Large scale data processing using MapReduce

As massive data sets become increasingly available, people are facing the problem of how to effectively process and understand these data. Traditional sequential computing models are giving way to parallel and distributed computing models, such as MapReduce, both due to the large size of the data sets and their high dimensionality. This dissertation, as in the same direction of other researches that are based on MapReduce, tries to develop effective techniques and applications using MapReduce that can help people solve large-scale problems. Three different problems are tackled in the dissertation. The first one deals with processing terabytes of raster data in a spatial data management system. Aerial imagery files are broken into tiles to enable data parallel computation. The second and third problems deal with dimension reduction techniques that can be used to handle data sets of high dimensionality. Three variants of the nonnegative matrix factorization technique are scaled up to factorize matrices of dimensions in the order of millions in MapReduce based on different matrix multiplication implementations. Two algorithms, which compute CANDECOMP/PARAFAC and Tucker tensor decompositions respectively, are parallelized in MapReduce based on carefully partitioning the data and arranging the computation to maximize data locality and parallelism.

Performance analysis of disk mirroring techniques

Unequaled improvements in processor and I/O speeds make many applications such as databases and operating systems to be increasingly I/O bound. Many schemes such as disk caching and disk mirroring have been proposed to address the problem. In this thesis we focus only on disk mirroring. In disk mirroring, a logical disk image is maintained on two physical disks allowing a single disk failure to be transparent to application programs. Although disk mirroring improves data availability and reliability, it has two major drawbacks. First, writes are expensive because both disks must be updated. Second, load balancing during failure mode operation is poor because all requests are serviced by the surviving disk. Distorted mirrors was proposed to address the write problem and interleaved declustering to address the load balancing problem. In this thesis we perform a comparative study of these two schemes under various operating modes. In addition we also study traditional mirroring to provide a common basis for comparison.

A mathematical resolution to log transformations and the binning effect in applied processing of data in flow cytometry

This dissertation develops a new mathematical approach that overcomes the effect of a data processing phenomenon known as "histogram binning" inherent to flow cytometry data. A real-time procedure is introduced to prove the effectiveness and fast implementation of such an approach on real-world data. The histogram binning effect is a dilemma posed by two seemingly antagonistic developments: (1) flow cytometry data in its histogram form is extended in its dynamic range to improve its analysis and interpretation, and (2) the inevitable dynamic range extension introduces an unwelcome side effect, the binning effect, which skews the statistics of the data, undermining as a consequence the accuracy of the analysis and the eventual interpretation of the data. Researchers in the field contended with such a dilemma for many years, resorting either to hardware approaches that are rather costly with inherent calibration and noise effects; or have developed software techniques based on filtering the binning effect but without successfully preserving the statistical content of the original data. The mathematical approach introduced in this dissertation is so appealing that a patent application has been filed. The contribution of this dissertation is an incremental scientific innovation based on a mathematical framework that will allow researchers in the field of flow cytometry to improve the interpretation of data knowing that its statistical meaning has been faithfully preserved for its optimized analysis. Furthermore, with the same mathematical foundation, proof of the origin of such an inherent artifact is provided. These results are unique in that new mathematical derivations are established to define and solve the critical problem of the binning effect faced at the experimental assessment level, providing a data platform that preserves its statistical content. In addition, a novel method for accumulating the log-transformed data was developed. This new method uses the properties of the transformation of statistical distributions to accumulate the output histogram in a non-integer and multi-channel fashion. Although the mathematics of this new mapping technique seem intricate, the concise nature of the derivations allow for an implementation procedure that lends itself to a real-time implementation using lookup tables, a task that is also introduced in this dissertation.

Consequences of interorganizational information systems: An empirical investigation of the effects of EDI use on interorganizational relationships in the retail industry

This dissertation examines the consequences of Electronic Data Interchange (EDI) use on interorganizational relations (IR) in the retail industry. EDI is a type of interorganizational information system that facilitates the exchange of business documents in structured, machine processable form. The research model links EDI use and three IR dimensions--structural, behavioral, and outcome. Based on relevant literature from organizational theory and marketing channels, fourteen hypotheses were proposed for the relationships among EDI use and the three IR dimensions.^ Data were collected through self-administered questionnaires from key informants in 97 retail companies (19% response rate). The hypotheses were tested using multiple regression analysis. The analysis supports the following hypothesis: (a) EDI use is positively related to information intensity and formalization, (b) formalization is positively related to cooperation, (c) information intensity is positively related to cooperation, (d) conflict is negatively related to performance and satisfaction, (e) cooperation is positively related to performance, and (f) performance is positively related to satisfaction. The results support the general premise of the model that the relationship between EDI use and satisfaction among channel members has to be viewed within an interorganizational context.^ Research on EDI is still in a nascent stage. By identifying and testing relevant interorganizational variables, this study offers insights for practitioners managing boundary-spanning activities in organizations using or planning to use EDI. Further, the thesis provides avenues for future research aimed at understanding the consequences of this interorganizational information technology. ^

