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- All Subjects: Computer Science
- Creators: Doupe, Adam
Description
Biological systems are complex in many dimensions as endless transportation and communication networks all function simultaneously. Our ability to intervene within both healthy and diseased systems is tied directly to our ability to understand and model core functionality. The progress in increasingly accurate and thorough high-throughput measurement technologies has provided a deluge of data from which we may attempt to infer a representation of the true genetic regulatory system. A gene regulatory network model, if accurate enough, may allow us to perform hypothesis testing in the form of computational experiments. Of great importance to modeling accuracy is the acknowledgment of biological contexts within the models -- i.e. recognizing the heterogeneous nature of the true biological system and the data it generates. This marriage of engineering, mathematics and computer science with systems biology creates a cycle of progress between computer simulation and lab experimentation, rapidly translating interventions and treatments for patients from the bench to the bedside. This dissertation will first discuss the landscape for modeling the biological system, explore the identification of targets for intervention in Boolean network models of biological interactions, and explore context specificity both in new graphical depictions of models embodying context-specific genomic regulation and in novel analysis approaches designed to reveal embedded contextual information. Overall, the dissertation will explore a spectrum of biological modeling with a goal towards therapeutic intervention, with both formal and informal notions of biological context, in such a way that will enable future work to have an even greater impact in terms of direct patient benefit on an individualized level.
ContributorsVerdicchio, Michael (Author) / Kim, Seungchan (Thesis advisor) / Baral, Chitta (Committee member) / Stolovitzky, Gustavo (Committee member) / Collofello, James (Committee member) / Arizona State University (Publisher)
Created2013
Description
With the increasing user demand for low latency, elastic provisioning of computing resources coupled with ubiquitous and on-demand access to real-time data, cloud computing has emerged as a popular computing paradigm to meet growing user demands. However, with the introduction and rising use of wear- able technology and evolving uses of smart-phones, the concept of Internet of Things (IoT) has become a prevailing notion in the currently growing technology industry. Cisco Inc. has projected a data creation of approximately 403 Zetabytes (ZB) by 2018. The combination of bringing benign devices and connecting them to the web has resulted in exploding service and data aggregation requirements, thus requiring a new and innovative computing platform. This platform should have the capability to provide robust real-time data analytics and resource provisioning to clients, such as IoT users, on-demand. Such a computation model would need to function at the edge-of-the-network, forming a bridge between the large cloud data centers and the distributed connected devices.
This research expands on the notion of bringing computational power to the edge- of-the-network, and then integrating it with the cloud computing paradigm whilst providing services to diverse IoT-based applications. This expansion is achieved through the establishment of a new computing model that serves as a platform for IoT-based devices to communicate with services in real-time. We name this paradigm as Gateway-Oriented Reconfigurable Ecosystem (GORE) computing. Finally, this thesis proposes and discusses the development of a policy management framework for accommodating our proposed computational paradigm. The policy framework is designed to serve both the hosted applications and the GORE paradigm by enabling them to function more efficiently. The goal of the framework is to ensure uninterrupted communication and service delivery between users and their applications.
This research expands on the notion of bringing computational power to the edge- of-the-network, and then integrating it with the cloud computing paradigm whilst providing services to diverse IoT-based applications. This expansion is achieved through the establishment of a new computing model that serves as a platform for IoT-based devices to communicate with services in real-time. We name this paradigm as Gateway-Oriented Reconfigurable Ecosystem (GORE) computing. Finally, this thesis proposes and discusses the development of a policy management framework for accommodating our proposed computational paradigm. The policy framework is designed to serve both the hosted applications and the GORE paradigm by enabling them to function more efficiently. The goal of the framework is to ensure uninterrupted communication and service delivery between users and their applications.
ContributorsDsouza, Clinton (Author) / Ahn, Gail-Joon (Thesis advisor) / Doupe, Adam (Committee member) / Dasgupta, Partha (Committee member) / Arizona State University (Publisher)
Created2015
Description
Android is currently the most widely used mobile operating system. The permission model in Android governs the resource access privileges of applications. The permission model however is amenable to various attacks, including re-delegation attacks, background snooping attacks and disclosure of private information. This thesis is aimed at understanding, analyzing and performing forensics on application behavior. This research sheds light on several security aspects, including the use of inter-process communications (IPC) to perform permission re-delegation attacks.
