Computer Sciences Commons^™

Building Towards Precision Medicine: Empowering Medical Professionals For The Next Revolution, Scott Mcgrath, Dario Ghersi

Interdisciplinary Informatics Faculty Publications

A new paradigm in disease classification, diagnosis and treatment is rapidly approaching. Known as precision medicine, this new healthcare model incorporates and integrates genetic information, microbiome data, and information on patients’ environment and lifestyle to better identify and classify disease processes, and to provide custom-tailored therapeutic solutions. In spite of its promises, precision medicine faces several challenges that need to be overcome to successfully implement this new healthcare model. In this paper we identify four main areas that require attention: data, tools and systems, regulations, and people. While there are important ongoing efforts for addressing the first three areas, we …

Identifying Enriched Drug Fragments As Possible Candidates For Metabolic Engineering, Sunandini Sharma, Kritika Karri, Ishwor Thapa, Dhundy Bastola, Dario Ghersi

Interdisciplinary Informatics Faculty Publications

Background: Fragment-based approaches have now become an important component of the drug discovery process. At the same time, pharmaceutical chemists are more often turning to the natural world and its extremely large and diverse collection of natural compounds to discover new leads that can potentially be turned into drugs. In this study we introduce and discuss a computational pipeline to automatically extract statistically overrepresented chemical fragments in therapeutic classes, and search for similar fragments in a large database of natural products. By systematically identifying enriched fragments in therapeutic groups, we are able to extract and focus on few fragments …

Evaluating Information Technology (It) Integration Risk Prior To Mergers And Acquisitions (M&A), Deepak Khazanchi, Vipin Arora

Information Systems and Quantitative Analysis Faculty Publications

Corporate mergers and acquisitions (M&A) are considered significant, from both a strategic and an economic point of view, across almost all sectors of the economy.¹ M&A is a complex process involving risk that ranges from financial and legal matters to sales and marketing challenges and everything in between. Despite well-established benefits of strategically driven expansion and integration of businesses through M&A, the consolidated organization exposes itself to a number of anticipated, unknown and unintended risk factors. The risk concerns the overall organizational integration of some or all of the previously distinct and interdependent assets, structures, business processes, technologies, systems, …

Dosocs: A System For Spdx 2.0 Document Creation And Storage, Matt Germonprez, Thomas Gurney, Sai Uday Shankar Korlimarla

Information Systems and Quantitative Analysis Faculty Publications

DoSOCS is a command-line tool for managing SPDX 2.0 documents and data. It can scan source code distributions to produce SPDX information, store that information in a relational database, and extract it in a plain-text format on request. DoSOCS enables the creation of SPDX documents for any software package, and can even be used in the creation and continuous maintenance of an inventory of all open-source software used in an organization.

Optimal Digital Control Of A Three-Phase Four-Leg Voltage Source Inverter, Ayhan Özdemi̇r, Zeki̇ye Erdem

Turkish Journal of Electrical Engineering and Computer Sciences

No abstract provided.

Internet-Based Multiuser In-Circuit Emulator Design For 8051 Microprocessors, Kubi̇lay Taşdelen, Aki̇f Kutlu

Turkish Journal of Electrical Engineering and Computer Sciences

A real-time, Internet-based 8051 microprocessor in-circuit emulator (MicroLabICE) was designed and run for microprocessor lessons for undergraduate and graduate programs of electrical, electronics, communication, and computer engineering. Users can run applications developed for the 8051 microprocessor online on a physical circuit not being limited to a specific time or place with the 8051 microprocessor in-circuit emulator (ICE). The programs prepared by users are transferred to the controller area network (CAN) through an online server and program the ICE experiment module. Codes loaded on the designed emulator experiment module are run step by step and values that 8051 microprocessor registers have …

Topics On Register Synthesis Problems, Weihua Liu

Theses and Dissertations--Computer Science

Pseudo-random sequences are ubiquitous in modern electronics and information technology. High speed generators of such sequences play essential roles in various engineering applications, such as stream ciphers, radar systems, multiple access systems, and quasi-Monte-Carlo simulation. Given a short prefix of a sequence, it is undesirable to have an efficient algorithm that can synthesize a generator which can predict the whole sequence. Otherwise, a cryptanalytic attack can be launched against the system based on that given sequence.

