ETDs

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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Representing, reasoning and answering questions about biological pathways various applications

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…

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
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Visual analytics methodologies on causality analysis

Description
Causality analysis is the process of identifying cause-effect relationships among variables. This process is challenging because causal relationships cannot be tested solely based on statistical indicators as additional information is always needed to reduce the ambiguity caused by factors beyond those covered by the statistical test. Traditionally, controlled experiments are…

Causality analysis is the process of identifying cause-effect relationships among variables. This process is challenging because causal relationships cannot be tested solely based on statistical indicators as additional information is always needed to reduce the ambiguity caused by factors beyond those covered by the statistical test. Traditionally, controlled experiments are carried out to identify causal relationships, but recently there is a growing interest in causality analysis with observational data due to the increasing availability of data and tools. This type of analysis will often involve automatic algorithms that extract causal relations from large amounts of data and rely on expert judgment to scrutinize and verify the relations. Over-reliance on these automatic algorithms is dangerous because models trained on observational data are susceptible to bias that can be difficult to spot even with expert oversight. Visualization has proven to be effective at bridging the gap between human experts and statistical models by enabling an interactive exploration and manipulation of the data and models. This thesis develops a visual analytics framework to support the interaction between human experts and automatic models in causality analysis. Three case studies were conducted to demonstrate the application of the visual analytics framework in which feature engineering, insight generation, correlation analysis, and causality inspections were showcased.
ContributorsWang, Hong, Ph.D (Author) / Maciejewski, Ross (Thesis advisor) / He, Jingrui (Committee member) / Davulcu, Hasan (Committee member) / Thies, Cameron (Committee member) / Arizona State University (Publisher)
Created2019