terms, and highly depending on a specialist to find similar terms. Therefore, this study combines semantic similarity measure and genetic algorithm to perform a better retrieval process for searching semantically similar terms. The semantic similarity measure is used to compute similitude strength between two terms. Then, the genetic algorithm is employed to perform batch retrievals and to handle the situation of the large search space of the Gene Ontology graph. The computational results are presented to show the effectiveness of the proposed algorithm.

Keywords: Gene Ontology, Semantic similarity measure, Genetic algorithm, Ontology search

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Authors: S. Sarumathi, N. Shanthi

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Due to the fast and flawless technological innovation there is a tremendous amount of data dumping all over the world in every domain such as Pattern Recognition, Machine Learning, Spatial Data Mining, Image Analysis, Fraudulent Analysis, World Wide Web etc., This issue turns to be more essential for developing several tools for data mining functionalities. The major aim of this paper is to analyze various tools which are used to build a resourceful analytical or descriptive model for handling large amount of information more efficiently and user friendly. In this survey the diverse tools are illustrated with their extensive technical paradigm, outstanding graphical interface and inbuilt multipath algorithms in which it is very useful for handling significant amount of data more indeed.

Keywords: Classification, Clustering, Data Mining, Machine learning, Visualization.

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