Linear feedback shift registers (LFSRs) are the most widely studied pseudorandom sequence generators. The LFSR synthesis problem can be solved by the Berlekamp-Massey algorithm, …

Secure And Authenticated Message Dissemination In Vehicular Ad Hoc Networks And An Incentive-Based Architecture For Vehicular Cloud, Kiho Lim

Theses and Dissertations--Computer Science

Vehicular ad hoc Networks (VANETs) allow vehicles to form a self-organized network. VANETs are likely to be widely deployed in the future, given the interest shown by industry in self-driving cars and satisfying their customers various interests. Problems related to Mobile ad hoc Networks (MANETs) such as routing, security, etc.have been extensively studied. Even though VANETs are special type of MANETs, solutions proposed for MANETs cannot be directly applied to VANETs because all problems related to MANETs have been studied for small networks. Moreover, in MANETs, nodes can move randomly. On the other hand, movement of nodes in VANETs are …

Verification And Automated Synthesis Of Memristor Crossbars, Arya Pourtabatabaie

Electronic Theses and Dissertations

The Memristor is a newly synthesized circuit element correlating differences in electrical charge and magnetic flux, which effectively acts as a nonlinear resistor with memory. The small size of this element and its potential for passive state preservation has opened great opportunities for data-level parallel computation, since the functions of memory and processing can be realized on the same physical device. In this research we present an in-depth study of memristor crossbars for combinational and sequential logic. We outline the structure of formulas which they are able to produce and henceforth the inherent powers and limitations of Memristive Crossbar Computing. …

Techniques For Automated Parameter Estimation In Computational Models Of Probabilistic Systems, Faraz Hussain

Electronic Theses and Dissertations

The main contribution of this dissertation is the design of two new algorithms for automatically synthesizing values of numerical parameters of computational models of complex stochastic systems such that the resultant model meets user-specified behavioral specifications. These algorithms are designed to operate on probabilistic systems – systems that, in general, behave differently under identical conditions. The algorithms work using an approach that combines formal verification and mathematical optimization to explore a model's parameter space. The problem of determining whether a model instantiated with a given set of parameter values satisfies the desired specification is first defined using formal verification terminology, …

Transcriptional And Post-Transcriptional Regulation Of Gene Expression, Jun Ding

Electronic Theses and Dissertations

Regulation of gene expression includes a variety of mechanisms to increase or decrease specific gene products. Gene expression can be regulated at any stage from transcription to post-transcription and it's essential to almost all living organisms, as it increases the versatility and adaptability by allowing the cell to express the needed proteins. In this dissertation, we comprehensively studied the gene regulation from both transcriptional and post-transcriptional points of view. Transcriptional regulation is by which cells regulate the transcription from DNA to RNA, thereby directing gene activity. Transcriptional factors (TFs) play a very important role in transcriptional regulation and they are …

Analysis Of Commutativity With State-Chart Graph Representation Of Concurrent Programs., Kishore Debnath

Electronic Theses and Dissertations

We present a new approach to check for Commutativity in concurrent programs from their run-time state-chart graphs. Two operations are said to be commutative if changing the order of their execution do not change the resultant effect on the working object. Commutative property is capable of boosting performance in concurrent transactions such that transactional concurrency is comparable to a non-blocking linearizable version of a similar data structure type. Transactional concurrency is a technique that analyses object semantics, as object states, to determine conflicts and recovery between conflicting operations. Processes that commute at object level can be executed concurrently at transaction …

Confluence Of Vision And Natural Language Processing For Cross-Media Semantic Relations Extraction, Amara Tariq

Electronic Theses and Dissertations

In this dissertation, we focus on extracting and understanding semantically meaningful relationships between data items of various modalities; especially relations between images and natural language. We explore the ideas and techniques to integrate such cross-media semantic relations for machine understanding of large heterogeneous datasets, made available through the expansion of the World Wide Web. The datasets collected from social media websites, news media outlets and blogging platforms usually contain multiple modalities of data. Intelligent systems are needed to automatically make sense out of these datasets and present them in such a way that humans can find the relevant pieces of …

A Study Of Holistic Strategies For The Recognition Of Characters In Natural Scene Images, Muhammad Ali

Electronic Theses and Dissertations

Recognition and understanding of text in scene images is an important and challenging task. The importance can be seen in the context of tasks such as assisted navigation for the blind, providing directions to driverless cars, e.g. Google car, etc. Other applications include automated document archival services, mining text from images, and so on. The challenge comes from a variety of factors, like variable typefaces, uncontrolled imaging conditions, and various sources of noise corrupting the captured images. In this work, we study and address the fundamental problem of recognition of characters extracted from natural scene images, and contribute three holistic …

Cleaning Up Minnesota's Archeological Record With Maid: The Minnesota Archeological Integrated Database, Andrew Allen Brown

All Graduate Theses, Dissertations, and Other Capstone Projects

Minnesota archeologists face many difficulties in conducting archeological research and managing the state's cultural resources such as a lack of standardized data formats and field/lab procedures, a lack of a centralized data repository, and insufficient existing databases. The purpose of this thesis is to build the foundation for a database system that addresses these difficulties along with being efficient and effective for entering, managing, and analyzing archeological data produced in the field and in the lab. The Minnesota Archeological Integrated Database is being built to be a long-lasting, constantly evolving system to be used by archeologists and cultural resource managers …

Retention Of Information Technology Employees, Sherry Ann Dixon

Walden Dissertations and Doctoral Studies

Business leaders often realize greater profitability when they have strategies to retain IT

employees. However, the cost to replace IT employees creates significant challenges for

business leaders. Given the growing impact of technology on operational costs, retention

of IT employees is imperative. This exploratory single case study sought to identify the

strategies that leaders use to increase IT employee retention. The population was 6

leaders from a military organization in Norfolk, Virginia, responsible for the retention of

IT employees. Herzberg's two-factor theory was the conceptual framework for this study.

