Search results for: biological data

Authors: Stuart Henry, Philip Morrow, John Winder, Bryan Scotney

Abstract:

The stereophotogrammetry modality is gaining more widespread use in the clinical setting. Registration and visualization of this data, in conjunction with conventional 3D volumetric image modalities, provides virtual human data with textured soft tissue and internal anatomical and structural information. In this investigation computed tomography (CT) and stereophotogrammetry data is acquired from 4 anatomical phantoms and registered using the trimmed iterative closest point (TrICP) algorithm. This paper fully addresses the issue of imaging artifacts around the stereophotogrammetry surface edge using the registered CT data as a reference. Several iterative algorithms are implemented to automatically identify and remove stereophotogrammetry surface edge outliers, improving the overall visualization of the combined stereophotogrammetry and CT data. This paper shows that outliers at the surface edge of stereophotogrammetry data can be successfully removed automatically.

Keywords: Data cleansing, stereophotogrammetry.

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Authors: A. F. Ali, D. M. Shawky

Abstract:

Discovering new biological knowledge from the highthroughput biological data is a major challenge to bioinformatics today. To address this challenge, we developed a new approach for protein classification. Proteins that are evolutionarily- and thereby functionally- related are said to belong to the same classification. Identifying protein classification is of fundamental importance to document the diversity of the known protein universe. It also provides a means to determine the functional roles of newly discovered protein sequences. Our goal is to predict the functional classification of novel protein sequences based on a set of features extracted from each protein sequence. The proposed technique used datasets extracted from the Structural Classification of Proteins (SCOP) database. A set of spectral domain features based on Fast Fourier Transform (FFT) is used. The proposed classifier uses multilayer back propagation (MLBP) neural network for protein classification. The maximum classification accuracy is about 91% when applying the classifier to the full four levels of the SCOP database. However, it reaches a maximum of 96% when limiting the classification to the family level. The classification results reveal that spectral domain contains information that can be used for classification with high accuracy. In addition, the results emphasize that sequence similarity measures are of great importance especially at the family level.

Keywords: Bioinformatics, Artificial Neural Networks, Protein Sequence Analysis, Feature Extraction.

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Authors: Yi Chao Huang, Yu Ling Liao, Chiu Shuang Lin

Abstract:

A data cutting and sorting method (DCSM) is proposed to optimize the performance of data mining. DCSM reduces the calculation time by getting rid of redundant data during the data mining process. In addition, DCSM minimizes the computational units by splitting the database and by sorting data with support counts. In the process of searching for the relationship between metabolic syndrome and lifestyles with the health examination database of an electronics manufacturing company, DCSM demonstrates higher search efficiency than the traditional Apriori algorithm in tests with different support counts.

Keywords: Data mining, Data cutting and sorting method, Apriori algorithm, Metabolic syndrome

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Authors: Mais Haj Qasem, Maen M. Al Assaf, Ali Rodan

Abstract:

Parallel hybrid storage systems consist of a hierarchy of different storage devices that vary in terms of data reading speed performance. As we ascend in the hierarchy, data reading speed becomes faster. Thus, migrating the application’ important data that will be accessed in the near future to the uppermost level will reduce the application I/O waiting time; hence, reducing its execution elapsed time. In this research, we implement trace-driven two-levels parallel hybrid storage system prototype that consists of HDDs and SSDs. The prototype uses data mining techniques to classify application’ data in order to determine its near future data accesses in parallel with the its on-demand request. The important data (i.e. the data that the application will access in the near future) are continuously migrated to the uppermost level of the hierarchy. Our simulation results show that our data migration approach integrated with data mining techniques reduces the application execution elapsed time when using variety of traces in at least to 22%.

Keywords: Data mining, hybrid storage system, recurrent neural network, support vector machine.

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Authors: Sarra Senhadji, Imene Benzeguimi, Zohra Yagoub

Abstract:

Big Data represents the recent technology of manipulating voluminous and unstructured data sets over multiple sources. Therefore, NOSQL appears to handle the problem of unstructured data. Association rules mining is one of the popular techniques of data mining to extract hidden relationship from transactional databases. The algorithm for finding association dependencies is well-solved with Map Reduce. The goal of our work is to reduce the time of generating of frequent itemsets by using Map Reduce and NOSQL database oriented document. A comparative study is given to evaluate the performances of our algorithm with the classical algorithm Apriori.

