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- Creators: Davulcu, Hasan
- Member of: ASU Electronic Theses and Dissertations
Description
Genes have widely different pertinences to the etiology and pathology of diseases. Thus, they can be ranked according to their disease-significance on a genomic scale, which is the subject of gene prioritization. Given a set of genes known to be related to a disease, it is reasonable to use them as a basis to determine the significance of other candidate genes, which will then be ranked based on the association they exhibit with respect to the given set of known genes. Experimental and computational data of various kinds have different reliability and relevance to a disease under study. This work presents a gene prioritization method based on integrated biological networks that incorporates and models the various levels of relevance and reliability of diverse sources. The method is shown to achieve significantly higher performance as compared to two well-known gene prioritization algorithms. Essentially, no bias in the performance was seen as it was applied to diseases of diverse ethnology, e.g., monogenic, polygenic and cancer. The method was highly stable and robust against significant levels of noise in the data. Biological networks are often sparse, which can impede the operation of associationbased gene prioritization algorithms such as the one presented here from a computational perspective. As a potential approach to overcome this limitation, we explore the value that transcription factor binding sites can have in elucidating suitable targets. Transcription factors are needed for the expression of most genes, especially in higher organisms and hence genes can be associated via their genetic regulatory properties. While each transcription factor recognizes specific DNA sequence patterns, such patterns are mostly unknown for many transcription factors. Even those that are known are inconsistently reported in the literature, implying a potentially high level of inaccuracy. We developed computational methods for prediction and improvement of transcription factor binding patterns. Tests performed on the improvement method by employing synthetic patterns under various conditions showed that the method is very robust and the patterns produced invariably converge to nearly identical series of patterns. Preliminary tests were conducted to incorporate knowledge from transcription factor binding sites into our networkbased model for prioritization, with encouraging results. Genes have widely different pertinences to the etiology and pathology of diseases. Thus, they can be ranked according to their disease-significance on a genomic scale, which is the subject of gene prioritization. Given a set of genes known to be related to a disease, it is reasonable to use them as a basis to determine the significance of other candidate genes, which will then be ranked based on the association they exhibit with respect to the given set of known genes. Experimental and computational data of various kinds have different reliability and relevance to a disease under study. This work presents a gene prioritization method based on integrated biological networks that incorporates and models the various levels of relevance and reliability of diverse sources. The method is shown to achieve significantly higher performance as compared to two well-known gene prioritization algorithms. Essentially, no bias in the performance was seen as it was applied to diseases of diverse ethnology, e.g., monogenic, polygenic and cancer. The method was highly stable and robust against significant levels of noise in the data. Biological networks are often sparse, which can impede the operation of associationbased gene prioritization algorithms such as the one presented here from a computational perspective. As a potential approach to overcome this limitation, we explore the value that transcription factor binding sites can have in elucidating suitable targets. Transcription factors are needed for the expression of most genes, especially in higher organisms and hence genes can be associated via their genetic regulatory properties. While each transcription factor recognizes specific DNA sequence patterns, such patterns are mostly unknown for many transcription factors. Even those that are known are inconsistently reported in the literature, implying a potentially high level of inaccuracy. We developed computational methods for prediction and improvement of transcription factor binding patterns. Tests performed on the improvement method by employing synthetic patterns under various conditions showed that the method is very robust and the patterns produced invariably converge to nearly identical series of patterns. Preliminary tests were conducted to incorporate knowledge from transcription factor binding sites into our networkbased model for prioritization, with encouraging results. To validate these approaches in a disease-specific context, we built a schizophreniaspecific network based on the inferred associations and performed a comprehensive prioritization of human genes with respect to the disease. These results are expected to be validated empirically, but computational validation using known targets are very positive.