The data was collected from semi-structured interviews with 6 leaders along …

The Successful Implementation Of Electronic Health Records At Small Rural Hospitals, Daniel Richardson

Walden Dissertations and Doctoral Studies

Electronic health records (EHRs) have been in use since the 1960s. U.S. rural hospital leaders and administrators face significant pressure to implement health information technology because of the American Recovery and Reinvestment Act of 2009. However, some leaders and managers of small rural hospital lack strategies to develop and implement EHRs. The focus of this descriptive phenomenological study was to explore lived experiences of hospital leaders and administrators who have used successful strategies to implement EHRs in small rural hospitals. Diffusion of innovation theory shaped the theoretical framework of this study. Data were collected through telephone interviews conducted with participants …

A Novel Recurrent Convolutional Neural Network For Ocean And Weather Forecasting, Robert James Firth

LSU Doctoral Dissertations

Numerical weather prediction is a computationally expensive task that requires not only the numerical solution to a complex set of non-linear partial differential equations, but also the creation of a parameterization scheme to estimate sub-grid scale phenomenon. The proposed method is an alternative approach to developing a mesoscale meteorological model – a modified recurrent convolutional neural network that learns to simulate the solution to these equations. Along with an appropriate time integration scheme and learning algorithm, this method can be used to create multi-day forecasts for a large region. The learning method presented is an extended form of Backpropagation Through …

Probabilistic And Deep Learning Algorithms For The Analysis Of Imagery Data, Saikat Basu

LSU Doctoral Dissertations

Accurate object classification is a challenging problem for various low to high resolution imagery data. This applies to both natural as well as synthetic image datasets. However, each object recognition dataset poses its own distinct set of domain-specific problems. In order to address these issues, we need to devise intelligent learning algorithms which require a deep understanding and careful analysis of the feature space. In this thesis, we introduce three new learning frameworks for the analysis of both airborne images (NAIP dataset) and handwritten digit datasets without and with noise (MNIST and n-MNIST respectively). First, we propose a probabilistic framework …

Finding, Understanding And Learning: Making Information Discovery Tasks Useful For Children And Teachers, Ion Madrazo Azpiazu, Nevena Dragovic, Maria Soledad Pera

Computer Science Faculty Publications and Presentations

We present our ongoing efforts on the development of a search environment tailored to 6-15 year-olds that can foster learning though retrieval of materials that not only satisfy the information needs of users but also match their reading abilities. YouUnderstood.me is an enhanced environment based on a popular search engine specifically designed to help students deal with search for learning tasks, and allow teachers to track their progress. An initial assessment conducted on YouUnderstood.me and well-known (children-oriented) search engines based on queries generated by K-9 students, showcases the need for this type of environment.

“One Size Doesn’T Fit All": Helping Users Find Events From Multiple Perspectives, Sean Maclachlan, Stacey Donohue, Nevena Dragovic, Maria Soledad Pera

Computer Science Faculty Publications and Presentations

In this demo, we showcase a novel mobile application that offers various ways to present recommendations to users. While the majority of the existing applications in the tourism domain either focus on event recommendation or event browsing, our mobile application acknowledges the fact that users have diffrent interests at different times and for different occasions. Consequently, while suggested events are filtered and ranked by proximity and date ranges to ensure they suit users' needs, each user is allowed to choose how to access these suggestions in one of four ways: search, categorized browsing, following, and traditional recommendations.

Anything Fun Going On?: A Simple Wizard To Avoid The Cold-Start Problem For Event Recommenders, Stacey Donohue, Nevena Dragovic, Maria Soledad Pera

Computer Science Faculty Publications and Presentations

In this demo, we showcase a set up wizard designed to bypass the cold start problem that often affects recommendation systems in the event domain. We have developed a mobile application for tourists, RelEVENT, which allows them to quickly and non-intrusively set up preferences and/or interests related to events. This will directly affect the degree to which they can receive personalized recommendations on-the-fly and become aware of events happening around town that might be appealing to them.

