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
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
Deep neural networks have been shown to be vulnerable to adversarial attacks. Typical attack strategies alter authentic data subtly so as to obtain adversarial samples that resemble the original but otherwise would cause a network's misbehavior such as a high misclassification rate. Various attack approaches have been reported, with some showing state-of-the-art performance in attacking certain networks. In the meanwhile, many defense mechanisms have been proposed in the literature, some of which are quite effective for guarding against typical attacks. Yet, most of these attacks fail when the targeted network modifies its architecture or uses another set of parameters and vice versa. Moreover, the emerging of more advanced deep neural networks, such as generative adversarial networks (GANs), has made the situation more complicated and the game between the attack and defense is continuing. This dissertation aims at exploring the venerability of the deep neural networks by investigating the mechanisms behind the success/failure of the existing attack and defense approaches. Therefore, several deep learning-based approaches have been proposed to study the problem from different perspectives. First, I developed an adversarial attack approach by exploring the unlearned region of a typical deep neural network which is often over-parameterized. Second, I proposed an end-to-end learning framework to analyze the images generated by different GAN models. Third, I developed a defense mechanism that can secure the deep neural network against adversarial attacks with a defense layer consisting of a set of orthogonal kernels. Substantial experiments are conducted to unveil the potential factors that contribute to attack/defense effectiveness. This dissertation also concludes with a discussion of possible future works of achieving a robust deep neural network.
ContributorsDing, Yuzhen (Author) / Li, Baoxin (Thesis advisor) / Davulcu, Hasan (Committee member) / Venkateswara, Hemanth Kumar Demakethepalli (Committee member) / Yang, Yezhou (Committee member) / Arizona State University (Publisher)
Created2022