Matching Items (37)
Description
Biological systems are complex in many dimensions as endless transportation and communication networks all function simultaneously. Our ability to intervene within both healthy and diseased systems is tied directly to our ability to understand and model core functionality. The progress in increasingly accurate and thorough high-throughput measurement technologies has provided a deluge of data from which we may attempt to infer a representation of the true genetic regulatory system. A gene regulatory network model, if accurate enough, may allow us to perform hypothesis testing in the form of computational experiments. Of great importance to modeling accuracy is the acknowledgment of biological contexts within the models -- i.e. recognizing the heterogeneous nature of the true biological system and the data it generates. This marriage of engineering, mathematics and computer science with systems biology creates a cycle of progress between computer simulation and lab experimentation, rapidly translating interventions and treatments for patients from the bench to the bedside. This dissertation will first discuss the landscape for modeling the biological system, explore the identification of targets for intervention in Boolean network models of biological interactions, and explore context specificity both in new graphical depictions of models embodying context-specific genomic regulation and in novel analysis approaches designed to reveal embedded contextual information. Overall, the dissertation will explore a spectrum of biological modeling with a goal towards therapeutic intervention, with both formal and informal notions of biological context, in such a way that will enable future work to have an even greater impact in terms of direct patient benefit on an individualized level.
ContributorsVerdicchio, Michael (Author) / Kim, Seungchan (Thesis advisor) / Baral, Chitta (Committee member) / Stolovitzky, Gustavo (Committee member) / Collofello, James (Committee member) / Arizona State University (Publisher)
Created2013
Description
Linear Temporal Logic is gaining increasing popularity as a high level specification language for robot motion planning due to its expressive power and scalability of LTL control synthesis algorithms. This formalism, however, requires expert knowledge and makes it inaccessible to non-expert users. This thesis introduces a graphical specification environment to create high level motion plans to control robots in the field by converting a visual representation of the motion/task plan into a Linear Temporal Logic (LTL) specification. The visual interface is built on the Android tablet platform and provides functionality to create task plans through a set of well defined gestures and on screen controls. It uses the notion of waypoints to quickly and efficiently describe the motion plan and enables a variety of complex Linear Temporal Logic specifications to be described succinctly and intuitively by the user without the need for the knowledge and understanding of LTL specification. Thus, it opens avenues for its use by personnel in military, warehouse management, and search and rescue missions. This thesis describes the construction of LTL for various scenarios used for robot navigation using the visual interface developed and leverages the use of existing LTL based motion planners to carry out the task plan by a robot.
ContributorsSrinivas, Shashank (Author) / Fainekos, Georgios (Thesis advisor) / Baral, Chitta (Committee member) / Burleson, Winslow (Committee member) / Arizona State University (Publisher)
Created2013
Description
Laboratory automation systems have seen a lot of technological advances in recent times. As a result, the software that is written for them are becoming increasingly sophisticated. Existing software architectures and standards are targeted to a wider domain of software development and need to be customized in order to use them for developing software for laboratory automation systems. This thesis proposes an architecture that is based on existing software architectural paradigms and is specifically tailored to developing software for a laboratory automation system. The architecture is based on fairly autonomous software components that can be distributed across multiple computers. The components in the architecture make use of asynchronous communication methodologies that are facilitated by passing messages between one another. The architecture can be used to develop software that is distributed, responsive and thread-safe. The thesis also proposes a framework that has been developed to implement the ideas proposed by the architecture. The framework is used to develop software that is scalable, distributed, responsive and thread-safe. The framework currently has components to control very commonly used laboratory automation devices such as mechanical stages, cameras, and also to do common laboratory automation functionalities such as imaging.