Android permission system is more of app-driven rather than user controlled, which means it is the applications that specify their permission requirement and the only thing which the user can do is choose not to install a particular application based on the requirements. Given the all or nothing choice, users succumb to pressures and needs to accept permissions requested. This thesis proposes a couple of ways for providing the users finer grained control of application privileges. The same methods can be used to evade the Permission Re-delegation attack.
This thesis also proposes and implements a novel methodology in Android that can be used to control the access privileges of an Android application, taking into consideration the context of the running application. This application-context based permission usage is further used to analyze a set of sample applications. We found the evidence of applications spoofing or divulging user sensitive information such as location information, contact information, phone id and numbers, in the background. Such activities can be used to track users for a variety of privacy-intrusive purposes. We have developed implementations that minimize several forms of privacy leaks that are routinely done by stock applications.
Android permission system is more of app-driven rather than user controlled, which means it is the applications that specify their permission requirement and the only thing which the user can do is choose not to install a particular application based on the requirements. Given the all or nothing choice, users succumb to pressures and needs to accept permissions requested. This thesis proposes a couple of ways for providing the users finer grained control of application privileges. The same methods can be used to evade the Permission Re-delegation attack.
This thesis also proposes and implements a novel methodology in Android that can be used to control the access privileges of an Android application, taking into consideration the context of the running application. This application-context based permission usage is further used to analyze a set of sample applications. We found the evidence of applications spoofing or divulging user sensitive information such as location information, contact information, phone id and numbers, in the background. Such activities can be used to track users for a variety of privacy-intrusive purposes. We have developed implementations that minimize several forms of privacy leaks that are routinely done by stock applications.
ContributorsGollapudi, Narasimha Aditya (Author) / Dasgupta, Partha (Thesis advisor) / Xue, Guoliang (Committee member) / Doupe, Adam (Committee member) / Arizona State University (Publisher)
Created2014
Description
The increasing number of continually connected mobile persons has created an environment conducive to real time user data gathering for many uses both public and private in nature. Publicly, one can envision no longer requiring a census to determine the demographic composition of the country and its sub regions. The information provided is vastly more up to date than that of a census and allows civil authorities to be more agile and preemptive with planning. Privately, advertisers take advantage of a persons stated opinions, demographics, and contextual (where and when) information in order to formulate and present pertinent offers.
Regardless of its use this information can be sensitive in nature and should therefore be under the control of the user. Currently, a user has little say in the manner that their information is processed once it has been released. An ad-hoc approach is currently in use, where the location based service providers each maintain their own policy over personal information usage.
In order to allow more user control over their personal information while still providing for targeted advertising, a systematic approach to the release of the information is needed. It is for that reason we propose a User-Centric Context Aware Spatiotemporal Anonymization framework. At its core the framework will unify the current spatiotemporal anonymization with that of traditional anonymization so that user specified anonymization requirement is met or exceeded while allowing for more demographic information to be released.
Regardless of its use this information can be sensitive in nature and should therefore be under the control of the user. Currently, a user has little say in the manner that their information is processed once it has been released. An ad-hoc approach is currently in use, where the location based service providers each maintain their own policy over personal information usage.
In order to allow more user control over their personal information while still providing for targeted advertising, a systematic approach to the release of the information is needed. It is for that reason we propose a User-Centric Context Aware Spatiotemporal Anonymization framework. At its core the framework will unify the current spatiotemporal anonymization with that of traditional anonymization so that user specified anonymization requirement is met or exceeded while allowing for more demographic information to be released.
ContributorsSanchez, Michael Andrew (Author) / Ahn, Gail-Joon (Thesis advisor) / Doupe, Adam (Committee member) / Dasgupta, Partha (Committee member) / Arizona State University (Publisher)
Created2014
Description
The rate at which new malicious software (Malware) is created is consistently increasing each year. These new malwares are designed to bypass the current anti-virus countermeasures employed to protect computer systems. Security Analysts must understand the nature and intent of the malware sample in order to protect computer systems from these attacks. The large number of new malware samples received daily by computer security companies require Security Analysts to quickly determine the type, threat, and countermeasure for newly identied samples. Our approach provides for a visualization tool to assist the Security Analyst in these tasks that allows the Analyst to visually identify relationships between malware samples.
