Computer Sciences Commons^™

Parallel Real-Time Scheduling Of Dags, Abusayeed Saifullah, David Ferry, Jing Li, Kunal Agrawal, Chenyang Lu, Christopher Gill

All Computer Science and Engineering Research

Recently, multi-core processors have become mainstream in processor design. To take full advantage of multi-core processing, computation-intensive real-time systems must exploit intra-task parallelism. In this paper, we address the open problem of real-time scheduling for a general model of deterministic parallel tasks, where each task is represented as a directed acyclic graph (DAG) with nodes having arbitrary execution requirements. We prove processor-speed augmentation bounds for both preemptive and non-preemptive real-time scheduling for general DAG tasks on multi-core processors. We first decompose each DAG into sequential tasks with their own release times and deadlines. Then we prove that these decomposed tasks …

Scanner: An Efficient And Accurate Trimming Tool For Illumina Next Generation Sequencing Reads, Xiang Zhou

All Computer Science and Engineering Research

Recent advances in High-Throughput Sequencing (HTS) technology have greatly facilitated the researches in bioinformatics field. With the ultra-high sequencing speed and improved base-calling accuracy, Illumina Genome Analyzer is currently the most widely used platform in the field. To use the raw reads generated from the sequencing machine, the 3’ adapter sequence attached to the real read in the process of ligation needs to be correctly trimmed. This is often done by some inhouse scripts or different packages with various parameters. They either use the Smith-Waterman algorithm or search for an exact match of the 3’ adapter sequence. In this report, …

Simple Analytic Performance Models For Streaming Data Applications Deployed On Diverse Architectures, Jonathan C. Beard, Roger D. Chamberlain, Mark A. Franklin

All Computer Science and Engineering Research

Modern hardware is inherently heterogeneous. With heterogeneity comes multiple abstraction layers that hide underlying complex systems. While hidden, this complexity makes quantitative performance modeling a difficult task. Designers of high-performance streaming applications for heterogeneous systems must contend with unpredictable and often non-generalizable models to predict performance of a particular application and hardware mapping. This paper outlines a computationally simple approach that can be used to model the overall throughput and buffering needs of a streaming application on heterogeneous hardware. The model presented is based upon a hybrid maximum flow and decomposed discrete queueing model. The utility of the model is …

Ewa Model With Recency Effect And Limited Memory, Hang Xie

All Computer Science and Engineering Research

Game theory is an important field in economics; it studies how people make decisions amid conflict and cooperation. Various experiments have been carried to study the way people play those games, and economists study those data for various purposes. There has been a rise of need for using artificial agents to simulate the game, since we could save the cost of hiring human subjects for the experiments, and we could gain more control over the experiment settings.

Self-Adapting Mac Layer For Wireless Sensor Networks, Mo Sha, Meng Xu, Chenyang Lu, Linh T.X. Phan, Tae-Suk Kim, Taerim Park

All Computer Science and Engineering Research

The integration of wireless sensors with mobile phones is gaining momentum as an enabling platform for numerous emerging applications. These mobile systems face dynamic environments where both application requirements and ambient wireless conditions change frequently. Despite the existence of many MAC protocols however, none can provide optimal performance along multiple dimensions, in particular when the conditions are frequently changing. Instead of pursuing a one-MAC-fit all approach we present a Self-Adapting MAC Layer (SAML) comprising (1) a Reconfigurable MAC Architecture (RMA) that can switch to different MAC protocols at run time and (2) a learning-based MAC Selection Engine that selects the …

Control In Networked Systems With Fuzzy Logic, Akhan Akbulut, Oğuzhan Öztaş

Turkish Journal of Electrical Engineering and Computer Sciences

Recently, the development of control systems based on network-based architecture is getting very high attention. Because of its fast data communication, network-based control is in high demand. However, there are some disadvantages, such as delays, data packet dropouts, and communication constraints. Network-based control systems are getting attention in the development of this architecture because of these disadvantages. Optimization of the system is supplied to improve the existing structure. The optimization is categorized into 2 main structures: software optimization and hardware optimization. The structure of the overall system is designed with these optimization strategies. A hierarchical and communicational structure has emerged …

Real-Time Multi-Core Virtual Machine Scheduling In Xen, Sisu Xi, Meng Xu, Chenyang Lu, Linh T.X. Phan, Christopher Gill, Olga Sokolsky, Insup Lee

All Computer Science and Engineering Research

Recent years have witnessed two major trends in the development of complex real-time systems. First, to reduce cost and enhance flexibility, multiple systems are sharing common computing platforms via virtualization technology, instead of being deployed separately on physically isolated hosts. Second, multicore processors are increasingly being used in real-time systems. The integration of real-time systems as virtual machines (VMs) atop common multicore platforms raises significant new research challenges in meeting the real-time performance requirements of multiple systems.

