Physical Sciences and Mathematics Commons^™

Parallel Sorting On Multi-Core Architecture, Wei Wang

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With the limitations given by the power consumption (power wall), memory wall and the instruction level parallelism, the computing industry has turned its direction to multi-core architectures. Nowadays, the multi-core and many-core architectures are becoming the trend of the processor design. But how to exploit these architectures is the primary challenge for the research community. To take advantage of the multi-core architectures, the software design has undergone fundamental changes.

Sorting is a fundamental, important problem in computer science. It is utilized in many applications such as databases and search engines. In this thesis, we will investigate and auto-tune two parallel …

Semi-Supervised Contrafold For Rna Secondary Structure Prediction: A Maximum Entropy Approach, Jianping Feng

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A novel probabilistic discriminative model based on conditional random fields, CONTRAfold, has recently been proposed for single sequence RNA secondary structure prediction. By incorporating most of the features which closely mirror the local interaction terms of thermodynamics-based models, the CONTRAfold model has outperformed both probabilistic and physics-based techniques, and received the highest single sequence prediction accuracies. CONTRAfold, like most other RNA secondary structure prediction techniques, requires a collection of RNA sequences with known secondary structure to serve as training data for the algorithm. Manual annotation of RNA sequences is both expensive and time-consuming, and there remains a great deal more …

Optimizing Memory Cost With Loop Transformations, Hailong Shi

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Embedded systems are usually constrained in terms of timing, power, and memory. Many embedded applications, especially in the multi-media and telecom domains, are inherently data dominant. These embedded DSP applications usually exhibit intensive computations in the form of multi-level loops. The performance of these embedded DSP applications mainly depends on the code quality of the loops and the memory hierarchy design. During the design phase of the embedded system, it is important to estimate the overall storage requirement to guide the memory system design and take advantage of the memory system by program transformations and loop transformations.

Loop transformations including …

Towards Optimal Resource Provisioning For Running Mapreduce Programs In Public Clouds, Fengguang Tian

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Running MapReduce programs in the public cloud introduces the important problem: how to optimize resource provisioning to minimize the financial charge for a specific job? In this thesis, We study the whole process of MapReduce processing and build up a cost function that explicitly models the relationship between the amount of input data, the available system resources (Map and Reduce slots), and the complexity of the Reduce function for the target MapReduce job. The model parameters can be learned from test runs with a small number of nodes on a small amount of data. Based on this cost model, we …

3-D Model Characterization And Identification From Intrinsic Landmarks, John L. Camp

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A method to automatically characterize and identify 3-D range scans based on intrinsic landmarks is presented. Intrinsic landmarks represent locally unique, intrinsic properties of a scanned surface, regardless of scale or rotation. The number, location, and characteristics of landmarks are used to characterize the scanned models. This method contains a selection process to identify stable, intrinsic landmarks for range scans as well as the identification of those scans. The selection process requires no user interaction or surface assumptions. It uses the principal curvatures at the range points to select the landmarks. First, a large number of landmarks are generated by …

Real Time Semantic Analysis Of Streaming Sensor Data, Harshal Kamlesh Patni

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The emergence of dynamic information sources - like social, mobile and sensors, has led to ginormous streams of real time data on the web also called, the era of Big Data [1]. Research studies suggest, these dynamic networks have created more data in the last three years than in the entire history of civilization, and this trend will only increase in the coming years [1]. Gigaom article on Big data shows, how the total information generated by these dynamic information sources has completely surpassed the total storage capacity. Thus keeping in mind the problem of ever-increasing data, this thesis focuses …

Interoperability Between Awsome And Other Tools Using Model Driven Architecture, Chitra Srinivasan

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AFIT Wide Spectrum Object Modeling Environment (AWSOME) is built on an Abstract Syntax Tree (AST) which is the meta-model of AWSOME. Transformations happen internally in AWSOME to transform anything in abstract to concrete. Earlier efforts in AWSOME were focused on developing tools to work on the AST. The goal of this thesis is to make AWSOME interoperable with other available tools. To achieve this goal, the Model Driven Architecture (MDA) concept is used. MDA is a framework aimed at portability, interoperability and reusability among different tools. Among many tools that use MDA context, EclipseUML 2008 and Dresden OCL Toolkit were …

Measuring Uncertainty Of Protein Secondary Structure, Alan Eugene Herner

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This dissertation develops and demonstrates a method to measure the uncertainty of secondary structure of protein sequences using Shannon's information theory. This method is applied to a newly developed large dataset of chameleon sequences and to several protein hinges culled from the Hinge Atlas. The uncertainty of the central residue in each tripeptide is computed for each amino acid in a sequence using Cuff and Barton's CB513 as the reference set. It is shown that while secondary structure uncertainty is relatively high in chameleon regions [avg = 1.27 bits] it is relatively low in the regions 1-7 residues nearest a …

A User Centered Design And Prototype Of A Mobile Reading Device For The Visually Impaired, Robert B. Keefer

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While mobile reading devices have been on the market and investigated by researchers in recent years, there is still work required to make these devices highly accessible to the visually impaired. A usability test with one such device revealed gaps in the current state of the art devices. These gaps focus mostly on the user interaction and his or her ability to quickly consume written reading material. In this dissertation a voice user interface (VUI) is presented that improves the ability of a blind user of a mobile reading device to interact with written material. The image processing techniques required …

Optimization Of Scientific Computation For Multicore Systems, Andrew B. Mcclain

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With the rapid growth of semiconductor technology, chip density has increased significantly. As the power exponent is setting hard limits to frequency increases, multi-core and chip level multi-processors have become prevalent in recent years to take advantage of the increasing chip density. In the new generation of processors, multi-core architecture design is becoming the major trend: IBM/SONY/Toshiba's Cell Broadband Engine processors contain nine cores; NVIDIA graphics processors contain more than 30 cores.

One of the biggest challenges is to efficiently utilize the computational power provided by multi-core systems. The second challenge to achieving high performance in a computer system is …