A mathematical resolution to log transformations and the binning effect in applied processing of data in flow cytometry

This dissertation develops a new mathematical approach that overcomes the effect of a data processing phenomenon known as “histogram binning” inherent to flow cytometry data. A real-time procedure is introduced to prove the effectiveness and fast implementation of such an approach on real-world data. The histogram binning effect is a dilemma posed by two seemingly antagonistic developments: (1) flow cytometry data in its histogram form is extended in its dynamic range to improve its analysis and interpretation, and (2) the inevitable dynamic range extension introduces an unwelcome side effect, the binning effect, which skews the statistics of the data, undermining as a consequence the accuracy of the analysis and the eventual interpretation of the data. ^ Researchers in the field contended with such a dilemma for many years, resorting either to hardware approaches that are rather costly with inherent calibration and noise effects; or have developed software techniques based on filtering the binning effect but without successfully preserving the statistical content of the original data. ^ The mathematical approach introduced in this dissertation is so appealing that a patent application has been filed. The contribution of this dissertation is an incremental scientific innovation based on a mathematical framework that will allow researchers in the field of flow cytometry to improve the interpretation of data knowing that its statistical meaning has been faithfully preserved for its optimized analysis. Furthermore, with the same mathematical foundation, proof of the origin of such an inherent artifact is provided. ^ These results are unique in that new mathematical derivations are established to define and solve the critical problem of the binning effect faced at the experimental assessment level, providing a data platform that preserves its statistical content. ^ In addition, a novel method for accumulating the log-transformed data was developed. This new method uses the properties of the transformation of statistical distributions to accumulate the output histogram in a non-integer and multi-channel fashion. Although the mathematics of this new mapping technique seem intricate, the concise nature of the derivations allow for an implementation procedure that lends itself to a real-time implementation using lookup tables, a task that is also introduced in this dissertation. ^

In Vivo Characterization of Myocardial Tissue Post Myocardial Infarction Using Combined Fluorescence and Diffuse Reflectance Spectroscopy

Accurately assessing the extent of myocardial tissue injury induced by Myocardial infarction (MI) is critical to the planning and optimization of MI patient management. With this in mind, this study investigated the feasibility of using combined fluorescence and diffuse reflectance spectroscopy to characterize a myocardial infarct at the different stages of its development. An animal study was conducted using twenty male Sprague-Dawley rats with MI. In vivo fluorescence spectra at 337 nm excitation and diffuse reflectance between 400 nm and 900 nm were measured from the heart using a portable fiber-optic spectroscopic system. Spectral acquisition was performed on - (1) the normal heart region; (2) the region immediately surrounding the infarct; and (3) the infarcted region - one, two, three and four weeks into MI development. The spectral data were divided into six subgroups according to the histopathological features associated with various degrees / severities of myocardial tissue injury as well as various stages of myocardial tissue remodeling, post infarction. Various data processing and analysis techniques were employed to recognize the representative spectral features corresponding to various histopathological features associated with myocardial infarction. The identified spectral features were utilized in discriminant analysis to further evaluate their effectiveness in classifying tissue injuries induced by MI. In this study, it was observed that MI induced significant alterations (p < 0.05) in the diffuse reflectance spectra, especially between 450 nm and 600 nm, from myocardial tissue within the infarcted and surrounding regions. In addition, MI induced a significant elevation in fluorescence intensities at 400 and 460 nm from the myocardial tissue from the same regions. The extent of these spectral alterations was related to the duration of the infarction. Using the spectral features identified, an effective tissue injury classification algorithm was developed which produced a satisfactory overall classification result (87.8%). The findings of this research support the concept that optical spectroscopy represents a useful tool to non-invasively determine the in vivo pathophysiological features of a myocardial infarct and its surrounding tissue, thereby providing valuable real-time feedback to surgeons during various surgical interventions for MI.

