## 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.

Resource Type
• Doctoral Dissertation
Date Range
2010 2019

## Recent Submissions

Reverse engineering gene regulatory networks (GRNs) is an important problem in the domain of Systems Biology. Learning GRNs is challenging due to the inherent complexity of the real regulatory networks and the heterogeneity of samples in available biomedical data. Real world biological data are commonly collected from broad surveys (profiling studies) and aggregate highly heterogeneous biological samples. Popular methods to learn GRNs simplistically assume a single universal regulatory network corresponding to available data. They neglect regulatory network adaptation due to change in underlying conditions and cellular phenotype or both. This dissertation presents a novel computational framework to learn common regulatory …

Contributors
Sen, Ina, Kim, Seungchan, Baral, Chitta, et al.
Created Date
2011

Automating aspects of biocuration through biomedical information extraction could significantly impact biomedical research by enabling greater biocuration throughput and improving the feasibility of a wider scope. An important step in biomedical information extraction systems is named entity recognition (NER), where mentions of entities such as proteins and diseases are located within natural-language text and their semantic type is determined. This step is critical for later tasks in an information extraction pipeline, including normalization and relationship extraction. BANNER is a benchmark biomedical NER system using linear-chain conditional random fields and the rich feature set approach. A case study with BANNER locating …

Contributors
Leaman, James Robert, Gonzalez, Graciela, Baral, Chitta, et al.
Created Date
2013

Answer Set Programming (ASP) is one of the most prominent and successful knowledge representation paradigms. The success of ASP is due to its expressive non-monotonic modeling language and its efficient computational methods originating from building propositional satisfiability solvers. The wide adoption of ASP has motivated several extensions to its modeling language in order to enhance expressivity, such as incorporating aggregates and interfaces with ontologies. Also, in order to overcome the grounding bottleneck of computation in ASP, there are increasing interests in integrating ASP with other computing paradigms, such as Constraint Programming (CP) and Satisfiability Modulo Theories (SMT). Due to the …

Contributors
Meng, Yunsong, Lee, Joohyung, Ahn, Gail-Joon, et al.
Created Date
2013

Question Answering has been under active research for decades, but it has recently taken the spotlight following IBM Watson's success in Jeopardy! and digital assistants such as Apple's Siri, Google Now, and Microsoft Cortana through every smart-phone and browser. However, most of the research in Question Answering aims at factual questions rather than deep ones such as How'' and Why'' questions. In this dissertation, I suggest a different approach in tackling this problem. We believe that the answers of deep questions need to be formally defined before found. Because these answers must be defined based on something, it is better …

Contributors
Vo, Nguyen Ha, Baral, Chitta, Lee, Joohyung, et al.
Created Date
2015

Science instructors need questions for use in exams, homework assignments, class discussions, reviews, and other instructional activities. Textbooks never have enough questions, so instructors must find them from other sources or generate their own questions. In order to supply instructors with biology questions, a semantic network approach was developed for generating open response biology questions. The generated questions were compared to professional authorized questions. To boost students’ learning experience, adaptive selection was built on the generated questions. Bayesian Knowledge Tracing was used as embedded assessment of the student’s current competence so that a suitable question could be selected based on …

Contributors
Zhang, Lishan, VanLehn, Kurt, Baral, Chitta, et al.
Created Date
2015

Different logic-based knowledge representation formalisms have different limitations either with respect to expressivity or with respect to computational efficiency. First-order logic, which is the basis of Description Logics (DLs), is not suitable for defeasible reasoning due to its monotonic nature. The nonmonotonic formalisms that extend first-order logic, such as circumscription and default logic, are expressive but lack efficient implementations. The nonmonotonic formalisms that are based on the declarative logic programming approach, such as Answer Set Programming (ASP), have efficient implementations but are not expressive enough for representing and reasoning with open domains. This dissertation uses the first-order stable model semantics, …

Contributors
Palla, Ravi Kiran Reddy, Lee, Joohyung, Baral, Chitta, et al.
Created Date
2012

As we migrate into an era of personalized medicine, understanding how bio-molecules interact with one another to form cellular systems is one of the key focus areas of systems biology. Several challenges such as the dynamic nature of cellular systems, uncertainty due to environmental influences, and the heterogeneity between individual patients render this a difficult task. In the last decade, several algorithms have been proposed to elucidate cellular systems from data, resulting in numerous data-driven hypotheses. However, due to the large number of variables involved in the process, many of which are unknown or not measurable, such computational approaches often …

Contributors
Ramesh, Archana, Kim, Seungchan, Langley, Patrick W, et al.
Created Date
2012

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 …

Contributors
Verdicchio, Michael Paul, Kim, Seungchan, Baral, Chitta, et al.
Created Date
2013

Teams are increasingly indispensable to achievements in any organizations. Despite the organizations' substantial dependency on teams, fundamental knowledge about the conduct of team-enabled operations is lacking, especially at the {\it social, cognitive} and {\it information} level in relation to team performance and network dynamics. The goal of this dissertation is to create new instruments to {\it predict}, {\it optimize} and {\it explain} teams' performance in the context of composite networks (i.e., social-cognitive-information networks). Understanding the dynamic mechanisms that drive the success of high-performing teams can provide the key insights into building the best teams and hence lift the productivity and …

Contributors
Li, Liangyue, Tong, Hanghang, Baral, Chitta, et al.
Created Date
2018