Keywords: Apriori, Association rules mining, Big Data, data mining, Hadoop, Map Reduce, MongoDB, NoSQL.

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Authors: Asok Adak, Debabrata Mazumder, Pratip Bandyopadhyay

Abstract:

Anaerobic Digestion has become a promising technology for biological transformation of organic fraction of the municipal solid wastes (MSW). In order to represent the kinetic behavior of such biological process and thereby to design a reactor system, development of a mathematical model is essential. Addressing this issue, a simplistic mathematical model has been developed for anaerobic digestion of MSW in a continuous flow reactor unit under homogeneous steady state condition. Upon simulated hydrolysis, the kinetics of biomass growth and substrate utilization rate are assumed to follow first order reaction kinetics. Simulation of this model has been conducted by studying sensitivity of various process variables. The model was simulated using typical kinetic data of anaerobic digestion MSW and typical MSW characteristics of Kolkata. The hydraulic retention time (HRT) and solid retention time (SRT) time were mainly estimated by varying different model parameters like efficiency of reactor, influent substrate concentration and biomass concentration. Consequently, design table and charts have also been prepared for ready use in the actual plant operation.

Keywords: Anaerobic digestion, municipal solid waste (MSW), process design model, simulation study, hydraulic retention time(HRT), solid retention time (SRT).

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Authors: Maria Paula Santos, Ana Lucas

Abstract:

Organizations support their operations and decision making on the data they have at their disposal, so the quality of these data is remarkably important and Data Quality (DQ) is currently a relevant issue, the literature being unanimous in pointing out that poor DQ can result in large costs for organizations. The literature review identified and described 24 Critical Success Factors (CSF) for Data Quality Management (DQM) that were presented to a panel of experts, who ordered them according to their degree of importance, using the Delphi method with the Q-sort technique, based on an online questionnaire. The study shows that the five most important CSF for DQM are: definition of appropriate policies and standards, control of inputs, definition of a strategic plan for DQ, organizational culture focused on quality of the data and obtaining top management commitment and support.

Keywords: Critical success factors, data quality, data quality management, Delphi, Q-Sort.

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Authors: Prakash G L, Thejaswini M, S H Manjula, K R Venugopal, L M Patnaik

Abstract:

Wireless sensor network can be applied to both abominable and military environments. A primary goal in the design of wireless sensor networks is lifetime maximization, constrained by the energy capacity of batteries. One well-known method to reduce energy consumption in such networks is data aggregation. Providing efcient data aggregation while preserving data privacy is a challenging problem in wireless sensor networks research. In this paper, we present privacy-preserving data aggregation scheme for additive aggregation functions. The Cluster-based Private Data Aggregation (CPDA)leverages clustering protocol and algebraic properties of polynomials. It has the advantage of incurring less communication overhead. The goal of our work is to bridge the gap between collaborative data collection by wireless sensor networks and data privacy. We present simulation results of our schemes and compare their performance to a typical data aggregation scheme TAG, where no data privacy protection is provided. Results show the efficacy and efficiency of our schemes.

Keywords: Aggregation, Clustering, Query Processing.

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Authors: Mughal Yar M, Israr Ul Haq, Bushra Noman

Abstract:

The stem cells have ability to differentiated themselves through mitotic cell division and various range of specialized cell types. Cellular differentiation is a way by which few specialized cell develops into more specialized.This paper studies the fundamental problem of computational schema for an artificial neural network based on chemical, physical and biological variables of state. By doing this type of study system could be model for a viable propagation of various economically important stem cells differentiation. This paper proposes various differentiation outcomes of artificial neural network into variety of potential specialized cells on implementing MATLAB version 2009. A feed-forward back propagation kind of network was created to input vector (five input elements) with single hidden layer and one output unit in output layer. The efficiency of neural network was done by the assessment of results achieved from this study with that of experimental data input and chosen target data. The propose solution for the efficiency of artificial neural network assessed by the comparatative analysis of “Mean Square Error" at zero epochs. There are different variables of data in order to test the targeted results.

