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- Genre: Doctoral Dissertation
- Creators: Davulcu, Hasan
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
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
Data-driven applications are becoming increasingly complex with support for processing events and data streams in a loosely-coupled distributed environment, providing integrated access to heterogeneous data sources such as relational databases and XML documents. This dissertation explores the use of materialized views over structured heterogeneous data sources to support multiple query optimization in a distributed event stream processing framework that supports such applications involving various query expressions for detecting events, monitoring conditions, handling data streams, and querying data. Materialized views store the results of the computed view so that subsequent access to the view retrieves the materialized results, avoiding the cost of recomputing the entire view from base data sources. Using a service-based metadata repository that provides metadata level access to the various language components in the system, a heuristics-based algorithm detects the common subexpressions from the queries represented in a mixed multigraph model over relational and structured XML data sources. These common subexpressions can be relational, XML or a hybrid join over the heterogeneous data sources. This research examines the challenges in the definition and materialization of views when the heterogeneous data sources are retained in their native format, instead of converting the data to a common model. LINQ serves as the materialized view definition language for creating the view definitions. An algorithm is introduced that uses LINQ to create a data structure for the persistence of these hybrid views. Any changes to base data sources used to materialize views are captured and mapped to a delta structure. The deltas are then streamed within the framework for use in the incremental update of the materialized view. Algorithms are presented that use the magic sets query optimization approach to both efficiently materialize the views and to propagate the relevant changes to the views for incremental maintenance. Using representative scenarios over structured heterogeneous data sources, an evaluation of the framework demonstrates an improvement in performance. Thus, defining the LINQ-based materialized views over heterogeneous structured data sources using the detected common subexpressions and incrementally maintaining the views by using magic sets enhances the efficiency of the distributed event stream processing environment.
ContributorsChaudhari, Mahesh Balkrishna (Author) / Dietrich, Suzanne W (Thesis advisor) / Urban, Susan D (Committee member) / Davulcu, Hasan (Committee member) / Chen, Yi (Committee member) / Arizona State University (Publisher)
Created2011
Description
The complexity of the systems that software engineers build has continuously grown since the inception of the field. What has not changed is the engineers' mental capacity to operate on about seven distinct pieces of information at a time. The widespread use of UML has led to more abstract software design activities, however the same cannot be said for reverse engineering activities. The introduction of abstraction to reverse engineering will allow the engineer to move farther away from the details of the system, increasing his ability to see the role that domain level concepts play in the system. In this thesis, we present a technique that facilitates filtering of classes from existing systems at the source level based on their relationship to concepts in the domain via a classification method using machine learning. We showed that concepts can be identified using a machine learning classifier based on source level metrics. We developed an Eclipse plugin to assist with the process of manually classifying Java source code, and collecting metrics and classifications into a standard file format. We developed an Eclipse plugin to act as a concept identifier that visually indicates a class as a domain concept or not. We minimized the size of training sets to ensure a useful approach in practice. This allowed us to determine that a training set of 7:5 to 10% is nearly as effective as a training set representing 50% of the system. We showed that random selection is the most consistent and effective means of selecting a training set. We found that KNN is the most consistent performer among the learning algorithms tested. We determined the optimal feature set for this classification problem. We discussed two possible structures besides a one to one mapping of domain knowledge to implementation. We showed that classes representing more than one concept are simply concepts at differing levels of abstraction. We also discussed composite concepts representing a domain concept implemented by more than one class. We showed that these composite concepts are difficult to detect because the problem is NP-complete.
ContributorsCarey, Maurice (Author) / Colbourn, Charles (Thesis advisor) / Collofello, James (Thesis advisor) / Davulcu, Hasan (Committee member) / Sarjoughian, Hessam S. (Committee member) / Ye, Jieping (Committee member) / Arizona State University (Publisher)
Created2013
Description
This dissertation presents the Temporal Event Query Language (TEQL), a new language for querying event streams. Event Stream Processing enables online querying of streams of events to extract relevant data in a timely manner. TEQL enables querying of interval-based event streams using temporal database operators. Temporal databases and temporal query languages have been a subject of research for more than 30 years and are a natural fit for expressing queries that involve a temporal dimension. However, operators developed in this context cannot be directly applied to event streams. The research extends a preexisting relational framework for event stream processing to support temporal queries. The language features and formal semantic extensions to extend the relational framework are identified. The extended framework supports continuous, step-wise evaluation of temporal queries. The incremental evaluation of TEQL operators is formalized to avoid re-computation of previous results. The research includes the development of a prototype that supports the integrated event and temporal query processing framework, with support for incremental evaluation and materialization of intermediate results. TEQL enables reporting temporal data in the output, direct specification of conditions over timestamps, and specification of temporal relational operators. Through the integration of temporal database operators with event languages, a new class of temporal queries is made possible for querying event streams. New features include semantic aggregation, extraction of temporal patterns using set operators, and a more accurate specification of event co-occurrence.
