Computer Sciences Commons^™

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 …

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 …

Understanding User-Generated Content On Social Media, Bala Meenakshi Nagarajan

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Over the last few years, there has been a growing public and enterprise fascination with 'social media' and its role in modern society. At the heart of this fascination is the ability for users to participate, collaborate, consume, create and share content via a variety of platforms such as blogs, micro-blogs, email, instant messaging services, social network services, collaborative wikis, social bookmarking sites, and multimedia sharing sites.

This dissertation is devoted to understanding informal user-generated textual content on social media platforms and using the results of the analysis to build Social Intelligence Applications.

The body of research presented in this …

Surveillance In A Smart Home Environment, Ryan Stewart Patrick

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A system for assisting the elderly in maintaining independent living is currently being designed. When mature, it is expected that this system will have the ability to track objects that a resident may lose periodically, detect falls within the home, and alert family members or health care professionals to abnormal behaviors.

This thesis addresses the early stages of this system's development. It presents a survey of the work that has previously been completed in the area of surveillance within a home environment, information on the physical characteristics of the system that is being designed, early results related to this system, …

Privacy-Preserving Attribute-Based Access Control In A Grid, Sang Mork Park

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A Grid community is composed of diverse stake holders, such as data resource providers, computing resource providers, service providers, and the users of the resources and services. In traditional security systems for Grids, most of the authentication and authorization mechanisms are based on the user's identity or the user's classification information. If the authorization mechanism is based on the user's identity, fine-grained access control policies can be implemented but the scalability of the security system would be limited. If the authorization mechanism is based on the user's classification, the scalability can be improved but the fine-grained access control policies may …

Prognosis: A Wearable System For Health Monitoring Of People At Risk, Alexandros A. Pantelopoulos

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Wearable Health Monitoring Systems (WHMS) have drawn a lot of attention from the research community and the industry during the last decade. The development of such systems has been motivated mainly by increasing healthcare costs and by the fact that the world population is ageing. In addition to that, RandD in WHMS has been propelled by recent technological advances in miniature bio-sensing devices, smart textiles, microelectronics and wireless communications techniques. These portable health systems can comprise various types of small physiological sensors, which enable continuous monitoring of a variety of human vital signs and other physiological parameters such as heart …

A Contrast Pattern Based Clustering Algorithm For Categorical Data, Neil Koberlein Fore

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The data clustering problem has received much attention in the data mining, machine learning, and pattern recognition communities over a long period of time. Many previous approaches to solving this problem require the use of a distance function. However, since clustering is highly explorative and is usually performed on data which are rather new, it is debatable whether users can provide good distance functions for the data. This thesis proposes a Contrast Pattern based Clustering (CPC) algorithm to construct clusters without a distance function, by focusing on the quality and diversity/richness of contrast patterns that contrast the clusters in a …

Evolution And Analysis Of Neuromorphic Flapping-Wing Flight Controllers, Sanjay Kumar Boddhu

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The control of insect-sized flapping-wing micro air vehicles is attracting increasing interest. Solution of the problem requires construction of a controller that is physically small, extremely power efficient, and capable. In addition, process variation in the creation of very small wings and armatures as well as the potential for accumulating damage and wear over the course of a vehicle's lifetime suggest that controllers be able to self-adapt to the specific and possibly changing nature of the vehicles in which they are embedded. Previous work with Evolvable Hardware Continuous Time Recurrent Neural Networks (CTRNNs) as applied to adaptive control of walking …

A Novel Synergistic Diagnosis Methodology For Identifying Abnormalities In Wireless Capsule Endoscopy Videos, Alexandros Karargyris

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Wireless Capsule Endoscopy (WCE) is a new technology that allows medical personnel to view the gastrointestinal (GI) mucosa. It is a swallowable miniature capsule device the size of a pill that transmits thousands of screenshots of the digestive tract to a wearable receiver. When the procedure finishes the video is uploaded to a workstation for viewing. Capsule Endoscopy has been established as a tool to identify various gastrointestinal (GI) conditions, such as blood-based abnormalities, polyps, ulcers, Crohn's disease in the small intestine, where the classical endoscopy is not regularly used.

As of 2009 the market is dominated by Given Imaging …

Algorithmic Techniques Employed In The Quantification And Characterization Of Nuclear Magnetic Resonance Spectroscopic Data, Paul Edward Anderson

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Nuclear magnetic resonance (NMR) based metabolomics is a developing research field with broad applicability, including the identification of biomarkers associated with pathophysiologic changes, sample classification based on the mechanism of toxicity, and clinical diagnosis. Intrinsic to these applications is the need for statistical and computational techniques to facilitate the associated data analysis. Further, a typical 1H NMR spectrum of pure proteins, biofluids, or tissue may contain thousands of resonances (i.e., peaks), thus, a pure visual inspection is insufficient to fully utilize the spectral information.