ContributorsKuppuswamy, Venkataramanan (Author) / Meldrum, Deirdre (Thesis advisor) / Collofello, James (Thesis advisor) / Sarjoughian, Hessam S. (Committee member) / Johnson, Roger (Committee member) / Arizona State University (Publisher)
Created2012
Description
The pay-as-you-go economic model of cloud computing increases the visibility, traceability, and verifiability of software costs. Application developers must understand how their software uses resources when running in the cloud in order to stay within budgeted costs and/or produce expected profits. Cloud computing's unique economic model also leads naturally to an earn-as-you-go profit model for many cloud based applications. These applications can benefit from low level analyses for cost optimization and verification. Testing cloud applications to ensure they meet monetary cost objectives has not been well explored in the current literature. When considering revenues and costs for cloud applications, the resource economic model can be scaled down to the transaction level in order to associate source code with costs incurred while running in the cloud. Both static and dynamic analysis techniques can be developed and applied to understand how and where cloud applications incur costs. Such analyses can help optimize (i.e. minimize) costs and verify that they stay within expected tolerances. An adaptation of Worst Case Execution Time (WCET) analysis is presented here to statically determine worst case monetary costs of cloud applications. This analysis is used to produce an algorithm for determining control flow paths within an application that can exceed a given cost threshold. The corresponding results are used to identify path sections that contribute most to cost excess. A hybrid approach for determining cost excesses is also presented that is comprised mostly of dynamic measurements but that also incorporates calculations that are based on the static analysis approach. This approach uses operational profiles to increase the precision and usefulness of the calculations.
ContributorsBuell, Kevin, Ph.D (Author) / Collofello, James (Thesis advisor) / Davulcu, Hasan (Committee member) / Lindquist, Timothy (Committee member) / Sen, Arunabha (Committee member) / Arizona State University (Publisher)
Created2012
Description
Access control is necessary for information assurance in many of today's applications such as banking and electronic health record. Access control breaches are critical security problems that can result from unintended and improper implementation of security policies. Security testing can help identify security vulnerabilities early and avoid unexpected expensive cost in handling breaches for security architects and security engineers. The process of security testing which involves creating tests that effectively examine vulnerabilities is a challenging task. Role-Based Access Control (RBAC) has been widely adopted to support fine-grained access control. However, in practice, due to its complexity including role management, role hierarchy with hundreds of roles, and their associated privileges and users, systematically testing RBAC systems is crucial to ensure the security in various domains ranging from cyber-infrastructure to mission-critical applications. In this thesis, we introduce i) a security testing technique for RBAC systems considering the principle of maximum privileges, the structure of the role hierarchy, and a new security test coverage criterion; ii) a MTBDD (Multi-Terminal Binary Decision Diagram) based representation of RBAC security policy including RHMTBDD (Role Hierarchy MTBDD) to efficiently generate effective positive and negative security test cases; and iii) a security testing framework which takes an XACML-based RBAC security policy as an input, parses it into a RHMTBDD representation and then generates positive and negative test cases. We also demonstrate the efficacy of our approach through case studies.
ContributorsGupta, Poonam (Author) / Ahn, Gail-Joon (Thesis advisor) / Collofello, James (Committee member) / Huang, Dijiang (Committee member) / Arizona State University (Publisher)
Created2014
Description
For this master's thesis, a unique set of cognitive prompts, designed to be delivered through a teachable robotic agent, were developed for students using Tangible Activities for Geometry (TAG), a tangible learning environment developed at Arizona State University. The purpose of these prompts is to enhance the affordances of the tangible learning environment and help researchers to better understand how we can design tangible learning environments to best support student learning. Specifically, the prompts explicitly encourage users to make use of their physical environment by asking students to perform a number of gestures and behaviors while prompting students about domain-specific knowledge. To test the effectiveness of these prompts that combine elements of cognition and physical movements, the performance and behavior of students who encounter these prompts while using TAG will be compared against the performance and behavior of students who encounter a more traditional set of cognitive prompts that would typically be used within a virtual learning environment. Following this study, data was analyzed using a novel modeling and analysis tool that combines enhanced log annotation using video and user model generation functionalities to highlight trends amongst students.
ContributorsThomas, Elissa (Author) / Burleson, Winslow (Thesis advisor) / Muldner, Katarzyna (Committee member) / Walker, Erin (Committee member) / Glenberg, Arthur (Committee member) / Arizona State University (Publisher)
Created2014
Description
Many web search improvements have been developed since the advent of the modern search engine, but one underrepresented area is the application of specific customizations to search results for educational web sites. In order to address this issue and improve the relevance of search results in automated learning environments, this work has integrated context-aware search principles with applications of preference based re-ranking and query modifications. This research investigates several aspects of context-aware search principles, specifically context-sensitive and preference based re-ranking of results which take user inputs as to their preferred content, and combines this with search query modifications which automatically search for a variety of modified terms based on the given search query, integrating these results into the overall re-ranking for the context. The result of this work is a novel web search algorithm which could be applied to any online learning environment attempting to collect relevant resources for learning about a given topic. The algorithm has been evaluated through user studies comparing traditional search results to the context-aware results returned through the algorithm for a given topic. These studies explore how this integration of methods could provide improved relevance in the search results returned when compared against other modern search engines.