ContributorsLee, Jang (Author) / Gonzalez, Graciela (Thesis advisor) / Ye, Jieping (Committee member) / Davulcu, Hasan (Committee member) / Gallitano-Mendel, Amelia (Committee member) / Arizona State University (Publisher)
Created2011
Description
Currently Java is making its way into the embedded systems and mobile devices like androids. The programs written in Java are compiled into machine independent binary class byte codes. A Java Virtual Machine (JVM) executes these classes. The Java platform additionally specifies the Java Native Interface (JNI). JNI allows Java code that runs within a JVM to interoperate with applications or libraries that are written in other languages and compiled to the host CPU ISA. JNI plays an important role in embedded system as it provides a mechanism to interact with libraries specific to the platform. This thesis addresses the overhead incurred in the JNI due to reflection and serialization when objects are accessed on android based mobile devices. It provides techniques to reduce this overhead. It also provides an API to access objects through its reference through pinning its memory location. The Android emulator was used to evaluate the performance of these techniques and we observed that there was 5 - 10 % performance gain in the new Java Native Interface.
ContributorsChandrian, Preetham (Author) / Lee, Yann-Hang (Thesis advisor) / Davulcu, Hasan (Committee member) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2011
Description
As pointed out in the keynote speech by H. V. Jagadish in SIGMOD'07, and also commonly agreed in the database community, the usability of structured data by casual users is as important as the data management systems' functionalities. A major hardness of using structured data is the problem of easily retrieving information from them given a user's information needs. Learning and using a structured query language (e.g., SQL and XQuery) is overwhelmingly burdensome for most users, as not only are these languages sophisticated, but the users need to know the data schema. Keyword search provides us with opportunities to conveniently access structured data and potentially significantly enhances the usability of structured data. However, processing keyword search on structured data is challenging due to various types of ambiguities such as structural ambiguity (keyword queries have no structure), keyword ambiguity (the keywords may not be accurate), user preference ambiguity (the user may have implicit preferences that are not indicated in the query), as well as the efficiency challenges due to large search space. This dissertation performs an expansive study on keyword search processing techniques as a gateway for users to access structured data and retrieve desired information. The key issues addressed include: (1) Resolving structural ambiguities in keyword queries by generating meaningful query results, which involves identifying relevant keyword matches, identifying return information, composing query results based on relevant matches and return information. (2) Resolving structural, keyword and user preference ambiguities through result analysis, including snippet generation, result differentiation, result clustering, result summarization/query expansion, etc. (3) Resolving the efficiency challenge in processing keyword search on structured data by utilizing and efficiently maintaining materialized views. These works deliver significant technical contributions towards building a full-fledged search engine for structured data.
ContributorsLiu, Ziyang (Author) / Chen, Yi (Thesis advisor) / Candan, Kasim S (Committee member) / Davulcu, Hasan (Committee member) / Jagadish, H V (Committee member) / Arizona State University (Publisher)
Created2011
Description
Most existing approaches to complex event processing over streaming data rely on the assumption that the matches to the queries are rare and that the goal of the system is to identify these few matches within the incoming deluge of data. In many applications, such as stock market analysis and user credit card purchase pattern monitoring, however the matches to the user queries are in fact plentiful and the system has to efficiently sift through these many matches to locate only the few most preferable matches. In this work, we propose a complex pattern ranking (CPR) framework for specifying top-k pattern queries over streaming data, present new algorithms to support top-k pattern queries in data streaming environments, and verify the effectiveness and efficiency of the proposed algorithms. The developed algorithms identify top-k matching results satisfying both patterns as well as additional criteria. To support real-time processing of the data streams, instead of computing top-k results from scratch for each time window, we maintain top-k results dynamically as new events come and old ones expire. We also develop new top-k join execution strategies that are able to adapt to the changing situations (e.g., sorted and random access costs, join rates) without having to assume a priori presence of data statistics. Experiments show significant improvements over existing approaches.