Partial Replica Location And Selection For Spatial Datasets, Yun Tian

Electronic Theses and Dissertations

As the size of scientific datasets continues to grow, we will not be able to store enormous datasets on a single grid node, but must distribute them across many grid nodes. The implementation of partial or incomplete replicas, which represent only a subset of a larger dataset, has been an active topic of research. Partial Spatial Replicas extend this functionality to spatial data, allowing us to distribute a spatial dataset in pieces over several locations. We investigate solutions to the partial spatial replica selection problems. First, we describe and develop two designs for an Spatial Replica Location Service (SRLS), which …

Standardized Construction Of Hpc Clusters For Academic Usage, Bradford Bazemore

Phi Kappa Phi Research Symposium (Archived)

A model for the standardization of design and implementation of HPC clusters to be used in universities is presented. Standardization is achieved by using an open-source operating system, network infrastructure, and software packages. The cluster is configured for universities intending to implement an HPC cluster for research or teaching use. No prior understanding of clusters is assumed but a basic understanding of programming, networking and computers in general is required.

Information Management Compliance: Frameworks For Governance & Assurance, Thomas B. Malvey

Senior Seminars

No abstract provided.

The Internet And How The Government Has Impacted Its Usage Today, Jonathan Hulse

Senior Seminars

No abstract provided.

Technology Use In The National Basketball Association: How Technology And Communication Has Changed, Katie Hottinger

Senior Seminars

No abstract provided.

Disulfide By Design 2.0: A Web-Based Tool For Disulfide Engineering In Proteins, Douglas B. Craig, Alan A. Dombkowski

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Disulfide engineering is an important biotechnological tool that has advanced a wide range of research. The introduction of novel disulfide bonds into proteins has been used extensively to improve protein stability, modify functional characteristics, and to assist in the study of protein dynamics. Successful use of this technology is greatly enhanced by software that can predict pairs of residues that will likely form a disulfide bond if mutated to cysteines.

Results

We had previously developed and distributed software for this purpose: Disulfide by Design (DbD). The original DbD program has been widely used; however, it has a number …

Regression Models For Readmission Prediction Using Electronic Medical Records, Yudi Niu

Wayne State University Theses

Hospital readmissions are not only expensive but are also potentially harmful, and most importantly, they are often preventable. Providing special care for a targeted group of patients who are at a high risk of readmission can significantly improve the chances of avoiding rehospitalization. Despite the significance of this problem, not many researchers have thoroughly investigated it due to the inherent complexities involved in analyzing and estimating the inherent predictive power of such complex hospitalization records. In this thesis, we propose using support vector machines and survival analysis methods to analyze data collected from Electronic Medical Records (EMR). We define the …

Analyzing Environmental Change And Prehistoric Hunter Behavior Through A 3d Time-Lapsed Model With Level Auto-Generation And Cultural Algorithms, Samuel Dustin Stanley

Wayne State University Theses

This paper describes a system containing two portions whose purpose it is to help further the Alpena-Amberley Land Bridge research project and similar archaeological research. The first portion is a "time engine" which one can utilize to navigate through time in order to see how environmental conditions evolved as time passed, or to run experiments during a desired time period. The second portion is a hunting blind cultural algorithm, which is built on top of the time engine as well as Palazzolo's program. In this portion, the AI hunting blinds react to the goals that they are trying to achieve, …

Performance Evaluation Of Voice Chat In Vechicular Ad-Hoc Networks, Vineeth Rakesh Mohan

Wayne State University Theses

Inter vehicle communication has emerged as an important area of research. With a rapid evolution of social networks, people are constantly looking for social interactions in all types of mobile environment. In this Thesis, we propose a voice chat model for Vehicle-to-Vehicle (V2V) communication that mimics a real-world group talk scenario, and measure its performance using Flood and Scalable broadcast (SBA) protocols. To evaluate the performance of the voice chat, we use different parameters such as group size, network density, transmission range and hop counts to show that our voice chat application is highly feasible in VANET environment. Furthermore, we …

On-The-Fly Tracing For Data-Centric Computing : Parallelization, Workflow And Applications, Lei Jiang

