Master of Science / Department of Computing and Information Sciences / Doina Caragea / The vast amount of data present on the internet calls for ways to label and organize this data according to specific categories, in order to facilitate search and browsing activities. This can be easily accomplished by making use of folksonomies and user provided tags. However, it can be difficult for users to provide meaningful tags. Tag recommendation systems can guide the users towards informative tags for online resources such as websites, pictures, etc. The aim of this thesis is to build a system for recommending tags to URLs available through a bookmark sharing service, called BibSonomy. We assume that the URLs for which we recommend tags do not have any prior tags assigned to them. Two approaches are proposed to address the tagging problem, both of them based on Latent Dirichlet Allocation (LDA) Blei et al. [2003]. LDA is a generative and probabilistic topic model which aims to infer the hidden topical structure in a collection of documents. According to LDA, documents can be seen as mixtures of topics, while topics can be seen as mixtures of words (in our case, tags). The first approach that we propose, called topic words based approach, recommends the top words in the top topics representing a resource as tags for that particular resource. The second approach, called topic distance based approach, uses the tags of the most similar training resources (identified using the KL-divergence Kullback and Liebler [1951]) to recommend tags for a test untagged resource. The dataset used in this work was made available through the ECML/PKDD Discovery Challenge 2009. We construct the documents that are provided as input to LDA in two ways, thus producing two different datasets. In the first dataset, we use only the description and the tags (when available) corresponding to a URL. In the second dataset, we crawl the URL content and use it to construct the document. Experimental results show that the LDA approach is not very effective at recommending tags for new untagged resources. However, using the resource content gives better results than using the description only. Furthermore, the topic distance based approach is better than the topic words based approach, when only the descriptions are used to construct documents, while the topic words based approach works better when the contents are used to construct documents.

Master of Science / Department of Computing and Information Sciences / Mitchell L. Neilsen / The United States Department of Agriculture (USDA) is currently researching the effectiveness of various earth dam designs and their ability to prevent erosion. This report utilizes experimental results from the USDA experimental hydraulic engineering research unit to develop computational fluid dynamics models using OpenFOAM. Several variations of smooth and stepped dam models are created and analyzed with OpenFOAM on multiple cores using Message Passing Interface. In this report, seven dam designs are analyzed to extract flow velocities and pressures and animations. This data and OpenFOAM models are helpful for determining potential erosion conditions.

Master of Science / Department of Computing and Information Sciences / Daniel A. Andresen / The aim of the project is to develop an Android application that lets its users to send notifications in case of an emergency or a panic situation. The users can send multiple text messages and emails on the press of a single button. The phone numbers, email ids and the contents of the text and email messages can be set from within the application. The text messages and emails sent, along with the content, also have the last known location of the user. This is very helpful in tracking the whereabouts of the person. The user can also call 911 directly from within the application, if the nature of the situation demands it. Additionally the user of the application may allow the app to track their location. If this option is selected, the application fetches the device’s location at about every 15 minutes and stores it in a database. This information is very useful and can be used in a variety of ways. One such use of the location data is from within the Android app where the user can view a map that shows their location history over a period of time for a particular day.

Master of Science / Department of Computing and Information Sciences / Mitchell L. Neilsen / The purpose of the project is to develop an Android application that is capable of detecting possible falls for the elderly. With the advancement of wireless communications, the world has become smarter and there has been increase in use of smart phones. Android, being an open source platform has made it simple for every individual to develop their own applications, which in turn can be used on Android devices. Falls among the elderly are a serious concern for both families as well as medical professionals, since falls are considered to be the eighth leading cause of death in the United States. Untreated fall injuries in adults 65 or older can result in serious risks and health complications, since 20% of falls require immediate medical attention and about one-tenth of the falls result in fractures. Thus, as mentioned, fall detection is a critical event requiring quick and accurate response, especially for elderly people living by themselves. This is the motivation behind developing an elderly support, which detects a fall and alerts the caretaker regarding the information. The elderly support is about tracking the person and notifying the caretaker if there is an occurrence. One of the main features of this Android application is that it notifies the caretaker with alert messages which contain all the necessary information. The alert messages contain useful information about the people in danger, such as his/her geo location and also corresponding directions on a map. In occasions of false alerts, the supervised person is given the ability to estimate the value of importance of a possible alert and to stop it before proceeding with further steps. This project is geared towards supporting the elderly. The mobile application is capable of detecting possible falls and through a user-friendly interface that can be used to alert relatives, doctors, and other people who take care of the elderly.

Master of Science / Department of Computing and Information Sciences / Eugene Vasserman / As medical systems expand to allow for the increase the number of devices, new ways to protect patient safety have be developed. The Integrated Clinical Environment, ICE, standard sets up a set of standards that define what an integrated hospital system is. Within the specification is a direct call for a forensic logger that can be used to review patient and system data. The MDCF is one implementation of the ICE standard, but it lacked a key component the ICE standard requires, a logger. Many loggers exist in industry, with varying rates of success and usefulness. A medically sound logger has to be able to completely retell exactly what happened during an event, including patient, device, and system information, so that the right medical professional can provide the best care. Several loggers have been built for MDCF, but few were practical due to the invasiveness of the service. A universal subscriber, a service that is able to connect to all publishing data streams, logging service was built for the MDCF which has the ability to record all information that passes over the MDCF messaging service. This implementation was then stress tested with varying numbers of devices and amounts of data. A reviewing tool was also built that allows for replay of device data that is similar to the original device UI. Future work will include looking into storing system information such as state changes within MDCF and system health. There is also a push to further integrate the forensic reviewer into the core MDCF UI.