ContributorsShiva, Foruhar Ali (Author) / Urban, Susan D (Thesis advisor) / Chen, Yi (Thesis advisor) / Davulcu, Hasan (Committee member) / Sarjoughian, Hessam S. (Committee member) / Arizona State University (Publisher)
Created2012
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
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
The pay-as-you-go economic model of cloud computing increases the visibility, traceability, and verifiability of software costs. Application developers must understand how their software uses resources when running in the cloud in order to stay within budgeted costs and/or produce expected profits. Cloud computing's unique economic model also leads naturally to an earn-as-you-go profit model for many cloud based applications. These applications can benefit from low level analyses for cost optimization and verification. Testing cloud applications to ensure they meet monetary cost objectives has not been well explored in the current literature. When considering revenues and costs for cloud applications, the resource economic model can be scaled down to the transaction level in order to associate source code with costs incurred while running in the cloud. Both static and dynamic analysis techniques can be developed and applied to understand how and where cloud applications incur costs. Such analyses can help optimize (i.e. minimize) costs and verify that they stay within expected tolerances. An adaptation of Worst Case Execution Time (WCET) analysis is presented here to statically determine worst case monetary costs of cloud applications. This analysis is used to produce an algorithm for determining control flow paths within an application that can exceed a given cost threshold. The corresponding results are used to identify path sections that contribute most to cost excess. A hybrid approach for determining cost excesses is also presented that is comprised mostly of dynamic measurements but that also incorporates calculations that are based on the static analysis approach. This approach uses operational profiles to increase the precision and usefulness of the calculations.
ContributorsBuell, Kevin, Ph.D (Author) / Collofello, James (Thesis advisor) / Davulcu, Hasan (Committee member) / Lindquist, Timothy (Committee member) / Sen, Arunabha (Committee member) / Arizona State University (Publisher)
Created2012
Description
Embedded Networked Systems (ENS) consist of various devices, which are embedded into physical objects (e.g., home appliances, vehicles, buidlings, people). With rapid advances in processing and networking technologies, these devices can be fully connected and pervasive in the environment. The devices can interact with the physical world, collaborate to share resources, and provide context-aware services. This dissertation focuses on collaboration in ENS to provide smart services. However, there are several challenges because the system must be - scalable to a huge number of devices; robust against noise, loss and failure; and secure despite communicating with strangers. To address these challenges, first, the dissertation focuses on designing a mobile gateway called Mobile Edge Computing Device (MECD) for Ubiquitous Sensor Networks (USN), a type of ENS. In order to reduce communication overhead with the server, an MECD is designed to provide local and distributed management of a network and data associated with a moving object (e.g., a person, car, pet). Furthermore, it supports collaboration with neighboring MECDs. The MECD is developed and tested for monitoring containers during shipment from Singapore to Taiwan and reachability to the remote server was a problem because of variance in connectivity (caused by high temperature variance) and high interference. The unreachability problem is addressed by using a mesh networking approach for collaboration of MECDs in sending data to a server. A hierarchical architecture is proposed in this regard to provide multi-level collaboration using dynamic mesh networks of MECDs at one layer. The mesh network is evaluated for an intelligent container scenario and results show complete connectivity with the server for temperature range from 25°C to 65°C. Finally, the authentication of mobile and pervasive devices in ENS for secure collaboration is investigated. This is a challenging problem because mutually unknown devices must be verified without knowledge of each other's identity. A self-organizing region-based authentication technique is proposed that uses environmental sound to autonomously verify if two devices are within the same region. The experimental results show sound could accurately authenticate devices within a small region.
ContributorsKim, Su-jin (Author) / Gupta, Sandeep K. S. (Thesis advisor) / Dasgupta, Partha (Committee member) / Davulcu, Hasan (Committee member) / Lee, Yann-Hang (Committee member) / Arizona State University (Publisher)
Created2010
Description
Cyber-systems and networks are the target of different types of cyber-threats and attacks, which are becoming more common, sophisticated, and damaging. Those attacks can vary in the way they are performed. However, there are similar strategies
and tactics often used because they are time-proven to be effective. The motivations behind cyber-attacks play an important role in designating how attackers plan and proceed to achieve their goals. Generally, there are three categories of motivation
are: political, economical, and socio-cultural motivations. These indicate that to defend against possible attacks in an enterprise environment, it is necessary to consider what makes such an enterprise environment a target. That said, we can understand
what threats to consider and how to deploy the right defense system. In other words, detecting an attack depends on the defenders having a clear understanding of why they become targets and what possible attacks they should expect. For instance,
attackers may preform Denial of Service (DoS), or even worse Distributed Denial of Service (DDoS), with intention to cause damage to targeted organizations and prevent legitimate users from accessing their services. However, in some cases, attackers are very skilled and try to hide in a system undetected for a long period of time with the incentive to steal and collect data rather than causing damages.