Data partitioning and replication management in distributed geographic information system (GIS) database

This research presents several components encompassing the scope of the objective of Data Partitioning and Replication Management in Distributed GIS Database. Modern Geographic Information Systems (GIS) databases are often large and complicated. Therefore data partitioning and replication management problems need to be addresses in development of an efficient and scalable solution. ^ Part of the research is to study the patterns of geographical raster data processing and to propose the algorithms to improve availability of such data. These algorithms and approaches are targeting granularity of geographic data objects as well as data partitioning in geographic databases to achieve high data availability and Quality of Service(QoS) considering distributed data delivery and processing. To achieve this goal a dynamic, real-time approach for mosaicking digital images of different temporal and spatial characteristics into tiles is proposed. This dynamic approach reuses digital images upon demand and generates mosaicked tiles only for the required region according to user's requirements such as resolution, temporal range, and target bands to reduce redundancy in storage and to utilize available computing and storage resources more efficiently. ^ Another part of the research pursued methods for efficient acquiring of GIS data from external heterogeneous databases and Web services as well as end-user GIS data delivery enhancements, automation and 3D virtual reality presentation. ^ There are vast numbers of computing, network, and storage resources idling or not fully utilized available on the Internet. Proposed "Crawling Distributed Operating System "(CDOS) approach employs such resources and creates benefits for the hosts that lend their CPU, network, and storage resources to be used in GIS database context. ^ The results of this dissertation demonstrate effective ways to develop a highly scalable GIS database. The approach developed in this dissertation has resulted in creation of TerraFly GIS database that is used by US government, researchers, and general public to facilitate Web access to remotely-sensed imagery and GIS vector information. ^

Statistical analysis and meta-analysis of microarray data

The microarray technology provides a high-throughput technique to study gene expression. Microarrays can help us diagnose different types of cancers, understand biological processes, assess host responses to drugs and pathogens, find markers for specific diseases, and much more. Microarray experiments generate large amounts of data. Thus, effective data processing and analysis are critical for making reliable inferences from the data. ^ The first part of dissertation addresses the problem of finding an optimal set of genes (biomarkers) to classify a set of samples as diseased or normal. Three statistical gene selection methods (GS, GS-NR, and GS-PCA) were developed to identify a set of genes that best differentiate between samples. A comparative study on different classification tools was performed and the best combinations of gene selection and classifiers for multi-class cancer classification were identified. For most of the benchmarking cancer data sets, the gene selection method proposed in this dissertation, GS, outperformed other gene selection methods. The classifiers based on Random Forests, neural network ensembles, and K-nearest neighbor (KNN) showed consistently god performance. A striking commonality among these classifiers is that they all use a committee-based approach, suggesting that ensemble classification methods are superior. ^ The same biological problem may be studied at different research labs and/or performed using different lab protocols or samples. In such situations, it is important to combine results from these efforts. The second part of the dissertation addresses the problem of pooling the results from different independent experiments to obtain improved results. Four statistical pooling techniques (Fisher inverse chi-square method, Logit method. Stouffer's Z transform method, and Liptak-Stouffer weighted Z-method) were investigated in this dissertation. These pooling techniques were applied to the problem of identifying cell cycle-regulated genes in two different yeast species. As a result, improved sets of cell cycle-regulated genes were identified. The last part of dissertation explores the effectiveness of wavelet data transforms for the task of clustering. Discrete wavelet transforms, with an appropriate choice of wavelet bases, were shown to be effective in producing clusters that were biologically more meaningful. ^

Design and implementation of a multisite data repository for pediatric epilepsy

This dissertation established a software-hardware integrated design for a multisite data repository in pediatric epilepsy. A total of 16 institutions formed a consortium for this web-based application. This innovative fully operational web application allows users to upload and retrieve information through a unique human-computer graphical interface that is remotely accessible to all users of the consortium. A solution based on a Linux platform with My-SQL and Personal Home Page scripts (PHP) has been selected. Research was conducted to evaluate mechanisms to electronically transfer diverse datasets from different hospitals and collect the clinical data in concert with their related functional magnetic resonance imaging (fMRI). What was unique in the approach considered is that all pertinent clinical information about patients is synthesized with input from clinical experts into 4 different forms, which were: Clinical, fMRI scoring, Image information, and Neuropsychological data entry forms. A first contribution of this dissertation was in proposing an integrated processing platform that was site and scanner independent in order to uniformly process the varied fMRI datasets and to generate comparative brain activation patterns. The data collection from the consortium complied with the IRB requirements and provides all the safeguards for security and confidentiality requirements. An 1-MR1-based software library was used to perform data processing and statistical analysis to obtain the brain activation maps. Lateralization Index (LI) of healthy control (HC) subjects in contrast to localization-related epilepsy (LRE) subjects were evaluated. Over 110 activation maps were generated, and their respective LIs were computed yielding the following groups: (a) strong right lateralization: (HC=0%, LRE=18%), (b) right lateralization: (HC=2%, LRE=10%), (c) bilateral: (HC=20%, LRE=15%), (d) left lateralization: (HC=42%, LRE=26%), e) strong left lateralization: (HC=36%, LRE=31%). Moreover, nonlinear-multidimensional decision functions were used to seek an optimal separation between typical and atypical brain activations on the basis of the demographics as well as the extent and intensity of these brain activations. The intent was not to seek the highest output measures given the inherent overlap of the data, but rather to assess which of the many dimensions were critical in the overall assessment of typical and atypical language activations with the freedom to select any number of dimensions and impose any degree of complexity in the nonlinearity of the decision space.