ContributorsVan Egmond, Eric (Author) / Burleson, Winslow (Thesis advisor) / Syrotiuk, Violet (Thesis advisor) / Nelson, Brian (Committee member) / Arizona State University (Publisher)
Created2014
Description
With the rise of mobile technology, the personal lives and sensitive information of everyday citizens are carried about without a thought to the risks involved. Despite this high possibility of harm, many fail to use simple security to protect themselves because they feel the benefits of securing their devices do not outweigh the cost to usability. The main issue is that beyond initial authentication, sessions are maintained using optional timeout mechanisms where a session will end if a user is inactive for a period of time. This interruption-based form of continuous authentication requires constant user intervention leading to frustration, which discourages its use. No solution currently exists that provides an implementation beyond the insecure and low usability of simple timeout and re-authentication. This work identifies the flaws of current mobile authentication techniques and provides a new solution that is not limiting to the user, has a system for secure, active continuous authentication, and increases the usability and security over current methods.
ContributorsRomo, James Tyler (Author) / Ahn, Gail-Joon (Thesis advisor) / Dasgupta, Partha (Committee member) / Burleson, Winslow (Committee member) / Arizona State University (Publisher)
Created2014
Description
Strong communities are important for society. One of the most important community builders, making friends, is poorly supported online. Dating sites support it but in romantic contexts. Other major social networks seem not to encourage it because either their purpose isn't compatible with introducing strangers or the prevalent methods of introduction aren't effective enough to merit use over real word alternatives. This paper presents a novel digital social network emphasizing creating friendships. Research has shown video chat communication can reach in-person levels of trust; coupled with a game environment to ease the discomfort people often have interacting with strangers and a recommendation engine, Zazzer, the presented system, allows people to meet and get to know each other in a manner much more true to real life than traditional methods. Its network also allows players to continue to communicate afterwards. The evaluation looks at real world use, measuring the frequency with which players choose the video chat game versus alternative, more traditional methods of online introduction. It also looks at interactions after the initial meeting to discover how effective video chat games are in creating sticky social connections. After initial use it became apparent a critical mass of users would be necessary to draw strong conclusions, however the collected data seemed to give preliminary support to the idea that video chat games are more effective than traditional ways of meeting online in creating new relationships.
ContributorsSorensen, Asael (Author) / VanLehn, Kurt (Thesis advisor) / Liu, Huan (Committee member) / Burleson, Winslow (Committee member) / Arizona State University (Publisher)
Created2011
Description
The main objective of this project was to create a framework for holistic ideation and research about the technical issues involved in creating a holistic approach. Towards that goal, we explored different components of ideation (both logical and intuitive), characterized ideation states, and found new ideation blocks with strategies used to overcome them. One of the major contributions of this research is the method by which easy traversal between different ideation methods with different components were facilitated, to support both creativity and functional quality. Another important part of the framework is the sensing of ideation states (blocks/ unfettered ideation) and investigation of matching ideation strategies most likely to facilitate progress. Some of the ideation methods embedded in the initial holistic test bed are Physical effects catalog, working principles catalog, TRIZ, Bio-TRIZ and Artifacts catalog. Repositories were created for each of those. This framework will also be used as a research tool to collect large amount of data from designers about their choice of ideation strategies used, and their effectiveness. Effective documentation of design ideation paths is also facilitated using this holistic approach. A computer tool facilitating holistic ideation was developed. Case studies were run on different designers to document their ideation states and their choice of ideation strategies to come up with a good solution to solve the same design problem.
ContributorsMohan, Manikandan (Author) / Shah, Jami J. (Thesis advisor) / Huebner, Kenneth (Committee member) / Burleson, Winslow (Committee member) / Arizona State University (Publisher)
Created2011