Common practice within the NMR-based metabolomics community is to evaluate and validate novel algorithms on empirical …

Semantic Provenance: Modeling, Querying, And Application In Scientific Discovery, Satya Sanket Sahoo

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Provenance metadata, describing the history or lineage of an entity, is essential for ensuring data quality, correctness of process execution, and computing trust values. Traditionally, provenance management issues have been dealt with in the context of workflow or relational database systems. However, existing provenance systems are inadequate to address the requirements of an emerging set of applications in the new eScience or Cyberinfrastructure paradigm and the Semantic Web. Provenance in these applications incorporates complex domain semantics on a large scale with a variety of uses, including accurate interpretation by software agents, trustworthy data integration, reproducibility, attribution for commercial or legal …

Visualization Of Complex Unsteady 3d Flow: Flowing Seed Points And Dynamically Evolving Seed Curves With Applications To Vortex Visualization In Cfd Simulations Of Ultra Low Reynolds Number Insect Flight, Christopher M. Koehler

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Three dimensional integration-based geometric visualization is a very powerful tool for analyzing flow phenomena in time dependent vector fields. Streamlines in particular have many perceptual benefits due to their ability to provide a snapshot of the vectors near key features of complex 3D flows at any instant in time. However, streamlines do not lend themselves well to animation. Subtle changes in the vector field at each time step lead to increasingly large changes between streamlines with the same seed point the longer they are integrated. Path lines, which show particle trajectories over time suffer from similar problems when attempting to …

A Cryptanalysis Methodology For The Reverse Engineering Of Encrypted Information In Images, Allan Anthony Rwabutaza

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Security is an important issue related to the storage and communication of data and information. In data and information security, cryptography and steganography are two of the most common security techniques. On one hand, there is cryptography, which is the secret communication between two parties by message scrambling on the sender's side and message unscrambling on the receiver's side so that only the intended receiver gets the secret message. On the other hand, there is steganography, which is the hiding of information in a medium in such a way that no one other than the sender or the intended receiver …

A System For Incorporating Time-Based Event-Condition-Action Rules Into Business Databases, Christina Marie Steidle

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Human beings handle time-based events continuously; however the passage of time does not play an active part in most business systems because they are typically driven by interaction from human users or other systems. In order to take an action based upon the passage of time it is necessary to build a framework which will monitor the progression of time and a way to define what events the system should be waiting for. This thesis describes such a system, and shows that the system performs as specified. With this system business users are able to build event-condition-action rules using a …

Computational Analysis Of Metabolomic Toxicological Data Derived From Nmr Spectroscopy, Benjamin J. Kelly

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Nuclear magnetic resonance (NMR) spectroscopy is a non-invasive method of acquiring metabolic profiles from biofluids. The most informative metabolomic features, or biomarkers, may provide keys to the early detection of changes within an organism such as those that result from exposure to a toxin. One major difficulty with typical NMR data, whether it come from a toxicological, medical or other source, is that it features a low sample size relative to the number of variables measured. Thus, traditional pattern recognition techniques are not always feasible. The "curse of dimensionality" is an important consideration in selecting appropriate statistical and pattern recognition …

Tyflos: A Wearable Navigation Prototype For Blind & Visually Impaired; Design, Modelling And Experimental Results, Dimitrios Dakopoulos

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The need for assistive devices has, had and will have a large merit in many engineering research arenas. This dissertation deals with the design, modeling, implementation and experimentation of the navigation component of a wearable assistive system for blind and visually impaired people, called TYFLOS (ΤΥΦΛΟΣ) which is the Greek word for "Blind".

The current prototype consists of two mini cameras attached to a pair of conventional eye-glasses, a 2D tactile display vibration array) which consists of 16 vibrating elements arranged in a 4x4 manner, attached to an elastic vest worn on the user's abdomen, a portable computer, an ear-speaker …

Investigation And Quantification Of Codon Usage Bias Trends In Prokaryotes, Amanda L. Hanes

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Organisms construct proteins out of individual amino acids using instructions encoded in the nucleotide sequence of a DNA molecule. The genetic code associates combinations of three nucleotides, called codons, with every amino acid. Most amino acids are associated with multiple synonymous codons, but although they result in the same amino acid and thus have no effect on the final protein, synonymous codons are not present in equal amounts in the genomes of most organisms. This phenomenon is known as codon usage bias, and the literature has shown that all organisms display a unique pattern of codon usage. Research also suggests …

Semantics Enriched Service Environments, Karthik Rajagopal Gomadam

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During the past seven years services centric computing has emerged as the preferred approach to architect complex software. Software is increasingly developed by integrating remotely existing components, popularly called services. This architectural paradigm, also called Service Oriented Architecture (SOA), brings with it the benefits of interoperability, agility and flexibility to software design and development. One can easily add or change new features to existing systems, either by the addition of new services or by replacing existing ones. Two popular approaches have emerged for realizing SOA. The first approach is based on the SOAP protocol for communication and the Web Service …

A Software Framework For The Design, Testing And Deployment Of Control Systems For Autonomous Robotics, Duane Stanley Bolick Jr.