This approach consists of three steps. First, the received samples are processed by a sandbox environment to perform a dynamic behavior analysis. Second, the reports of the dynamic behavior analysis are parsed to extract identifying features which are matched against other known and analyzed samples. Lastly, those matches that are determined to express a relationship are visualized as an edge connected pair of nodes in an undirected graph.
This approach consists of three steps. First, the received samples are processed by a sandbox environment to perform a dynamic behavior analysis. Second, the reports of the dynamic behavior analysis are parsed to extract identifying features which are matched against other known and analyzed samples. Lastly, those matches that are determined to express a relationship are visualized as an edge connected pair of nodes in an undirected graph.
ContributorsHolmes, James Edward (Author) / Ahn, Gail-Joon (Thesis advisor) / Dasgupta, Partha (Committee member) / Doupe, Adam (Committee member) / Arizona State University (Publisher)
Created2014
Description
Given the process of tumorigenesis, biological signaling pathways have become of interest in the field of oncology. Many of the regulatory mechanisms that are altered in cancer are directly related to signal transduction and cellular communication. Thus, identifying signaling pathways that have become deregulated may provide useful information to better understanding altered regulatory mechanisms within cancer. Many methods that have been created to measure the distinct activity of signaling pathways have relied strictly upon transcription profiles. With advancements in comparative genomic hybridization techniques, copy number data has become extremely useful in providing valuable information pertaining to the genomic landscape of cancer. The purpose of this thesis is to develop a methodology that incorporates both gene expression and copy number data to identify signaling pathways that have become deregulated in cancer. The central idea is that copy number data may significantly assist in identifying signaling pathway deregulation by justifying the aberrant activity being measured in gene expression profiles. This method was then applied to four different subtypes of breast cancer resulting in the identification of signaling pathways associated with distinct functionalities for each of the breast cancer subtypes.
ContributorsTrevino, Robert (Author) / Kim, Seungchan (Thesis advisor) / Ringner, Markus (Committee member) / Liu, Huan (Committee member) / Arizona State University (Publisher)
Created2011
Description
In many classication problems data samples cannot be collected easily, example in drug trials, biological experiments and study on cancer patients. In many situations the data set size is small and there are many outliers. When classifying such data, example cancer vs normal patients the consequences of mis-classication are probably more important than any other data type, because the data point could be a cancer patient or the classication decision could help determine what gene might be over expressed and perhaps a cause of cancer. These mis-classications are typically higher in the presence of outlier data points. The aim of this thesis is to develop a maximum margin classier that is suited to address the lack of robustness of discriminant based classiers (like the Support Vector Machine (SVM)) to noise and outliers. The underlying notion is to adopt and develop a natural loss function that is more robust to outliers and more representative of the true loss function of the data. It is demonstrated experimentally that SVM's are indeed susceptible to outliers and that the new classier developed, here coined as Robust-SVM (RSVM), is superior to all studied classier on the synthetic datasets. It is superior to the SVM in both the synthetic and experimental data from biomedical studies and is competent to a classier derived on similar lines when real life data examples are considered.
ContributorsGupta, Sidharth (Author) / Kim, Seungchan (Thesis advisor) / Welfert, Bruno (Committee member) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2011
Description
Reverse engineering gene regulatory networks (GRNs) is an important problem in the domain of Systems Biology. Learning GRNs is challenging due to the inherent complexity of the real regulatory networks and the heterogeneity of samples in available biomedical data. Real world biological data are commonly collected from broad surveys (profiling studies) and aggregate highly heterogeneous biological samples. Popular methods to learn GRNs simplistically assume a single universal regulatory network corresponding to available data. They neglect regulatory network adaptation due to change in underlying conditions and cellular phenotype or both. This dissertation presents a novel computational framework to learn common regulatory interactions and networks underlying the different sets of relatively homogeneous samples from real world biological data. The characteristic set of samples/conditions and corresponding regulatory interactions defines the cellular context (context). Context, in this dissertation, represents the deterministic transcriptional activity within the specific cellular regulatory mechanism. The major contributions of this framework include - modeling and learning context specific GRNs; associating enriched samples with contexts to interpret contextual interactions using biological knowledge; pruning extraneous edges from the context-specific GRN to improve the precision of the final GRNs; integrating multisource data to learn inter and intra domain interactions and increase confidence in obtained GRNs; and finally, learning combinatorial conditioning factors from the data to identify regulatory cofactors. The framework, Expattern, was applied to both real world and synthetic data. Interesting insights were obtained into mechanism of action of drugs on analysis of NCI60 drug activity and gene expression data. Application to refractory cancer data and Glioblastoma multiforme yield GRNs that were readily annotated with context-specific phenotypic information. Refractory cancer GRNs also displayed associations between distinct cancers, not observed through only clustering. Performance comparisons on multi-context synthetic data show the framework Expattern performs better than other comparable methods.