Keywords: Computational shcmin, meiosis, mitosis, neuralnetwork, Stem cell SOM;

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Authors: M. Abbasi Dezfouli, S. Mazraeh, M. H. Yektaie

Abstract:

Wireless sensor networks (WSN) consists of many sensor nodes that are placed on unattended environments such as military sites in order to collect important information. Implementing a secure protocol that can prevent forwarding forged data and modifying content of aggregated data and has low delay and overhead of communication, computing and storage is very important. This paper presents a new protocol for concealed data aggregation (CDA). In this protocol, the network is divided to virtual cells, nodes within each cell produce a shared key to send and receive of concealed data with each other. Considering to data aggregation in each cell is locally and implementing a secure authentication mechanism, data aggregation delay is very low and producing false data in the network by malicious nodes is not possible. To evaluate the performance of our proposed protocol, we have presented computational models that show the performance and low overhead in our protocol.

Keywords: Wireless Sensor Networks, Security, Concealed Data Aggregation.

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Authors: Faruq A. Al-Omari, Nabeel I. Al-Fayoumi

Abstract:

In this paper, we present a new algorithm for clustering data in large datasets using image processing approaches. First the dataset is mapped into a binary image plane. The synthesized image is then processed utilizing efficient image processing techniques to cluster the data in the dataset. Henceforth, the algorithm avoids exhaustive search to identify clusters. The algorithm considers only a small set of the data that contains critical boundary information sufficient to identify contained clusters. Compared to available data clustering techniques, the proposed algorithm produces similar quality results and outperforms them in execution time and storage requirements.

Keywords: Data clustering, Data mining, Image-mapping, Pattern discovery, Predictive analysis.

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Authors: M. Abbasi Dezfouli, S. Mazraeh, M. H. Yektaie

Abstract:

Wireless sensor networks (WSN) consists of many sensor nodes that are placed on unattended environments such as military sites in order to collect important information. Implementing a secure protocol that can prevent forwarding forged data and modifying content of aggregated data and has low delay and overhead of communication, computing and storage is very important. This paper presents a new protocol for concealed data aggregation (CDA). In this protocol, the network is divided to virtual cells, nodes within each cell produce a shared key to send and receive of concealed data with each other. Considering to data aggregation in each cell is locally and implementing a secure authentication mechanism, data aggregation delay is very low and producing false data in the network by malicious nodes is not possible. To evaluate the performance of our proposed protocol, we have presented computational models that show the performance and low overhead in our protocol.

Keywords: Wireless Sensor Networks, Security, Concealed Data Aggregation.

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Authors: D Sudheer Reddy, N Gopal Reddy, P V Radhadevi, J Saibaba, Geeta Varadan

Abstract:

Smoothing or filtering of data is first preprocessing step for noise suppression in many applications involving data analysis. Moving average is the most popular method of smoothing the data, generalization of this led to the development of Savitzky-Golay filter. Many window smoothing methods were developed by convolving the data with different window functions for different applications; most widely used window functions are Gaussian or Kaiser. Function approximation of the data by polynomial regression or Fourier expansion or wavelet expansion also gives a smoothed data. Wavelets also smooth the data to great extent by thresholding the wavelet coefficients. Almost all smoothing methods destroys the peaks and flatten them when the support of the window is increased. In certain applications it is desirable to retain peaks while smoothing the data as much as possible. In this paper we present a methodology called as peak-wise smoothing that will smooth the data to any desired level without losing the major peak features.

Keywords: smoothing, moving average, peakwise smoothing, spatialdensity models, planar shape models, wavelets.

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Authors: Andrew Jester, Ross Lee, Pritpal Singh

Abstract:

As the world transitions to a more sustainable energy economy, the deployment of energy storage technologies is expected to increase to develop a more resilient grid system. However, current technologies are associated with various environmental and safety issues throughout their entire lifecycle; therefore, a new battery technology is desirable for grid applications to curtail these risks. Biological cells, such as human neurons and electrocytes in the electric eel, can serve as a more sustainable design template for a new bio-inspired (i.e., biomimetic) battery. Within biological cells, an electrochemical gradient across the cell membrane forms the membrane potential, which serves as the driving force for ion transport into/out of the cell akin to the charging/discharging of a battery cell. This work serves as the first step for developing such a biomimetic battery cell, starting with the fabrication and characterization of ion-selective membranes to facilitate ion transport through the cell. Performance characteristics (e.g., cell voltage, power density, specific energy, roundtrip efficiency) for the cell under investigation are compared to incumbent battery technologies and biological cells to assess the readiness level for this emerging technology. Using a Na+-Form Nafion-117 membrane, the cell in this work successfully demonstrated behavior like human neurons; these findings will inform how cell components can be re-engineered to enhance device performance.