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Simulation and control of robotic agents are common enough tasks among computer science and engineering researchers that there exists a large variety of software applications, toolkits, and programming frameworks designed to facilitate such research. The intent of this project is to provide an autonomous robotics simulation and control framework with sufficiently useful tools and reference implementations so as to be immediately useful to basic users, as well as easily understood and extended by software developers and robotics researchers.

As such, this document describes the implementation of a general networking toolkit, an autonomous robotics extension framework, and an autonomous robotics simulator …

Burst Scheduling, Grooming And Qos Provisioning In Optical Burst-Switched Networks, Yuqi Fan

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The demand of network capacity has been increasing steadily with more users than ever connected to the Internet through broadband access and the popularity of video based applications, such as YouTube. Optical wavelength division multiplexing (WDM) networks are expected to form the next-generation backbone network and to fulfill the insatiable appetite for bandwidth.

Wavelength routed WDM optical networks offer the granularity of switching at a fiber, waveband, or a wavelength level. The finest granularity offered is at a wavelength level by provisioning lightpaths for different clients/services. All-optical packet switching is still deemed technically infeasible and its competitiveness as a backbone …

Improving Remote Homology Detection Using A Sequence Property Approach, Gina Marie Cooper

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Understanding the structure and function of proteins is a key part of understanding biological systems. Although proteins are complex biological macromolecules, they are made up of only 20 basic building blocks known as amino acids. The makeup of a protein can be described as a sequence of amino acids. One of the most important tools in modern bioinformatics is the ability to search for biological sequences (such as protein sequences) that are similar to a given query sequence. There are many tools for doing this (Altschul et al., 1990, Hobohm and Sander, 1995, Thomson et al., 1994, Karplus and Barrett, …

Design And Performance Analysis Of A Secure Proces-Sor Scan-Sp With Crypto-Biometric Capabilities, Raghudeep Kannavara

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Secure computing is gaining importance in recent times as computing capability is increasingly becoming distributed and information is everywhere. Prevention of piracy and digital rights management has become very important. Information security is mandatory rather than an additional feature. Numerous software techniques have been proposed to provide certain level of copyright and intellectual property protection. Techniques like obfuscation attempt to transform the code into a form that is harder to reverse engineer. Tamper-proofing causes a program to malfunction when it detects that it has been modified. Software watermarking embeds copyright notice in the software code to allow the owners of …

Semantic And Role-Based Access Control For Data Grid Systems, Vineela Muppavarapu

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A Grid is an integration infrastructure for sharing and coordinated use of diverseresources in dynamic, distributed virtual organizations (VOs). A Data Grid is an architecture for the access, exchange, and sharing of data in the Grid environment. Distributed data resources can be diverse in their formats, schema, quality, access mechanisms, ownership, access policies, and capabilities. In recent years, several organizations have started utilizing Grid technologies to deploy data-intensive and/or computation-intensive applications. As more and more organizations are sharing data resources and participating in Data Grids, the complexity and heterogeneity of the systems is increasing constantly, but their management techniques are …

Automated Transforms Of Software Models: A Design Pattern Approach, Brandon Adam Gump

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In the realm of software development, projects are plagued by continuous maintenance at the source code level as well as tedious transformations from formal specifications to source code. Such work consumes a large amount of time only to create complicated, un-intelligible, and un-reusable code that is completely detached from initial design rational. To cope with these problems, The Air Force Institute of Technology (AFIT) Wide Spectrum Object Modeling Environment (AWSOME) was designed to generate specifications that can be transformed into abstract designs and finally into source code. The specifications are written in the AFIT Wide-spectrum Language (AWL) and parsed in …

Extracting, Representing And Mining Semantic Metadata From Text: Facilitating Knowledge Discovery In Biomedicine, Cartic Ramakrishnan

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The information access paradigm offered by most contemporary text information systems is a search-and-sift paradigm where users have to manually glean and aggregate relevant information from the large number of documents that are typically returned in response to keyword queries. Expecting the users to glean and aggregate information has lead to several inadequacies in these information systems. Owing to the size of many text databases, search-and-sift is a very tedious often requiring repeated keyword searches refining or generalizing queries terms. A more serious limitation arises from the lack of automated mechanisms to aggregate content across different documents to discover new …

Evolutionary Methodology For Optimization Of Image Transforms Subject To Quantization Noise, Michael Ray Peterson

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Lossy image compression algorithms sacrifice perfect imagereconstruction in favor of decreased storage requirements. Modelossy compression schemes, such as JPEG2000, rely upon the discrete wavelet transform (DWT) to achieve high levels of compression while minimizing the loss of information for image reconstruction. Some compression applications require higher levels of compression than those achieved through application of the DWT and entropy coding. In such lossy systems, quantization provides high compression rates at the cost of increased distortion. Unfortunately, as the amount of quantization increases, the performance of the DWT for accurate image reconstruction deteriorates. Previous research demonstrates that a genetic algorithm can …