ContributorsWang, Xinxin (Author) / Candan, K. Selcuk (Thesis advisor) / Chen, Yi (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2011
Description
Source selection is one of the foremost challenges for searching deep-web. For a user query, source selection involves selecting a subset of deep-web sources expected to provide relevant answers to the user query. Existing source selection models employ query-similarity based local measures for assessing source quality. These local measures are necessary but not sufficient as they are agnostic to source trustworthiness and result importance, which, given the autonomous and uncurated nature of deep-web, have become indispensible for searching deep-web. SourceRank provides a global measure for assessing source quality based on source trustworthiness and result importance. SourceRank's effectiveness has been evaluated in single-topic deep-web environments. The goal of the thesis is to extend sourcerank to a multi-topic deep-web environment. Topic-sensitive sourcerank is introduced as an effective way of extending sourcerank to a deep-web environment containing a set of representative topics. In topic-sensitive sourcerank, multiple sourcerank vectors are created, each biased towards a representative topic. At query time, using the topic of query keywords, a query-topic sensitive, composite sourcerank vector is computed as a linear combination of these pre-computed biased sourcerank vectors. Extensive experiments on more than a thousand sources in multiple domains show 18-85% improvements in result quality over Google Product Search and other existing methods.
ContributorsJha, Manishkumar (Author) / Kambhampati, Subbarao (Thesis advisor) / Liu, Huan (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2011
Description
This thesis research attempts to observe, measure and visualize the communication patterns among developers of an open source community and analyze how this can be inferred in terms of progress of that open source project. Here I attempted to analyze the Ubuntu open source project's email data (9 subproject log archives over a period of five years) and focused on drawing more precise metrics from different perspectives of the communication data. Also, I attempted to overcome the scalability issue by using Apache Pig libraries, which run on a MapReduce framework based Hadoop Cluster. I described four metrics based on which I observed and analyzed the data and also presented the results which show the required patterns and anomalies to better understand and infer the communication. Also described the usage experience with Pig Latin (scripting language of Apache Pig Libraries) for this research and how they brought the feature of scalability, simplicity, and visibility in this data intensive research work. These approaches are useful in project monitoring, to augment human observation and reporting, in social network analysis, to track individual contributions.
ContributorsMotamarri, Lakshminarayana (Author) / Santanam, Raghu (Thesis advisor) / Ye, Jieping (Thesis advisor) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2011
Description
Analysis of political texts, which contains a huge amount of personal political opinions, sentiments, and emotions towards powerful individuals, leaders, organizations, and a large number of people, is an interesting task, which can lead to discover interesting interactions between the political parties and people. Recently, political blogosphere plays an increasingly important role in politics, as a forum for debating political issues. Most of the political weblogs are biased towards their political parties, and they generally express their sentiments towards their issues (i.e. leaders, topics etc.,) and also towards issues of the opposing parties. In this thesis, I have modeled the above interactions/debate as a sentimental bi-partite graph, a bi-partite graph with Blogs forming vertices of a disjoint set, and the issues (i.e. leaders, topics etc.,) forming the other disjoint set,and the edges between the two sets representing the sentiment of the blogs towards the issues. I have used American Political blog data to model the sentimental bi- partite graph, in particular, a set of popular political liberal and conservative blogs that have clearly declared positions. These blogs contain discussion about social, political, economic issues and related key individuals in their conservative/liberal view. To be more focused and more polarized, 22 most popular liberal/conservative blogs of a particular time period, May 2008 - October 2008(because of high intensity of debate and discussions), just before the presidential elections, was considered, involving around 23,800 articles. This thesis involves solving the questions: a) which is the most liberal/conservative blogs on the web? b) Who is on which side of debate and what are the issues? c) Who are the important leaders? d) How do you model the relationship between the participants of the debate and the underlying issues?