In vivo characterization of myocardial tissue post myocardial infarction using combined fluorescence and diffuse reflectance spectroscopy

Accurately assessing the extent of myocardial tissue injury induced by Myocardial infarction (MI) is critical to the planning and optimization of MI patient management. With this in mind, this study investigated the feasibility of using combined fluorescence and diffuse reflectance spectroscopy to characterize a myocardial infarct at the different stages of its development. An animal study was conducted using twenty male Sprague-Dawley rats with MI. In vivo fluorescence spectra at 337 nm excitation and diffuse reflectance between 400 nm and 900 nm were measured from the heart using a portable fiber-optic spectroscopic system. Spectral acquisition was performed on (1) the normal heart region; (2) the region immediately surrounding the infarct; and (3) the infarcted region—one, two, three and four weeks into MI development. The spectral data were divided into six subgroups according to the histopathological features associated with various degrees/severities of myocardial tissue injury as well as various stages of myocardial tissue remodeling, post infarction. Various data processing and analysis techniques were employed to recognize the representative spectral features corresponding to various histopathological features associated with myocardial infarction. The identified spectral features were utilized in discriminant analysis to further evaluate their effectiveness in classifying tissue injuries induced by MI. In this study, it was observed that MI induced significant alterations (p < 0.05) in the diffuse reflectance spectra, especially between 450 nm and 600 nm, from myocardial tissue within the infarcted and surrounding regions. In addition, MI induced a significant elevation in fluorescence intensities at 400 and 460 nm from the myocardial tissue from the same regions. The extent of these spectral alterations was related to the duration of the infarction. Using the spectral features identified, an effective tissue injury classification algorithm was developed which produced a satisfactory overall classification result (87.8%). The findings of this research support the concept that optical spectroscopy represents a useful tool to non-invasively determine the in vivo pathophysiological features of a myocardial infarct and its surrounding tissue, thereby providing valuable real-time feedback to surgeons during various surgical interventions for MI.

Database As A Tool For Hospitality Management

In his discussion - Database As A Tool For Hospitality Management - William O'Brien, Assistant Professor, School of Hospitality Management at Florida International University, O’Brien offers at the outset, “Database systems offer sweeping possibilities for better management of information in the hospitality industry. The author discusses what such systems are capable of accomplishing.” The author opens with a bit of background on database system development, which also lends an impression as to the complexion of the rest of the article; uh, it’s a shade technical. “In early 1981, Ashton-Tate introduced dBase 11. It was the first microcomputer database management processor to offer relational capabilities and a user-friendly query system combined with a fast, convenient report writer,” O’Brien informs. “When 16-bit microcomputers such as the IBM PC series were introduced late the following year, more powerful database products followed: dBase 111, Friday!, and Framework. The effect on the entire business community, and the hospitality industry in particular, has been remarkable”, he further offers with his informed outlook. Professor O’Brien offers a few anecdotal situations to illustrate how much a comprehensive data-base system means to a hospitality operation, especially when billing is involved. Although attitudes about computer systems, as well as the systems themselves have changed since this article was written, there is pertinent, fundamental information to be gleaned. In regards to the digression of the personal touch when a customer is engaged with a computer system, O’Brien says, “A modern data processing system should not force an employee to treat valued customers as numbers…” He also cautions, “Any computer system that decreases the availability of the personal touch is simply unacceptable.” In a system’s ability to process information, O’Brien suggests that in the past businesses were so enamored with just having an automated system that they failed to take full advantage of its capabilities. O’Brien says that a lot of savings, in time and money, went un-noticed and/or under-appreciated. Today, everyone has an integrated system, and the wise business manager is the business manager who takes full advantage of all his resources. O’Brien invokes the 80/20 rule, and offers, “…the last 20 percent of results costs 80 percent of the effort. But times have changed. Everyone is automating data management, so that last 20 percent that could be ignored a short time ago represents a significant competitive differential.” The evolution of data systems takes center stage for much of the article; pitfalls also emerge.

