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.
Displaying 1 - 10 of 35
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
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 non-monotonic nature of the ASP semantics, such enhancements turned out to be non-trivial and the existing extensions are not fully satisfactory. We observe that one main reason for the difficulties rooted in the propositional semantics of ASP, which is limited in handling first-order constructs (such as aggregates and ontologies) and functions (such as constraint variables in CP and SMT) in natural ways. This dissertation presents a unifying view on these extensions by viewing them as instances of formulas with generalized quantifiers and intensional functions. We extend the first-order stable model semantics by by Ferraris, Lee, and Lifschitz to allow generalized quantifiers, which cover aggregate, DL-atoms, constraints and SMT theory atoms as special cases. Using this unifying framework, we study and relate different extensions of ASP. We also present a tight integration of ASP with SMT, based on which we enhance action language C+ to handle reasoning about continuous changes. Our framework yields a systematic approach to study and extend non-monotonic languages.
ContributorsMeng, Yunsong (Author) / Lee, Joohyung (Thesis advisor) / Ahn, Gail-Joon (Committee member) / Baral, Chitta (Committee member) / Fainekos, Georgios (Committee member) / Lifschitz, Vladimir (Committee member) / Arizona State University (Publisher)
Created2013
Description
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 composition, industrial manufacturing, business process management, cybersecurity, space exploration, deep ocean exploration, and logistics all benefit from applying domain-independent automated planning technique. Naturally, actually carrying out such case studies has much to offer. For example, we may extract the lesson that reasoning carefully about deadlines is rather crucial to planning in practice. More generally, effectively automating specifically temporal planning is well-motivated from applications. Entirely abstractly, the aim is to improve the theory of automated temporal planning by distilling from its practice. My thesis is that the key feature of computational interest is concurrency. To support, I demonstrate by way of compilation methods, worst-case counting arguments, and analysis of algorithmic properties such as completeness that the more immediately pressing computational obstacles (facing would-be temporal generalizations of classical planning systems) can be dealt with in theoretically efficient manner. So more accurately the technical contribution here is to demonstrate: The computationally significant obstacle to automated temporal planning that remains is just concurrency.
ContributorsCushing, William Albemarle (Author) / Kambhampati, Subbarao (Thesis advisor) / Weld, Daniel S. (Committee member) / Smith, David E. (Committee member) / Baral, Chitta (Committee member) / Davalcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2012
Description
Modeling dynamic systems is an interesting problem in Knowledge Representation (KR) due to their usefulness in reasoning about real-world environments. In order to effectively do this, a number of different formalisms have been considered ranging from low-level languages, such as Answer Set Programming (ASP), to high-level action languages, such as C+ and BC. These languages show a lot of promise over many traditional approaches as they allow a developer to automate many tasks which require reasoning within dynamic environments in a succinct and elaboration tolerant manner. However, despite their strengths, they are still insufficient for modeling many systems, especially those of non-trivial scale or that require the ability to cope with exceptions which occur during execution, such as unexpected events or unintended consequences to actions which have been performed. In order to address these challenges, a theoretical framework is created which focuses on improving the feasibility of applying KR techniques to such problems. The framework is centered on the action language BC+, which integrates many of the strengths of existing KR formalisms, and provides the ability to perform efficient reasoning in an incremental fashion while handling exceptions which occur during execution. The result is a developer friendly formalism suitable for performing reasoning in an online environment. Finally, the newly enhanced Cplus2ASP 2 is introduced, which provides a number of improvements over the original version. These improvements include implementing BC+ among several additional languages, providing enhanced developer support, and exhibiting a significant performance increase over its predecessors and similar systems.