Image Understanding is a long-established discipline in computer vision, which encompasses a body of advanced image processing techniques, that are used to locate (“where”), characterize and recognize (“what”) objects, regions, and their attributes in the image. However, the notion of “understanding” (and the goal of artificial intelligent machines) goes beyond factual recall of the recognized components and includes reasoning and thinking beyond what can be seen (or perceived). Understanding is often evaluated by asking questions of increasing difficulty. Thus, the expected functionalities of an intelligent Image Understanding system can be expressed in terms of the functionalities that are required to …

Contributors
Aditya, Somak, Baral, Chitta, Yang, Yezhou, et al.
Created Date
2018

Automated planning problems classically involve finding a sequence of actions that transform an initial state to some state satisfying a conjunctive set of goals with no temporal constraints. But in many real-world problems, the best plan may involve satisfying only a subset of goals or missing defined goal deadlines. For example, this may be required when goals are logically conflicting, or when there are time or cost constraints such that achieving all goals on time may be too expensive. In this case, goals and deadlines must be declared as soft. I call these partial satisfaction planning (PSP) problems. In this …

Contributors
Benton, J., Kambhampati, Subbarao, Baral, Chitta, et al.
Created Date
2012

As robotic technology and its various uses grow steadily more complex and ubiquitous, humans are coming into increasing contact with robotic agents. A large portion of such contact is cooperative interaction, where both humans and robots are required to work on the same application towards achieving common goals. These application scenarios are characterized by a need to leverage the strengths of each agent as part of a unified team to reach those common goals. To ensure that the robotic agent is truly a contributing team-member, it must exhibit some degree of autonomy in achieving goals that have been delegated to …

Contributors
Talamadupula, Kartik, Kambhampati, Subbarao, Baral, Chitta, et al.
Created Date
2014

Current work in planning assumes that user preferences and/or domain dynamics are completely specified in advance, and aims to search for a single solution plan to satisfy these. In many real world scenarios, however, providing a complete specification of user preferences and domain dynamics becomes a time-consuming and error-prone task. More often than not, a user may provide no knowledge or at best partial knowledge of her preferences with respect to a desired plan. Similarly, a domain writer may only be able to determine certain parts, not all, of the model of some actions in a domain. Such modeling issues …

Contributors
Nguyen, Tuan Anh, Kambhampati, Subbarao, Baral, Chitta, et al.
Created Date
2014

Reasoning about the activities of cyber threat actors is critical to defend against cyber attacks. However, this task is difficult for a variety of reasons. In simple terms, it is difficult to determine who the attacker is, what the desired goals are of the attacker, and how they will carry out their attacks. These three questions essentially entail understanding the attacker’s use of deception, the capabilities available, and the intent of launching the attack. These three issues are highly inter-related. If an adversary can hide their intent, they can better deceive a defender. If an adversary’s capabilities are not well …

Contributors
Nunes, Eric, Shakarian, Paulo, Ahn, Gail-Joon, et al.
Created Date
2018

Knowledge Representation (KR) is one of the prominent approaches to Artificial Intelligence (AI) that is concerned with representing knowledge in a form that computer systems can utilize to solve complex problems. Answer Set Programming (ASP), based on the stable model semantics, is a widely-used KR framework that facilitates elegant and efficient representations for many problem domains that require complex reasoning. However, while ASP is effective on deterministic problem domains, it is not suitable for applications involving quantitative uncertainty, for example, those that require probabilistic reasoning. Furthermore, it is hard to utilize information that can be statistically induced from data with …

Contributors
Wang, Yi, Lee, Joohyung, Baral, Chitta, et al.
Created Date
2019

Reasoning about actions forms the basis of many tasks such as prediction, planning, and diagnosis in a dynamic domain. Within the reasoning about actions community, a broad class of languages, called action languages, has been developed together with a methodology for their use in representing and reasoning about dynamic domains. With a few notable exceptions, the focus of these efforts has largely centered around single-agent systems. Agents rarely operate in a vacuum however, and almost in parallel, substantial work has been done within the dynamic epistemic logic community towards understanding how the actions of an agent may effect not just …

Contributors
Gelfond, Gregory, Baral, Chitta, Kambhampati, Subbarao, et al.
Created Date
2018

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 …

Contributors
Zhao, Jicheng, Baral, Chitta, Kambhampati, Subbarao, et al.
Created Date
2010

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 …

Contributors
Anwar, Saadat, Baral, Chitta, Inoue, Katsumi, et al.
Created Date
2014

Reasoning with commonsense knowledge is an integral component of human behavior. It is due to this capability that people know that a weak person may not be able to lift someone. It has been a long standing goal of the Artificial Intelligence community to simulate such commonsense reasoning abilities in machines. Over the years, many advances have been made and various challenges have been proposed to test their abilities. The Winograd Schema Challenge (WSC) is one such Natural Language Understanding (NLU) task which was also proposed as an alternative to the Turing Test. It is made up of textual question …

Contributors
Sharma, Arpit, Baral, Chitta, Lee, Joohyung, et al.
Created Date
2019

In this dissertation I develop a deep theory of temporal planning well-suited to analyzing, understanding, and improving the state of the art implementations (as of 2012). At face-value the work is strictly theoretical; nonetheless its impact is entirely real and practical. The easiest portion of that impact to highlight concerns the notable improvements to the format of the temporal fragment of the International Planning Competitions (IPCs). Particularly: the theory I expound upon here is the primary cause of--and justification for--the altered (i) selection of benchmark problems, and (ii) notion of "winning temporal planner". For higher level motivation: robotics, web service …

Contributors
Cushing, William Albemarle, Kambhampati, Subbarao, Weld, Daniel S, et al.
Created Date
2012