Identifying And Scheduling Loop Chains Using Directives, Ian J. Bertolacci, Michelle Mills Strout, Stephen Guzik, Jordan Riley, Catherine Olschanowsky

Computer Science Faculty Publications and Presentations

Exposing opportunities for parallelization while explicitly managing data locality is the primary challenge to porting and optimizing existing computational science simulation codes to improve performance and accuracy. OpenMP provides many mechanisms for expressing parallelism, but it primarily remains the programmer’s responsibility to group computations to improve data locality. The loopchain abstraction, where data access patterns are included with the specification of parallel loops, provides compilers with sufficient information to automate the parallelism versus data locality tradeoff. In this paper, we present a loop chain pragma and an extension to the omp for to enable the specification of loop chains and …

A New Dictionary-Based Preprocessor That Uses Radix-190 Numbering, Mete Eray Şenergi̇n, Erhan Ali̇ri̇za İnce

Turkish Journal of Electrical Engineering and Computer Sciences

Various scholarly works in the literature have pointed out that placing a preprocessor in front of a standard postcompressor would help achieve higher gains while compressing natural-language text files. Ever since, there has been much research on preprocessors to improve the gain attained by concatenated systems. With the same goal in mind our paper proposes a new word-based preprocessor named METEHAN190 (M190) and contrasts its performance with four other state-of-the-art preprocessors. Throughout the experiments source files from the Wall Street Journal (WSJ) archive, and the Calgary, Canterbury, Gutenberg, and Pizza and Chili corpora were used. Postcompressors adapted were Prediction by …

Lifetime Maximization Of Wireless Sensor Networks Using Particle Swarm Optimization, Aleem Kabeer Mir, Muhammad Zubair, Ijaz Mansoor Qureshi

Turkish Journal of Electrical Engineering and Computer Sciences

Wireless sensor networks have multiple applications in intelligent environment and structural monitoring. The major challenge in wireless sensor networks is the power constraint. This paper deals with minimizing the energy utilization of wireless sensor nodes and maximizing their overall life span. The objective of our proposed scheme is to find a method for grouping sensors into the maximum number of distinct sensor cover sets to totally monitor the required area. This problem can be solved by using the disjoint cover set problem. Present optimization techniques take much time and deliver unsatisfactory results in large-scale networks. This paper proposes a technique …

To The Memory Of R. Freivalds, Efim Kinber

School of Computer Science & Engineering Faculty Publications

The paper contains author’s memories of his mentor and teacher R. M. Freivalds.

The Inevitability Of Playing Politics As Chair: Advantages And Pitfalls, Domenick Pinto

School of Computer Science & Engineering Faculty Publications

Politics is a term often frowned upon as it pertains to the role of an academic leader. However as chair for almost 29 years it has become an essential yet sometimes unwanted aspect of the daily rigors of the position. This session explores the advantages and pitfalls of “playing politics” as a department chair.

Cp-Nets: From Theory To Practice, Thomas E. Allen

Theses and Dissertations--Computer Science

Conditional preference networks (CP-nets) exploit the power of ceteris paribus rules to represent preferences over combinatorial decision domains compactly. CP-nets have much appeal. However, their study has not yet advanced sufficiently for their widespread use in real-world applications. Known algorithms for deciding dominance---whether one outcome is better than another with respect to a CP-net---require exponential time. Data for CP-nets are difficult to obtain: human subjects data over combinatorial domains are not readily available, and earlier work on random generation is also problematic. Also, much of the research on CP-nets makes strong, often unrealistic assumptions, such as that decision variables must …

Preferences: Optimization, Importance Learning And Strategic Behaviors, Ying Zhu

Theses and Dissertations--Computer Science

Preferences are fundamental to decision making and play an important role in artificial intelligence. Our research focuses on three group of problems based on the preference formalism Answer Set Optimization (ASO): preference aggregation problems such as computing optimal (near optimal) solutions, strategic behaviors in preference representation, and learning ranks (weights) for preferences.

In the first group of problems, of interest are optimal outcomes, that is, outcomes that are optimal with respect to the preorder defined by the preference rules. In this work, we consider computational problems concerning optimal outcomes. We propose, implement and study methods to compute an optimal outcome; …

Statistical Properties Of Pseudorandom Sequences, Ting Gu

Theses and Dissertations--Computer Science

Random numbers (in one sense or another) have applications in computer simulation, Monte Carlo integration, cryptography, randomized computation, radar ranging, and other areas. It is impractical to generate random numbers in real life, instead sequences of numbers (or of bits) that appear to be ``random" yet repeatable are used in real life applications. These sequences are called pseudorandom sequences. To determine the suitability of pseudorandom sequences for applications, we need to study their properties, in particular, their statistical properties. The simplest property is the minimal period of the sequence. That is, the shortest number of steps until the sequence repeats. …