ContributorsBabb, Joseph (Author) / Lee, Joohyung (Thesis advisor) / Lee, Yann-Hang (Committee member) / Baral, Chitta (Committee member) / Arizona State University (Publisher)
Created2014
Description
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 requires new concepts on what a solution should be, and novel techniques in solving the problem. When user preferences are incomplete, rather than presenting a single plan, the planner must instead provide a set of plans containing one or more plans that are similar to the one that the user prefers. This research first proposes the usage of different measures to capture the quality of such plan sets. These are domain-independent distance measures based on plan elements if no knowledge of the user preferences is given, or the Integrated Preference Function measure in case incomplete knowledge of such preferences is provided. It then investigates various heuristic approaches to generate plan sets in accordance with these measures, and presents empirical results demonstrating the promise of the methods. The second part of this research addresses planning problems with incomplete domain models, specifically those annotated with possible preconditions and effects of actions. It formalizes the notion of plan robustness capturing the probability of success for plans during execution. A method of assessing plan robustness based on the weighted model counting approach is proposed. Two approaches for synthesizing robust plans are introduced. The first one compiles the robust plan synthesis problems to the conformant probabilistic planning problems. The second approximates the robustness measure with lower and upper bounds, incorporating them into a stochastic local search for estimating distance heuristic to a goal state. The resulting planner outperforms a state-of-the-art planner that can handle incomplete domain models in both plan quality and planning time.
ContributorsNguyễn, Tuấn Anh (Author) / Kambhampati, Subbarao (Thesis advisor) / Baral, Chitta (Committee member) / Do, Minh (Committee member) / Lee, Joohyung (Committee member) / Smith, David E. (Committee member) / Arizona State University (Publisher)
Created2014
Description
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 it. Indeed, a significant portion of the utility of such human-robot teams derives from the delegation of goals to the robot, and autonomy on the part of the robot in achieving those goals. In order to be considered truly autonomous, the robot must be able to make its own plans to achieve the goals assigned to it, with only minimal direction and assistance from the human.
Automated planning provides the solution to this problem -- indeed, one of the main motivations that underpinned the beginnings of the field of automated planning was to provide planning support for Shakey the robot with the STRIPS system. For long, however, automated planners suffered from scalability issues that precluded their application to real world, real time robotic systems. Recent decades have seen a gradual abeyance of those issues, and fast planning systems are now the norm rather than the exception. However, some of these advances in speedup and scalability have been achieved by ignoring or abstracting out challenges that real world integrated robotic systems must confront.
In this work, the problem of planning for human-hobot teaming is introduced. The central idea -- the use of automated planning systems as mediators in such human-robot teaming scenarios -- and the main challenges inspired from real world scenarios that must be addressed in order to make such planning seamless are presented: (i) Goals which can be specified or changed at execution time, after the planning process has completed; (ii) Worlds and scenarios where the state changes dynamically while a previous plan is executing; (iii) Models that are incomplete and can be changed during execution; and (iv) Information about the human agent's plan and intentions that can be used for coordination. These challenges are compounded by the fact that the human-robot team must execute in an open world, rife with dynamic events and other agents; and in a manner that encourages the exchange of information between the human and the robot. As an answer to these challenges, implemented solutions and a fielded prototype that combines all of those solutions into one planning system are discussed. Results from running this prototype in real world scenarios are presented, and extensions to some of the solutions are offered as appropriate.
Automated planning provides the solution to this problem -- indeed, one of the main motivations that underpinned the beginnings of the field of automated planning was to provide planning support for Shakey the robot with the STRIPS system. For long, however, automated planners suffered from scalability issues that precluded their application to real world, real time robotic systems. Recent decades have seen a gradual abeyance of those issues, and fast planning systems are now the norm rather than the exception. However, some of these advances in speedup and scalability have been achieved by ignoring or abstracting out challenges that real world integrated robotic systems must confront.
In this work, the problem of planning for human-hobot teaming is introduced. The central idea -- the use of automated planning systems as mediators in such human-robot teaming scenarios -- and the main challenges inspired from real world scenarios that must be addressed in order to make such planning seamless are presented: (i) Goals which can be specified or changed at execution time, after the planning process has completed; (ii) Worlds and scenarios where the state changes dynamically while a previous plan is executing; (iii) Models that are incomplete and can be changed during execution; and (iv) Information about the human agent's plan and intentions that can be used for coordination. These challenges are compounded by the fact that the human-robot team must execute in an open world, rife with dynamic events and other agents; and in a manner that encourages the exchange of information between the human and the robot. As an answer to these challenges, implemented solutions and a fielded prototype that combines all of those solutions into one planning system are discussed. Results from running this prototype in real world scenarios are presented, and extensions to some of the solutions are offered as appropriate.