Master of Science / Department of Computer Science / Eugene Vasserman / There is continuing growth in the need to secure critical infrastructures from malicious adversaries. These adversaries can attack systems from different forms. They can physically break in and steal something important, or they can attack from the cyber realm in order to steal critical information. This project combines the modeling process for physical spaces along with a logic reasoning tool that can identify the state of a networked device in order to analyze large enterprise systems for combined cyber-physical vulnerabilities. Using a pure model checker would not be able to handle the near infinite states that a computer or networked device may be in. Therefore this new approach combines the use of a logic analyzer tool that with a well-defined set of rules that reasons about the security and trustworthiness of devices in the model. While there has been long study of how to secure a building from intrusion, and much research about defense against cyber attacks, there is always a large gap between the two in practice. This approach may no longer be sufficient against today’s adversaries and offers little to no defense against insider threats. Combining the two in this new form allows for a more complete security view and protection against more advanced adversaries. Then this thesis shows how this approach meets a series of requirements for an effective vulnerability analysis. This is achieved by executing a model based on a real world facility with a series of induced faults that would on their own not be enough to be a vulnerability but tied together would have series consequences. This thesis shows how this approach can then be used to detail potentially unseen vulnerabilities and develop fixes for them to help create a more secure facility.

Master of Science / Department of Computing and Information Sciences / Daniel A. Andresen / Tutorials and Quiz Android Mobile application is an application which gives you brief tutorials on various programming languages and technologies to the user who has installed this application. It gives video tutorials and training on different technologies. The mobile application also contains sample code, interview questions, and answers. This application also conducts a quiz to the user who is interested in a particular technology for checking their knowledge on the subject. It has different levels like Basic Level and Advanced Level quiz. This application conducts a quiz in the form of multiple choice questions. After the completion of the quiz the application generates reports based on the quiz conducted. The user can also test their knowledge on those technologies based on a timed quiz, we can include the above technology questions in this application. We can give a time frame for each question and all the questions are to be answered in that specified time period. Say for example we can give 20 seconds to answer a question. If the user gives an incorrect answer, will be exited out of the quiz.

Master of Science / Computing and Information Sciences / Daniel A. Andresen / One among the many inventions of Benjamin Franklin is the Glass Armonica, a musical instrument whose sound source was a series of resonating glass vessels. However, the Irish musician Richard Pockrich is typically credited as the first to play an instrument composed of glass vessels, called the Glass Harp in 1741, by rubbing his fingers around the rims. In this project “Singing Wine Glasses”, the principle of Franklin’s glass armonica is demonstrated with a wine glass. One hand is used to hold the glass steady at the base. The rim of glass is gently pressed with a moistened finger of the other hand and drawn in a circle around. When the pressure and amount of moisture are just right, the slight friction between the finger and the rim of glass causes vibrations in the sides of the glass. At a particular frequency, called the resonant frequency, the sides of the glass will vibrate most easily. The resonant frequency of wine glasses is typically within the range of human hearing (20-20,000 Hz), so the resulting resonant vibration is heard as a tone. The glass starts to sing when the vibration gets the molecules moving at their natural frequency. The resonant frequency changes with the amount of water filled in the glass. This android application deals with virtual glasses that serve the purpose of wine glasses filled with different amounts of water. Swiping on the glass edges would produce music, as per Franklin’s principle. The users would be free to select the number of glasses they want to play, and the amount of water-level in each glass. This application would also come with an enhanced feature of sustaining a particular note until the finger is released from the glass.

Doctor of Philosophy / Department of Computing and Information Sciences / Gurdip Singh / Many frameworks have been proposed which provide distributed algorithms encapsulated as middleware services to simplify application design. The developers of such algorithms are faced with two opposing forces. One is to design generic algorithms that are reusable in a large number of applications. Efficiency considerations, on the other hand, force the algorithms to be customized to specific operational contexts. This problem is often attacked by simply re-implementing all or large portions of an algorithm. We propose InDiGO, an infrastructure which allows design of generic but customizable algorithms and provides tools to customize such algorithms for specific applications. InDiGO provides the following capabilities: (a) Tools to generate intermediate representations of an application which can be leveraged for analysis, (b) Mechanisms to allow developers to design customizable algorithms by exposing design knowledge in terms of configurable options, and (c) An optimization engine to analyze an application to derive the information necessary to optimize the algorithms. Specifically, we optimize algorithms by removing communication which is redundant in the context of a specific application. We perform three types of optimizations: static optimization, dynamic optimization and physical topology-based optimization. We present experimental results to demonstrate the advantages of our infrastructure.

Master of Science / Department of Computing and Information Sciences / William H. Hsu / Alternative splicing is a mechanism for generating different gene transcripts (called iso- forms) from the same genomic sequence. Finding alternative splicing events experimentally is both expensive and time consuming. Computational methods in general, and EST analy- sis and machine learning algorithms in particular, can be used to complement experimental methods in the process of identifying alternative splicing events. In this thesis, I first iden- tify alternative splicing exons by analyzing EST-genome alignment. Next, I explore the predictive power of a rich set of features that have been experimentally shown to affect al- ternative splicing. I use these features to build support vector machine (SVM) classifiers for distinguishing between alternatively spliced exons and constitutive exons. My results show that simple, linear SVM classifiers built from a rich set of features give results comparable to those of more sophisticated SVM classifiers that use more basic sequence features. Finally, I use feature selection methods to identify computationally the most informative features for the prediction problem considered.