Keywords: Battery, biomimetic, electrocytes, human neurons, ion-selective membranes, membrane potential.

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Authors: Seyed Mohammad Hossein Moossavizadeh, Mehran Mohsenzadeh, Nasrin Arshadi

Abstract:

the data quality is a kind of complex and unstructured concept, which is concerned by information systems managers. The reason of this attention is the high amount of Expenses for maintenance and cleaning of the inefficient data. Such a data more than its expenses of lack of quality, cause wrong statistics, analysis and decisions in organizations. Therefor the managers intend to improve the quality of their information systems' data. One of the basic subjects of quality improvement is the evaluation of the amount of it. In this paper, we present a precautionary method, which with its application the data of information systems would have a better quality. Our method would cover different dimensions of data quality; therefor it has necessary integrity. The presented method has tested on three dimensions of accuracy, value-added and believability and the results confirm the improvement and integrity of this method.

Keywords: Data quality, precaution, information system, measurement, improvement.

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Authors: Jia-Yu Dai, Don-Lin Yang, Jungpin Wu, Ming-Chuan Hung

Abstract:

In an era of knowledge explosion, the growth of data increases rapidly day by day. Since data storage is a limited resource, how to reduce the data space in the process becomes a challenge issue. Data compression provides a good solution which can lower the required space. Data mining has many useful applications in recent years because it can help users discover interesting knowledge in large databases. However, existing compression algorithms are not appropriate for data mining. In [1, 2], two different approaches were proposed to compress databases and then perform the data mining process. However, they all lack the ability to decompress the data to their original state and improve the data mining performance. In this research a new approach called Mining Merged Transactions with the Quantification Table (M2TQT) was proposed to solve these problems. M2TQT uses the relationship of transactions to merge related transactions and builds a quantification table to prune the candidate itemsets which are impossible to become frequent in order to improve the performance of mining association rules. The experiments show that M2TQT performs better than existing approaches.

Keywords: Association rule, data mining, merged transaction, quantification table.

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Authors: K. A. Laptinskiy, S. A. Burikov, A. M. Vervald, S. A. Dolenko, T. A. Dolenko

Abstract:

The article presents the results of the application of artificial neural networks to separate the fluorescent contribution of nanodiamonds used as biomarkers, adsorbents and carriers of drugs in biomedicine, from a fluorescent background of own biological fluorophores. The principal possibility of solving this problem is shown. Use of neural network architecture let to detect fluorescence of nanodiamonds against the background autofluorescence of egg white with high accuracy - better than 3 ug/ml.

Keywords: Artificial neural networks, fluorescence, data aggregation.

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Authors: M. A. Hasan, M. R. Islam, R. A. Tarefder

Abstract:

Currently, there are few user friendly Weigh-in- Motion (WIM) data analysis softwares available which can produce traffic input data for the recently developed AASHTOWare pavement Mechanistic-Empirical (ME) design software. However, these softwares have only rudimentary Quality Control (QC) processes. Therefore, they cannot properly deal with erroneous WIM data. As the pavement performance is highly sensible to the quality of WIM data, it is highly recommended to use more refined QC process on raw WIM data to get a good result. This study develops a userfriendly software, which can produce traffic input for the ME design software. This software takes the raw data (Class and Weight data) collected from the WIM station and processes it with a sophisticated QC procedure. Traffic data such as traffic volume, traffic distribution, axle load spectra, etc. can be obtained from this software; which can directly be used in the ME design software.

Keywords: Weigh-in-motion, software, axle load spectra, traffic distribution, AASHTOWare.

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Authors: Iliana Marinova, Valentin Mateev

Abstract:

In this paper a computer system for electromagnetic properties measurements is designed. The system employs Agilent 4294A precision impedance analyzer to measure the amplitude and the phase of a signal applied over a tested biological tissue sample. Measured by the developed computer system data could be used for tissue characterization in wide frequency range from 40Hz to 110MHz. The computer system can interface with output devices acquiring flexible testing process.