File Control: The Heart Of Business Computer Management

In his study - File Control: The Heart Of Business Computer Management - William G. O'Brien, Assistant Professor, The School of Hospitality Management at Florida International University, initially informs you: “Even though computers are an everyday part of the hospitality industry, many managers lack the knowledge and experience to control and protect the files in these systems. The author offers guidelines which can minimize or prevent damage to the business as a whole.” Our author initially opens this study with some anecdotal instances illustrating the failure of hospitality managers to exercise due caution with regard to computer supported information systems inside their restaurants and hotels. “Of the three components that make up any business computer system (data files, programs, and hard-ware), it is files that are most important, perhaps irreplaceable, to the business,” O’Brien informs you. O’Brien breaks down the noun, files, into two distinct categories. They are, the files of extrinsic value, and its counterpart the files of intrinsic value. An example of extrinsic value files would be a restaurant’s wine inventory. “As sales are made and new shipments are received, the computer updates the file,” says O’Brien. “This information might come directly from a point-of-sale terminal or might be entered manually by an employee,” he further explains. On the intrinsic side of the equation, O’Brien wants you to know that the information itself is the valuable part of this type of file. Its value is over and above the file’s informational purpose as a pragmatic business tool, as it is in inventory control. “The information is money in the legal sense For instance, figures moved about in banking system computers do not represent dollars; they are dollars,” O’Brien explains. “If the record of a dollar amount is erased from all computer files, then that money ceases to exist,” he warns. This type of information can also be bought and sold, such as it is in customer lists to advertisers. Files must be protected O’Brien stresses. “File security requires a systematic approach,” he discloses. O’Brien goes on to explain important elements to consider when evaluating file information. File back-up is also an important factor to think about, along with file storage/safety concerns. “Sooner or later, every property will have its fire, flood, careless mistake, or disgruntled employee,” O’Brien closes. “…good file control can minimize or prevent damage to the business as a whole.”

Pulsed parabolic equation model of acoustic transmission (PPEMAT)

Underwater sound is very important in the field of oceanography where it is used for remote sensing in much the same way that radar is used in atmospheric studies. One way to mathematically model sound propagation in the ocean is by using the parabolic-equation method, a technique that allows range dependent environmental parameters. More importantly, this method can model sound transmission where the source emits either a pure tone or a short pulse of sound. Based on the parabolic approximation method and using the split-step Fourier algorithm, a computer model for underwater sound propagation was designed and implemented. This computer model differs from previous models in its use of the interactive mode, structured programming, modular design, and state-of-the-art graphics displays. In addition, the model maximizes the efficiency of computer time through synchronization of loosely coupled dual processors and the design of a restart capability. Since the model is designed for adaptability and for users with limited computer skills, it is anticipated that it will have many applications in the scientific community.

Intelligent retrieval system for conditions of contract documents in construction

The outcome of this research is an Intelligent Retrieval System for Conditions of Contract Documents. The objective of the research is to improve the method of retrieving data from a computer version of a construction Conditions of Contract document. SmartDoc, a prototype computer system has been developed for this purpose. The system provides recommendations to aid the user in the process of retrieving clauses from the construction Conditions of Contract document. The prototype system integrates two computer technologies: hypermedia and expert systems. Hypermedia is utilized to provide a dynamic way for retrieving data from the document. Expert systems technology is utilized to build a set of rules that activate the recommendations to aid the user during the process of retrieval of clauses. The rules are based on experts knowledge. The prototype system helps the user retrieve related clauses that are not explicitly cross-referenced but, according to expert experience, are relevant to the topic that the user is interested in.

Optimal kernel development for real-time communications

The purpose of this research is to develop an optimal kernel which would be used in a real-time engineering and communications system. Since the application is a real-time system, relevant real-time issues are studied in conjunction with kernel related issues. The emphasis of the research is the development of a kernel which would not only adhere to the criteria of a real-time environment, namely determinism and performance, but also provide the flexibility and portability associated with non-real-time environments. The essence of the research is to study how the features found in non-real-time systems could be applied to the real-time system in order to generate an optimal kernel which would provide flexibility and architecture independence while maintaining the performance needed by most of the engineering applications. Traditionally, development of real-time kernels has been done using assembly language. By utilizing the powerful constructs of the C language, a real-time kernel was developed which addressed the goals of flexibility and portability while still meeting the real-time criteria. The implementation of the kernel is carried out using the powerful 68010/20/30/40 microprocessor based systems.