ContributorsSen, Ina (Author) / Kim, Seungchan (Thesis advisor) / Baral, Chitta (Committee member) / Bittner, Michael (Committee member) / Konjevod, Goran (Committee member) / Arizona State University (Publisher)
Created2011
Description
Threshold logic has been studied by at least two independent group of researchers. One group of researchers studied threshold logic with the intention of building threshold logic circuits. The earliest research to this end was done in the 1960's. The major work at that time focused on studying mathematical properties of threshold logic as no efficient circuit implementations of threshold logic were available. Recently many post-CMOS (Complimentary Metal Oxide Semiconductor) technologies that implement threshold logic have been proposed along with efficient CMOS implementations. This has renewed the effort to develop efficient threshold logic design automation techniques. This work contributes to this ongoing effort. Another group studying threshold logic did so, because the building block of neural networks - the Perceptron, is identical to the threshold element implementing a threshold function. Neural networks are used for various purposes as data classifiers. This work contributes tangentially to this field by proposing new methods and techniques to study and analyze functions implemented by a Perceptron After completion of the Human Genome Project, it has become evident that most biological phenomenon is not caused by the action of single genes, but due to the complex interaction involving a system of genes. In recent times, the `systems approach' for the study of gene systems is gaining popularity. Many different theories from mathematics and computer science has been used for this purpose. Among the systems approaches, the Boolean logic gene model has emerged as the current most popular discrete gene model. This work proposes a new gene model based on threshold logic functions (which are a subset of Boolean logic functions). The biological relevance and utility of this model is argued illustrated by using it to model different in-vivo as well as in-silico gene systems.
ContributorsLinge Gowda, Tejaswi (Author) / Vrudhula, Sarma (Thesis advisor) / Shrivastava, Aviral (Committee member) / Chatha, Karamvir (Committee member) / Kim, Seungchan (Committee member) / Arizona State University (Publisher)
Created2012
Description
Due to the shortcomings of modern Mobile Device Management solutions, businesses
have begun to incorporate forensics to analyze their mobile devices and respond
to any incidents of malicious activity in order to protect their sensitive data. Current
forensic tools, however, can only look a static image of the device being examined,
making it difficult for a forensic analyst to produce conclusive results regarding the
integrity of any sensitive data on the device. This research thesis expands on the
use of forensics to secure data by implementing an agent on a mobile device that can
continually collect information regarding the state of the device. This information is
then sent to a separate server in the form of log files to be analyzed using a specialized
tool. The analysis tool is able to look at the data collected from the device over time
and perform specific calculations, according to the user's specifications, highlighting
any correlations or anomalies among the data which might be considered suspicious
to a forensic analyst. The contribution of this paper is both an in-depth explanation
on the implementation of an iOS application to be used to improve the mobile forensics
process as well as a proof-of-concept experiment showing how evidence collected
over time can be used to improve the accuracy of a forensic analysis.
have begun to incorporate forensics to analyze their mobile devices and respond
to any incidents of malicious activity in order to protect their sensitive data. Current
forensic tools, however, can only look a static image of the device being examined,
making it difficult for a forensic analyst to produce conclusive results regarding the
integrity of any sensitive data on the device. This research thesis expands on the
use of forensics to secure data by implementing an agent on a mobile device that can
continually collect information regarding the state of the device. This information is
then sent to a separate server in the form of log files to be analyzed using a specialized
tool. The analysis tool is able to look at the data collected from the device over time
and perform specific calculations, according to the user's specifications, highlighting
any correlations or anomalies among the data which might be considered suspicious
to a forensic analyst. The contribution of this paper is both an in-depth explanation
on the implementation of an iOS application to be used to improve the mobile forensics
process as well as a proof-of-concept experiment showing how evidence collected
over time can be used to improve the accuracy of a forensic analysis.
ContributorsWhitaker, Jeremy (Author) / Ahn, Gail-Joon (Thesis advisor) / Doupe, Adam (Committee member) / Yau, Stephen (Committee member) / Arizona State University (Publisher)
Created2015