LSU Doctoral Dissertations

As data-centric computing becomes the trend in science and engineering, more and more hardware systems, as well as middleware frameworks, are emerging to handle the intensive computations associated with big data. At the programming level, it is crucial to have corresponding programming paradigms for dealing with big data. Although MapReduce is now a known programming model for data-centric computing where parallelization is completely replaced by partitioning the computing task through data, not all programs particularly those using statistical computing and data mining algorithms with interdependence can be re-factorized in such a fashion. On the other hand, many traditional automatic parallelization …

Logical Linked Data Compression, Amit Krishna Joshi, Pascal Hitzler, Guozhu Dong

Computer Science and Engineering Faculty Publications

Linked data has experienced accelerated growth in recent years. With the continuing proliferation of structured data, demand for RDF compression is becoming increasingly important. In this study, we introduce a novel lossless compression technique for RDF datasets, called Rule Based Compression (RB Compression) that compresses datasets by generating a set of new logical rules from the dataset and removing triples that can be inferred from these rules. Unlike other compression techniques, our approach not only takes advantage of syntactic verbosity and data redundancy but also utilizes semantic associations present in the RDF graph. Depending on the nature of the dataset, …

Stochastic Optimization: Theory And Applications, Bin Wang, Lotfollah Najjar, Neal N. Xiong, Rung Ching Chen

Information Systems and Quantitative Analysis Faculty Publications

As an important branch of applied mathematics, optimization theory, especially stochastic optimization, becomes an important tool for solving multiobjective decision-making problems in random process recently. Many kinds of industrial, biological, engineering, and economic problems can be viewed as stochastic systems, for example, area of communication, gene, signal processing, geography, civil engineering, aerospace, banking, and so forth. Stochastic optimization is suitable to solve the decision-making problems in these stochastic systems.

Call Graph Based Metrics To Evaluate Software Design Quality, H. Abandah, Izzat M. Alsmadi

Computer Science Faculty Publications (Archived)

Software defects prediction was introduced to support development and maintenance activities such as improving the software quality through finding errors or patterns of errors early in the software development process. Software defects prediction is playing the role of maintenance facilitation in terms of effort, time and more importantly the cost prediction for software maintenance and evolution activities. In this research, software call graph model is used to evaluate its ability to predict quality related attributes in developed software products. As a case study, the call graph model is generated for several applications in order to represent and reflect the degree …

Efficient Assessment And Evaluation For Websites Vulnerabilities Using Snort, M. Dabbour, Izzat M. Alsmadi, E. Alsukhni

Computer Science Faculty Publications (Archived)

An endless number of methods or ways exists to access illegally a web server or a website. The task of defending a system (e.g. network, server, website, etc.) is complex and challenging. SNORT is one of the popular open source tools that can be used to detect and possibly prevent illegal access and attacks for networks and websites. However, this largely depends on the way SNORT rules are designed and implemented. In this paper, we investigated in details several examples of SNORT rules and how they can be tuned to improve websites protection. We demonstrated practical methods to design and …

Impact Of Programming Features On Code Readability, Y. Tashtoush, Z. Odat, Izzat M. Alsmadi, M. Yatim

Computer Science Faculty Publications (Archived)

Readability is one important quality attributes for software source codes. Readability has also significant relation or impact with other quality attributes such as: reusability, maintainability, reliability, complexity, and portability metrics. This research develops a novel approach called Impact of Programming Features on Code Readability (IPFCR), to examine the influence of various programming features and the effect of these features on code readability. A code Readability Tool (CRT) is developed to evaluate the IPFCR readability features or attributes. In order to assess the level if impact that each one of the 25 proposed readability features may have, positively or negatively on …

Software Development For A 3d Gravity Inversion And Application To Study Of The Border Ranges Fault System, South-Central Alaska, Rolando Cardenas

Open Access Theses & Dissertations

The Border Ranges Fault System (BRFS) bounds the Cook Inlet and Susitna Basins, and is an important petroleum province within south-central Alaska. A primary goal of our research is to test several plausible models of structure along the BRFS using a novel three-dimensional inversion technique utilizing gravity data, constrained with other geophysical, borehole and surface geological information. This research involves the development of 3D inversion modeling software using C++ Builder from Embarcadero's XE2 Suite. The novel inversion approach directly models known geology with a priori uncertainties assigned to the geologic model to allow researchers to compare alternative interpretations. This technique …

Automatic Memory Management Policies For Low Power, Memory Limited, And Delay Intolerant Devices, Md Abu Jahid