Nowadays, not only the variety of attack types and the way they are launched are important. However, advancement in technology is another factor to consider. Over the last decades, we have experienced various new technologies. Obviously, in the beginning, new technologies will have their own limitations before they stand out. There are a number of related technical areas whose understanding is still less than satisfactory, and in which long-term research is needed. On the other hand, these new technologies can boost the advancement of deploying security solutions and countermeasures when they are carefully adapted. That said, Software Defined Networking i(SDN), its related security threats and solutions, and its adaption in enterprise environments bring us new chances to enhance our security solutions. To reach the optimal level of deploying SDN technology in enterprise environments, it is important to consider re-evaluating current deployed security solutions in traditional networks before deploying them to SDN-based infrastructures. Although DDoS attacks are a bit sinister, there are other types of cyber-threats that are very harmful, sophisticated, and intelligent. Thus, current security defense solutions to detect DDoS cannot detect them. These kinds of attacks are complex, persistent, and stealthy, also referred to Advanced Persistent Threats (APTs) which often leverage the bot control and remotely access valuable information. APT uses multiple stages to break into a network. APT is a sort of unseen, continuous and long-term penetrative network and attackers can bypass the existing security detection systems. It can modify and steal the sensitive data as well as specifically cause physical damage the target system. In this dissertation, two cyber-attack motivations are considered: sabotage, where the motive is the destruction; and information theft, where attackers aim to acquire invaluable information (customer info, business information, etc). I deal with two types of attacks (DDoS attacks and APT attacks) where DDoS attacks are classified under sabotage motivation category, and the APT attacks are classified under information theft motivation category. To detect and mitigate each of these attacks, I utilize the ease of programmability in SDN and its great platform for implementation, dynamic topology changes, decentralized network management, and ease of deploying security countermeasures.
and tactics often used because they are time-proven to be effective. The motivations behind cyber-attacks play an important role in designating how attackers plan and proceed to achieve their goals. Generally, there are three categories of motivation
are: political, economical, and socio-cultural motivations. These indicate that to defend against possible attacks in an enterprise environment, it is necessary to consider what makes such an enterprise environment a target. That said, we can understand
what threats to consider and how to deploy the right defense system. In other words, detecting an attack depends on the defenders having a clear understanding of why they become targets and what possible attacks they should expect. For instance,
attackers may preform Denial of Service (DoS), or even worse Distributed Denial of Service (DDoS), with intention to cause damage to targeted organizations and prevent legitimate users from accessing their services. However, in some cases, attackers are very skilled and try to hide in a system undetected for a long period of time with the incentive to steal and collect data rather than causing damages.
Nowadays, not only the variety of attack types and the way they are launched are important. However, advancement in technology is another factor to consider. Over the last decades, we have experienced various new technologies. Obviously, in the beginning, new technologies will have their own limitations before they stand out. There are a number of related technical areas whose understanding is still less than satisfactory, and in which long-term research is needed. On the other hand, these new technologies can boost the advancement of deploying security solutions and countermeasures when they are carefully adapted. That said, Software Defined Networking i(SDN), its related security threats and solutions, and its adaption in enterprise environments bring us new chances to enhance our security solutions. To reach the optimal level of deploying SDN technology in enterprise environments, it is important to consider re-evaluating current deployed security solutions in traditional networks before deploying them to SDN-based infrastructures. Although DDoS attacks are a bit sinister, there are other types of cyber-threats that are very harmful, sophisticated, and intelligent. Thus, current security defense solutions to detect DDoS cannot detect them. These kinds of attacks are complex, persistent, and stealthy, also referred to Advanced Persistent Threats (APTs) which often leverage the bot control and remotely access valuable information. APT uses multiple stages to break into a network. APT is a sort of unseen, continuous and long-term penetrative network and attackers can bypass the existing security detection systems. It can modify and steal the sensitive data as well as specifically cause physical damage the target system. In this dissertation, two cyber-attack motivations are considered: sabotage, where the motive is the destruction; and information theft, where attackers aim to acquire invaluable information (customer info, business information, etc). I deal with two types of attacks (DDoS attacks and APT attacks) where DDoS attacks are classified under sabotage motivation category, and the APT attacks are classified under information theft motivation category. To detect and mitigate each of these attacks, I utilize the ease of programmability in SDN and its great platform for implementation, dynamic topology changes, decentralized network management, and ease of deploying security countermeasures.
ContributorsAlshamrani, Adel (Author) / Huang, Dijiang (Thesis advisor) / Doupe, Adam (Committee member) / Ahn, Gail-Joon (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2018