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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
Description
Turing test has been a benchmark scale for measuring the human level intelligence in computers since it was proposed by Alan Turing in 1950. However, for last 60 years, the applications such as ELIZA, PARRY, Cleverbot and Eugene Goostman, that claimed to pass the test. These applications are either based

Turing test has been a benchmark scale for measuring the human level intelligence in computers since it was proposed by Alan Turing in 1950. However, for last 60 years, the applications such as ELIZA, PARRY, Cleverbot and Eugene Goostman, that claimed to pass the test. These applications are either based on tricks to fool humans on a textual chat based test or there has been a disagreement between AI communities on them passing the test. This has led to the school of thought that it might not be the ideal test for predicting the human level intelligence in machines.

Consequently, the Winograd Schema Challenge has been suggested as an alternative to the Turing test. As opposed to deciding the intelligent behavior with the help of chat servers, like it was done in the Turing test, the Winograd Schema Challenge is a question answering test. It consists of sentence and question pairs such that the answer to the question depends on the resolution of a definite pronoun or adjective in the sentence. The answers are fairly intuitive for humans but they are difficult for machines because it requires some sort of background or commonsense knowledge about the sentence.

In this thesis, I propose a novel technique to solve the Winograd Schema Challenge. The technique has three basic modules at its disposal, namely, a Semantic Parser that parses the English text (both sentences and questions) into a formal representation, an Automatic Background Knowledge Extractor that extracts the Background Knowledge pertaining to the given Winograd sentence, and an Answer Set Programming Reasoning Engine that reasons on the given Winograd sentence and the corresponding Background Knowledge. The applicability of the technique is illustrated by solving a subset of Winograd Schema Challenge pertaining to a certain type of Background Knowledge. The technique is evaluated on the subset and a notable accuracy is achieved.
ContributorsSharma, Arpita (Author) / Baral, Chita (Thesis advisor) / Lee, Joohyung (Committee member) / Pon-Barry, Heather (Committee member) / Arizona State University (Publisher)
Created2014
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Description
With the inception of World Wide Web, the amount of data present on the internet is tremendous. This makes the task of navigating through this enormous amount of data quite difficult for the user. As users struggle to navigate through this wealth of information, the need for the development of

With the inception of World Wide Web, the amount of data present on the internet is tremendous. This makes the task of navigating through this enormous amount of data quite difficult for the user. As users struggle to navigate through this wealth of information, the need for the development of an automated system that can extract the required information becomes urgent. The aim of this thesis is to develop a Question Answering system to ease the process of information retrieval.

Question Answering systems have been around for quite some time and are a sub-field of information retrieval and natural language processing. The task of any Question Answering system is to seek an answer to a free form factual question. The difficulty of pinpointing and verifying the precise answer makes question answering more challenging than simple information retrieval done by search engines. Text REtrieval Conference (TREC) is a yearly conference which provides large - scale infrastructure and resources to support research in information retrieval domain. TREC has a question answering track since 1999 where the questions dataset contains a list of factual questions (Vorhees & Tice, 1999). DBpedia (Bizer et al., 2009) is a community driven effort to extract and structure the data present in Wikipedia.

The research objective of this thesis is to develop a novel approach to Question Answering based on a composition of conventional approaches of Information Retrieval and Natural Language processing. The focus is also on exploring the use of a structured and annotated knowledge base as opposed to an unstructured knowledge base. The knowledge base used here is DBpedia and the final system is evaluated on the TREC 2004 questions dataset.
ContributorsChandurkar, Avani (Author) / Bansal, Ajay (Thesis advisor) / Bansal, Srividya (Committee member) / Lindquist, Timothy (Committee member) / Arizona State University (Publisher)
Created2016
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Description
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

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 to be more structural in natural language text; I define Knowledge Description Graphs (KDGs), a graphical structure containing information about events, entities, and classes. We then propose formulations and algorithms to construct KDGs from a frame-based knowledge base, define the answers of various ``How'' and ``Why'' questions with respect to KDGs, and suggest how to obtain the answers from KDGs using Answer Set Programming. Moreover, I discuss how to derive missing information in constructing KDGs when the knowledge base is under-specified and how to answer many factual question types with respect to the knowledge base.

After having the answers of various questions with respect to a knowledge base, I extend our research to use natural language text in specifying deep questions and knowledge base, generate natural language text from those specification. Toward these goals, I developed NL2KR, a system which helps in translating natural language to formal language. I show NL2KR's use in translating ``How'' and ``Why'' questions, and generating simple natural language sentences from natural language KDG specification. Finally, I discuss applications of the components I developed in Natural Language Understanding.
ContributorsVo, Nguyen Ha (Author) / Baral, Chitta (Thesis advisor) / Lee, Joohyung (Committee member) / VanLehn, Kurt (Committee member) / Tran, Son Cao (Committee member) / Arizona State University (Publisher)
Created2015
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Description
Question answering is a challenging problem and a long term goal of Artificial Intelligence. There are many approaches proposed to solve this problem, including end to end machine learning systems, Information Retrieval based approaches and Textual Entailment. Despite being popular, these methods find difficulty in solving problems that require multi

Question answering is a challenging problem and a long term goal of Artificial Intelligence. There are many approaches proposed to solve this problem, including end to end machine learning systems, Information Retrieval based approaches and Textual Entailment. Despite being popular, these methods find difficulty in solving problems that require multi level reasoning and combining independent pieces of knowledge, for example, a question like "What adaptation is necessary in intertidal ecosystems but not in reef ecosystems?'', requires the system to consider qualities, behaviour or features of an organism living in an intertidal ecosystem and compare with that of an organism in a reef ecosystem to find the answer. The proposed solution is to solve a genre of questions, which is questions based on "Adaptation, Variation and Behavior in Organisms", where there are various different independent sets of knowledge required for answering questions along with reasoning. This method is implemented using Answer Set Programming and Natural Language Inference (which is based on machine learning ) for finding which of the given options is more probable to be the answer by matching it with the knowledge base. To evaluate this approach, a dataset of questions and a knowledge base in the domain of "Adaptation, Variation and Behavior in Organisms" is created.
ContributorsBatni, Vaishnavi (Author) / Baral, Chitta (Thesis advisor) / Anwar, Saadat (Committee member) / Yang, Yezhou (Committee member) / Arizona State University (Publisher)
Created2019