ContributorsThirumalai, Dananjayan (Author) / Davulcu, Hasan (Thesis advisor) / Sarjoughian, Hessam S. (Committee member) / Sen, Arunabha (Committee member) / Arizona State University (Publisher)
Created2012
Description
Situations of sensory overload are steadily becoming more frequent as the ubiquity of technology approaches reality--particularly with the advent of socio-communicative smartphone applications, and pervasive, high speed wireless networks. Although the ease of accessing information has improved our communication effectiveness and efficiency, our visual and auditory modalities--those modalities that today's computerized devices and displays largely engage--have become overloaded, creating possibilities for distractions, delays and high cognitive load; which in turn can lead to a loss of situational awareness, increasing chances for life threatening situations such as texting while driving. Surprisingly, alternative modalities for information delivery have seen little exploration. Touch, in particular, is a promising candidate given that it is our largest sensory organ with impressive spatial and temporal acuity. Although some approaches have been proposed for touch-based information delivery, they are not without limitations including high learning curves, limited applicability and/or limited expression. This is largely due to the lack of a versatile, comprehensive design theory--specifically, a theory that addresses the design of touch-based building blocks for expandable, efficient, rich and robust touch languages that are easy to learn and use. Moreover, beyond design, there is a lack of implementation and evaluation theories for such languages. To overcome these limitations, a unified, theoretical framework, inspired by natural, spoken language, is proposed called Somatic ABC's for Articulating (designing), Building (developing) and Confirming (evaluating) touch-based languages. To evaluate the usefulness of Somatic ABC's, its design, implementation and evaluation theories were applied to create communication languages for two very unique application areas: audio described movies and motor learning. These applications were chosen as they presented opportunities for complementing communication by offloading information, typically conveyed visually and/or aurally, to the skin. For both studies, it was found that Somatic ABC's aided the design, development and evaluation of rich somatic languages with distinct and natural communication units.
ContributorsMcDaniel, Troy Lee (Author) / Panchanathan, Sethuraman (Thesis advisor) / Davulcu, Hasan (Committee member) / Li, Baoxin (Committee member) / Santello, Marco (Committee member) / Arizona State University (Publisher)
Created2012
Description
Muslim radicalism is recognized as one of the greatest security threats for the United States and the rest of the world. Use of force to eliminate specific radical entities is ineffective in containing radicalism as a whole. There is a need to understand the origin, ideologies and behavior of Radical and Counter-Radical organizations and how they shape up over a period of time. Recognizing and supporting counter-radical organizations is one of the most important steps towards impeding radical organizations. A lot of research has already been done to categorize and recognize organizations, to understand their behavior, their interactions with other organizations, their target demographics and the area of influence. We have a huge amount of information which is a result of the research done over these topics. This thesis provides a powerful and interactive way to navigate through all this information, using a Visualization Dashboard. The dashboard makes it easier for Social Scientists, Policy Analysts, Military and other personnel to visualize an organization's propensity towards violence and radicalism. It also tracks the peaking religious, political and socio-economic markers, their target demographics and locations. A powerful search interface with parametric search helps in narrowing down to specific scenarios and view the corresponding information related to the organizations. This tool helps to identify moderate Counter-Radical organizations and also has the potential of predicting the orientation of various organizations based on the current information.
ContributorsNair, Shreejay (Author) / Davulcu, Hasan (Thesis advisor) / Dasgpta, Partha (Committee member) / Sen, Arunabha (Committee member) / Arizona State University (Publisher)
Created2012
Description
Navigating within non-linear structures is a challenge for all users when the space is large but the problem is most pronounced when the users are blind or visually impaired. Such users access digital content through screen readers like JAWS which read out the text on the screen. However presentation of non-linear narratives in such a manner without visual cues and information about spatial dependencies is very inefficient for such users. The NSDL Science Literacy StrandMaps are visual layouts to help students and teachers browse educational resources. A Strandmap shows relationships between concepts and how they build upon one another across grade levels. NSDL Strandmaps are non-linear narratives which need to be presented to users who are blind in an effective way. A good summary of the Strandmap can give the users an idea about the concepts that are explained in it. This can help them decide whether to view the map or not. In addition, a preview-based navigation mechanism can help users decide which direction they want to take, based on a preview of upcoming content in each direction. Given a non-linear narrative like a Strandmap which has both text and structure, and a word limit w, the goal of this thesis is to find the best way to create its summary. The following approaches are considered: – Purely Text-based Approach using a Multi-document Text Summarizer – Purely Structure-based Approach using PageRank – Approaches Combining both Text and Structure → CUTS-Based Approach (Topic Segmentation) → PageRank with Content Since no reference summaries for such structures were available, user studies were conducted to evaluate these algorithms. PageRank with Content approach performed the best. Another important conclusion was that text and structure are intertwined in a Strandmap by design.
ContributorsGaur, Shruti (Author) / Candan, Kasim Selcuk (Thesis advisor) / Sundaram, Hari (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2011