Keywords: Electromagnetic properties, human tissue, bioimpedance, measurement system.

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Authors: T. S. Myers, J. Trevathan

Abstract:

Improvements in the data fusion and data analysis phase of research are imperative due to the exponential growth of sensed data. Currently, there are developments in the Semantic Sensor Web community to explore efficient methods for reuse, correlation and integration of web-based data sets and live data streams. This paper describes the integration of remotely sensed data with web-available static data for use in observational hypothesis testing and the analysis phase of research. The Semantic Reef system combines semantic technologies (e.g., well-defined ontologies and logic systems) with scientific workflows to enable hypothesis-based research. A framework is presented for how the data fusion concepts from the Semantic Reef architecture map to the Smart Environment Monitoring and Analysis Technologies (SEMAT) intelligent sensor network initiative. The data collected via SEMAT and the inferred knowledge from the Semantic Reef system are ingested to the Tropical Data Hub for data discovery, reuse, curation and publication.

Keywords: Information architecture, Semantic technologies Sensor networks, Ontologies.

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Authors: Bogdan Walek, Cyril Klimes

Abstract:

Current tools for data migration between documentoriented and relational databases have several disadvantages. We propose a new approach for data migration between documentoriented and relational databases. During data migration the relational schema of the target (relational database) is automatically created from collection of XML documents. Proposed approach is verified on data migration between document-oriented database IBM Lotus/ Notes Domino and relational database implemented in relational database management system (RDBMS) MySQL.

Keywords: data migration, database, document-oriented database, XML, relational schema

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Authors: Fuad M. Alkoot

Abstract:

DNA data have been used in forensics for decades. However, current research looks at using the DNA as a biometric identity verification modality. The goal is to improve the speed of identification. We aim at using gene data that was initially used for autism detection to find if and how accurate is this data for identification applications. Mainly our goal is to find if our data preprocessing technique yields data useful as a biometric identification tool. We experiment with using the nearest neighbor classifier to identify subjects. Results show that optimal classification rate is achieved when the test set is corrupted by normally distributed noise with zero mean and standard deviation of 1. The classification rate is close to optimal at higher noise standard deviation reaching 3. This shows that the data can be used for identity verification with high accuracy using a simple classifier such as the k-nearest neighbor (k-NN). 

Keywords: Biometrics, identity verification, genetic data, k-nearest neighbor.

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Authors: J. Chojnacki, E. Dulcet, A. Grieger

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The entomopathogenic nematodes Steinernema feltiaeare are components of many biological pesticides. The biological pesticides are applicated by means a spraying machines. The influence of high pressure operating time on viability of nematodes has been experimentally investigated in order to explain if static pressure inside of the sprayers installation was able to destroy nematodes. The value of pressure was 55 MPa and its maximum operating time was 3 hours. Changes were found in viability of pressurized samples of nematodes, mixed with water.

Keywords: Entomopathogenic nematodes, biopesticides, highpressure, sprayer.

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Authors: Joon-young Jung, Dong-oh Kang, Chang-seok Bae

Abstract:

Power consumption is rapidly increased in data centers because the number of data center is increased and more the scale of data center become larger. Therefore, it is one of key research items to reduce power consumption in data center. The peak power of a typical server is around 250 watts. When a server is idle, it continues to use around 60% of the power consumed when in use, though vendors are putting effort into reducing this “idle" power load. Servers tend to work at only around a 5% to 20% utilization rate, partly because of response time concerns. An average of 10% of servers in their data centers was unused. In those reason, we propose dynamic power management system to reduce power consumption in green data center. Experiment result shows that about 55% power consumption is reduced at idle time.

Keywords: Data Center, Green IT, Management Server, Power Saving.

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Authors: Paula Simões, Isabel Natário

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This paper reviews a number of theoretical aspects for implementing an explicit spatial perspective in econometrics for modelling non-continuous data, in general, and count data, in particular. It provides an overview of the several spatial econometric approaches that are available to model data that are collected with reference to location in space, from the classical spatial econometrics approaches to the recent developments on spatial econometrics to model count data, in a Bayesian hierarchical setting. Considerable attention is paid to the inferential framework, necessary for structural consistent spatial econometric count models, incorporating spatial lag autocorrelation, to the corresponding estimation and testing procedures for different assumptions, to the constrains and implications embedded in the various specifications in the literature. This review combines insights from the classical spatial econometrics literature as well as from hierarchical modeling and analysis of spatial data, in order to look for new possible directions on the processing of count data, in a spatial hierarchical Bayesian econometric context.