Open Access Theses & Dissertations

Mobile devices such as smartphones and tablets are energy and memory limited, and implement graphical user interfaces that are intolerant of computational delays. Mobile device platforms supporting apps implemented in languages that require automatic memory man- agement, such as the Dalvik (Java) virtual machine within Google's Android, have become dominant. It is essential that automatic memory management avoid causing unacceptable interface delays while responsibly managing energy and memory resource usage. Dalvik's automatic memory management policies for heap growth and garbage collection scheduling utilize heuristics tuned to minimize memory footprint. These policies result in only marginally acceptable response times and garbage …

Using Emotion As Inferred From Prosody In Language Modeling, Shreyas Ashok Karkhedkar

Open Access Theses & Dissertations

Research has focused on using prosody as an alternative source of information for language modeling. However, prosody is a surface phenomenon and to develop deeper models of language production, the underlying mental processes need to be considered. There are several cognitive factors, such as dialog-states and formulation, that have been given attention. However, emotion { as a cognitive factor, has been neglected so far. Speakers' emotional state plays an important role in spoken dialog. Participants seem to infer each others emotional state from multiple cues and react accordingly. In particular, these states manifest themselves moment-by-moment in the speakers voice. This …

Model Fusion: A New Approach To Processing Heterogeneous Data, Omar Ochoa

Open Access Theses & Dissertations

In many practical situations, it is necessary to extract

information from data of different types. For example, in geosciences, several sources of data can be used to determine the interior structure of the earth: the first arriving waves from earthquakes and from man-made sources, measurements of the earth's gravity field, measurements of the dispersion of surface waves generated by earthquakes, etc. At present, most existing data processing techniques deal only with data of one type.

A joint use of all the information derived from multiple types of data sources is an important theoretical and practical challenge. Such a joint use …

Strong Coupled Quark Matter And Drawbacks Of Its Bcs-Bec Crossover, Israel Portillo Vazquez

Open Access Theses & Dissertations

It was found many years ago, that the ground state wave functions of the Bardeen-Cooper-Schrieer (BCS) superconductivity in a degenerate Fermi gas and the Bose-Einstein condensation (BEC) of composite molecules are essentially the same, and those two states can be smoothly connected through a crossover. This BCS-BEC crossover has being recently extended to relativistic Fermi System. This thesis is dedicated to exploring the possible crossover from BEC to BCS phase on strong-interacting matter and its implications for the system Equation of State. The study will be concentrated on dierent phases of dense quark-matter for vanishing temperatures and densities beyond hadronic …

Extracting Fuzzy Measures From Sample Data: Optimization Algorithms And Applications, Xiaojing Wang

Open Access Theses & Dissertations

In Multi-Criteria Decision Making (MCDM), decisions are based on several criteria that are usually conflicting and non-homogenously satisfied. We use non-additive (fuzzy) measures combined with the Choquet integral to solve MCDM problems, for they allow to model and aggregate the levels of satisfaction of the several criteria of the problem at hand by considering the relationship between these criteria. In practice, it is difficult to identify such fuzzy measures. An automated process is then necessary and can be used when sample data is available. Several optimization approaches have been used to extract fuzzy measures from sample data, for example, genetic …

Determining The Benefit Of Human Input In Human-In-The-Loop Robotic Systems, Christine Elizabeth Bringes

USF Tampa Graduate Theses and Dissertations

This work analyzes human-in-the-loop robotic systems to determine where human input can be most beneficial to a collaborative task. This is accomplished by implementing a pick-and-place task using a human-in-the-loop robotic system and determining which segments of the task, when replaced by human guidance, provide the most improvement to overall task performance and require the least cognitive effort.

The first experiment entails implementing a pick and place task on a commercial robotic arm. Initially, we look at a pick-and-place task that is segmented into two main areas: coarse approach towards a goal object and fine pick motion. For the fine …

Efficient And Private Processing Of Analytical Queries In Scientific Datasets, Anand Kumar

USF Tampa Graduate Theses and Dissertations

Large amount of data is generated by applications used in basic-science research and development applications. The size of data introduces great challenges in storage, analysis and preserving privacy. This dissertation proposes novel techniques to efficiently analyze the data and reduce storage space requirements through a data compression technique while preserving privacy and providing data security.

We present an efficient technique to compute an analytical query called spatial distance histogram (SDH) using spatiotemporal properties of the data. Special spatiotemporal properties present in the data are exploited to process SDH efficiently on the fly. General purpose graphics processing units (GPGPU or just …