ContributorsTalamadupula, Kartik (Author) / Kambhampati, Subbarao (Thesis advisor) / Baral, Chitta (Committee member) / Liu, Huan (Committee member) / Scheutz, Matthias (Committee member) / Smith, David E. (Committee member) / Arizona State University (Publisher)
Created2014
Description
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 interactions and networks underlying the different sets of relatively homogeneous samples from real world biological data. The characteristic set of samples/conditions and corresponding regulatory interactions defines the cellular context (context). Context, in this dissertation, represents the deterministic transcriptional activity within the specific cellular regulatory mechanism. The major contributions of this framework include - modeling and learning context specific GRNs; associating enriched samples with contexts to interpret contextual interactions using biological knowledge; pruning extraneous edges from the context-specific GRN to improve the precision of the final GRNs; integrating multisource data to learn inter and intra domain interactions and increase confidence in obtained GRNs; and finally, learning combinatorial conditioning factors from the data to identify regulatory cofactors. The framework, Expattern, was applied to both real world and synthetic data. Interesting insights were obtained into mechanism of action of drugs on analysis of NCI60 drug activity and gene expression data. Application to refractory cancer data and Glioblastoma multiforme yield GRNs that were readily annotated with context-specific phenotypic information. Refractory cancer GRNs also displayed associations between distinct cancers, not observed through only clustering. Performance comparisons on multi-context synthetic data show the framework Expattern performs better than other comparable methods.
ContributorsSen, Ina (Author) / Kim, Seungchan (Thesis advisor) / Baral, Chitta (Committee member) / Bittner, Michael (Committee member) / Konjevod, Goran (Committee member) / Arizona State University (Publisher)
Created2011
Description
Action language C+ is a formalism for describing properties of actions, which is based on nonmonotonic causal logic. The definite fragment of C+ is implemented in the Causal Calculator (CCalc), which is based on the reduction of nonmonotonic causal logic to propositional logic. This thesis describes the language of CCalc in terms of answer set programming (ASP), based on the translation of nonmonotonic causal logic to formulas under the stable model semantics. I designed a standard library which describes the constructs of the input language of CCalc in terms of ASP, allowing a simple modular method to represent CCalc input programs in the language of ASP. Using the combination of system F2LP and answer set solvers, this method achieves functionality close to that of CCalc while taking advantage of answer set solvers to yield efficient computation that is orders of magnitude faster than CCalc for many benchmark examples. In support of this, I created an automated translation system Cplus2ASP that implements the translation and encoding method and automatically invokes the necessary software to solve the translated input programs.
ContributorsCasolary, Michael (Author) / Lee, Joohyung (Thesis advisor) / Ahn, Gail-Joon (Committee member) / Baral, Chitta (Committee member) / Arizona State University (Publisher)
Created2011
Description
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, which extends both first-order logic and ASP, to relate circumscription to ASP, and to integrate DLs and ASP, thereby partially overcoming the limitations of the formalisms. By exploiting the relationship between circumscription and ASP, well-known action formalisms, such as the situation calculus, the event calculus, and Temporal Action Logics, are reformulated in ASP. The advantages of these reformulations are shown with respect to the generality of the reasoning tasks that can be handled and with respect to the computational efficiency. The integration of DLs and ASP presented in this dissertation provides a framework for integrating rules and ontologies for the semantic web. This framework enables us to perform nonmonotonic reasoning with DL knowledge bases. Observing the need to integrate action theories and ontologies, the above results are used to reformulate the problem of integrating action theories and ontologies as a problem of integrating rules and ontologies, thus enabling us to use the computational tools developed in the context of the latter for the former.
ContributorsPalla, Ravi (Author) / Lee, Joohyung (Thesis advisor) / Baral, Chitta (Committee member) / Kambhampati, Subbarao (Committee member) / Lifschitz, Vladimir (Committee member) / Arizona State University (Publisher)
Created2012