Keywords: Spatial data analysis, spatial econometrics, Bayesian hierarchical models, count data.

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Authors: M. Awawdeh, A. Fedi

Abstract:

The application of data mining to environmental monitoring has become crucial for a number of tasks related to emergency management. Over recent years, many tools have been developed for decision support system (DSS) for emergency management. In this article a graphical user interface (GUI) for environmental monitoring system is presented. This interface allows accomplishing (i) data collection and observation and (ii) extraction for data mining. This tool may be the basis for future development along the line of the open source software paradigm.

Keywords: Data Mining, Environmental data, Mathematical Models, Matlab Graphical User Interface.

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Authors: Dong Hoon Lim

Abstract:

A series of microarray experiments produces observations of differential expression for thousands of genes across multiple conditions. Principal component analysis(PCA) has been widely used in multivariate data analysis to reduce the dimensionality of the data in order to simplify subsequent analysis and allow for summarization of the data in a parsimonious manner. PCA, which can be implemented via a singular value decomposition(SVD), is useful for analysis of microarray data. For application of PCA using SVD we use the DNA microarray data for the small round blue cell tumors(SRBCT) of childhood by Khan et al.(2001). To decide the number of components which account for sufficient amount of information we draw scree plot. Biplot, a graphic display associated with PCA, reveals important features that exhibit relationship between variables and also the relationship of variables with observations.

Keywords: Principal component analysis, singular value decomposition, microarray data, SRBCT

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Authors: Youngji Yoo, Cheong-Sool Park, Jun Seok Kim, Young-Hak Lee, Sung-Shick Kim, Jun-Geol Baek

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In the semiconductor manufacturing process, large amounts of data are collected from various sensors of multiple facilities. The collected data from sensors have several different characteristics due to variables such as types of products, former processes and recipes. In general, Statistical Quality Control (SQC) methods assume the normality of the data to detect out-of-control states of processes. Although the collected data have different characteristics, using the data as inputs of SQC will increase variations of data, require wide control limits, and decrease performance to detect outof- control. Therefore, it is necessary to separate similar data groups from mixed data for more accurate process control. In the paper, we propose a regression tree using split algorithm based on Pearson distribution to handle non-normal distribution in parametric method. The regression tree finds similar properties of data from different variables. The experiments using real semiconductor manufacturing process data show improved performance in fault detecting ability.

Keywords: Semiconductor, non-normal mixed process data, clustering, Statistical Quality Control (SQC), regression tree, Pearson distribution system.

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Authors: H. B. Kekre, Tanuja K. Sarode

Abstract:

Mostly transforms are used for speech data compressions which are lossy algorithms. Such algorithms are tolerable for speech data compression since the loss in quality is not perceived by the human ear. However the vector quantization (VQ) has a potential to give more data compression maintaining the same quality. In this paper we propose speech data compression algorithm using vector quantization technique. We have used VQ algorithms LBG, KPE and FCG. The results table shows computational complexity of these three algorithms. Here we have introduced a new performance parameter Average Fractional Change in Speech Sample (AFCSS). Our FCG algorithm gives far better performance considering mean absolute error, AFCSS and complexity as compared to others.

Keywords: Vector Quantization, Data Compression, Encoding, , Speech coding.

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Authors: Eun-Jung Ko, Hyung-Jik Lee, Jeun-Woo Lee

Abstract:

In ubiqutious healthcare environment, user's health data are transfered to the remote healthcare server by the user's wearable system or mobile phone. These collected user's health data should be managed and analyzed in the healthcare server, so that care giver or user can monitor user's physiological state. In this paper, we designed and developed the intelligent Healthcare Server to manage the user's health data using CDSS and ontology. Our system can analyze user's health data semantically using CDSS and ontology, and report the result of user's physiological raw data to the user and care giver.

Keywords: u-healthcare, CDSS, healthcare server, health data, ontology.

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