ASU Electronic Theses and Dissertations
This collection includes most of the ASU Theses and Dissertations from 2011 to present. ASU Theses and Dissertations are available in downloadable PDF format; however, a small percentage of items are under embargo. Information about the dissertations/theses includes degree information, committee members, an abstract, supporting data or media.
In addition to the electronic theses found in the ASU Digital Repository, ASU Theses and Dissertations can be found in the ASU Library Catalog.
Dissertations and Theses granted by Arizona State University are archived and made available through a joint effort of the ASU Graduate College and the ASU Libraries. For more information or questions about this collection contact or visit the Digital Repository ETD Library Guide or contact the ASU Graduate College at gradformat@asu.edu.
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- Creators: Davulcu, Hasan
- Creators: Zhao, Jicheng
Description
Biological organisms are made up of cells containing numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted, manifesting as disease symptoms. Thus, understanding these biochemical processes and their interrelationships is a primary task in biomedical research and a prerequisite for activities including diagnosing diseases and drug development. Scientists studying these interconnected processes have identified various pathways involved in drug metabolism, diseases, and signal transduction, etc. High-throughput technologies, new algorithms and speed improvements over the last decade have resulted in deeper knowledge about biological systems, leading to more refined pathways. Such pathways tend to be large and complex, making it difficult for an individual to remember all aspects. Thus, computer models are needed to represent and analyze them. The refinement activity itself requires reasoning with a pathway model by posing queries against it and comparing the results against the real biological system. Many existing models focus on structural and/or factoid questions, relying on surface-level information. These are generally not the kind of questions that a biologist may ask someone to test their understanding of biological processes. Examples of questions requiring understanding of biological processes are available in introductory college level biology text books. Such questions serve as a model for the question answering system developed in this thesis. Thus, the main goal of this thesis is to develop a system that allows the encoding of knowledge about biological pathways to answer questions demonstrating understanding of the pathways. To that end, a language is developed to specify a pathway and pose questions against it. Some existing tools are modified and used to accomplish this goal. The utility of the framework developed in this thesis is illustrated with applications in the biological domain. Finally, the question answering system is used in real world applications by extracting pathway knowledge from text and answering questions related to drug development.
ContributorsAnwar, Saadat (Author) / Baral, Chitta (Thesis advisor) / Inoue, Katsumi (Committee member) / Chen, Yi (Committee member) / Davulcu, Hasan (Committee member) / Lee, Joohyung (Committee member) / Arizona State University (Publisher)
Created2014
Description
Goal specification is an important aspect of designing autonomous agents. A goal does not only refer to the set of states for the agent to reach. A goal also defines restrictions on the paths the agent should follow. Temporal logics are widely used in goal specification. However, they lack the ability to represent goals in a non-deterministic domain, goals that change non-monotonically, and goals with preferences. This dissertation defines new goal specification languages by extending temporal logics to address these issues. First considered is the goal specification in non-deterministic domains, in which an agent following a policy leads to a set of paths. A logic is proposed to distinguish paths of the agent from all paths in the domain. In addition, to address the need of comparing policies for finding the best ones, a language capable of quantifying over policies is proposed. As policy structures of agents play an important role in goal specification, languages are also defined by considering different policy structures. Besides, after an agent is given an initial goal, the agent may change its expectations or the domain may change, thus goals that are previously specified may need to be further updated, revised, partially retracted, or even completely changed. Non-monotonic goal specification languages that can make these changes in an elaboration tolerant manner are needed. Two languages that rely on labeling sub-formulas and connecting multiple rules are developed to address non-monotonicity in goal specification. Also, agents may have preferential relations among sub-goals, and the preferential relations may change as agents achieve other sub-goals. By nesting a comparison operator with other temporal operators, a language with dynamic preferences is proposed. Various goals that cannot be expressed in other languages are expressed in the proposed languages. Finally, plans are given for some goals specified in the proposed languages.
ContributorsZhao, Jicheng (Author) / Baral, Chitta (Thesis advisor) / Kambhampati, Subbarao (Committee member) / Lee, Joohyung (Committee member) / Lifschitz, Vladimir (Committee member) / Liu, Huan (Committee member) / Arizona State University (Publisher)
Created2010