Matching Items (22)
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
Laboratory automation systems have seen a lot of technological advances in recent times. As a result, the software that is written for them are becoming increasingly sophisticated. Existing software architectures and standards are targeted to a wider domain of software development and need to be customized in order to use them for developing software for laboratory automation systems. This thesis proposes an architecture that is based on existing software architectural paradigms and is specifically tailored to developing software for a laboratory automation system. The architecture is based on fairly autonomous software components that can be distributed across multiple computers. The components in the architecture make use of asynchronous communication methodologies that are facilitated by passing messages between one another. The architecture can be used to develop software that is distributed, responsive and thread-safe. The thesis also proposes a framework that has been developed to implement the ideas proposed by the architecture. The framework is used to develop software that is scalable, distributed, responsive and thread-safe. The framework currently has components to control very commonly used laboratory automation devices such as mechanical stages, cameras, and also to do common laboratory automation functionalities such as imaging.
ContributorsKuppuswamy, Venkataramanan (Author) / Meldrum, Deirdre (Thesis advisor) / Collofello, James (Thesis advisor) / Sarjoughian, Hessam S. (Committee member) / Johnson, Roger (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
Access control is necessary for information assurance in many of today's applications such as banking and electronic health record. Access control breaches are critical security problems that can result from unintended and improper implementation of security policies. Security testing can help identify security vulnerabilities early and avoid unexpected expensive cost in handling breaches for security architects and security engineers. The process of security testing which involves creating tests that effectively examine vulnerabilities is a challenging task. Role-Based Access Control (RBAC) has been widely adopted to support fine-grained access control. However, in practice, due to its complexity including role management, role hierarchy with hundreds of roles, and their associated privileges and users, systematically testing RBAC systems is crucial to ensure the security in various domains ranging from cyber-infrastructure to mission-critical applications. In this thesis, we introduce i) a security testing technique for RBAC systems considering the principle of maximum privileges, the structure of the role hierarchy, and a new security test coverage criterion; ii) a MTBDD (Multi-Terminal Binary Decision Diagram) based representation of RBAC security policy including RHMTBDD (Role Hierarchy MTBDD) to efficiently generate effective positive and negative security test cases; and iii) a security testing framework which takes an XACML-based RBAC security policy as an input, parses it into a RHMTBDD representation and then generates positive and negative test cases. We also demonstrate the efficacy of our approach through case studies.
ContributorsGupta, Poonam (Author) / Ahn, Gail-Joon (Thesis advisor) / Collofello, James (Committee member) / Huang, Dijiang (Committee member) / Arizona State University (Publisher)
Created2014
Description
Corporations invest considerable resources to create, preserve and analyze
their data; yet while organizations are interested in protecting against
unauthorized data transfer, there lacks a comprehensive metric to discriminate
what data are at risk of leaking.
This thesis motivates the need for a quantitative leakage risk metric, and
provides a risk assessment system, called Whispers, for computing it. Using
unsupervised machine learning techniques, Whispers uncovers themes in an
organization's document corpus, including previously unknown or unclassified
data. Then, by correlating the document with its authors, Whispers can
identify which data are easier to contain, and conversely which are at risk.
Using the Enron email database, Whispers constructs a social network segmented
by topic themes. This graph uncovers communication channels within the
organization. Using this social network, Whispers determines the risk of each
topic by measuring the rate at which simulated leaks are not detected. For the
Enron set, Whispers identified 18 separate topic themes between January 1999
and December 2000. The highest risk data emanated from the legal department
with a leakage risk as high as 60%.
their data; yet while organizations are interested in protecting against
unauthorized data transfer, there lacks a comprehensive metric to discriminate
what data are at risk of leaking.
This thesis motivates the need for a quantitative leakage risk metric, and
provides a risk assessment system, called Whispers, for computing it. Using
unsupervised machine learning techniques, Whispers uncovers themes in an
organization's document corpus, including previously unknown or unclassified
data. Then, by correlating the document with its authors, Whispers can
identify which data are easier to contain, and conversely which are at risk.
Using the Enron email database, Whispers constructs a social network segmented
by topic themes. This graph uncovers communication channels within the
organization. Using this social network, Whispers determines the risk of each
topic by measuring the rate at which simulated leaks are not detected. For the
Enron set, Whispers identified 18 separate topic themes between January 1999
and December 2000. The highest risk data emanated from the legal department
with a leakage risk as high as 60%.
ContributorsWright, Jeremy (Author) / Syrotiuk, Violet (Thesis advisor) / Davulcu, Hasan (Committee member) / Yau, Stephen (Committee member) / Arizona State University (Publisher)
Created2014
Description
This thesis proposed a novel approach to establish the trust model in a social network scenario based on users' emails. Email is one of the most important social connections nowadays. By analyzing email exchange activities among users, a social network trust model can be established to judge the trust rate between each two users. The whole trust checking process is divided into two steps: local checking and remote checking. Local checking directly contacts the email server to calculate the trust rate based on user's own email communication history. Remote checking is a distributed computing process to get help from user's social network friends and built the trust rate together. The email-based trust model is built upon a cloud computing framework called MobiCloud. Inside MobiCloud, each user occupies a virtual machine which can directly communicate with others. Based on this feature, the distributed trust model is implemented as a combination of local analysis and remote analysis in the cloud. Experiment results show that the trust evaluation model can give accurate trust rate even in a small scale social network which does not have lots of social connections. With this trust model, the security in both social network services and email communication could be improved.
ContributorsZhong, Yunji (Author) / Huang, Dijiang (Thesis advisor) / Dasgupta, Partha (Committee member) / Syrotiuk, Violet (Committee member) / Arizona State University (Publisher)
Created2011
Description
Introductory programming courses, also known as CS1, have a specific set of expected outcomes related to the learning of the most basic and essential computational concepts in computer science (CS). However, two of the most often heard complaints in such courses are that (1) they are divorced from the reality of application and (2) they make the learning of the basic concepts tedious. The concepts introduced in CS1 courses are highly abstract and not easily comprehensible. In general, the difficulty is intrinsic to the field of computing, often described as "too mathematical or too abstract." This dissertation presents a small-scale mixed method study conducted during the fall 2009 semester of CS1 courses at Arizona State University. This study explored and assessed students' comprehension of three core computational concepts - abstraction, arrays of objects, and inheritance - in both algorithm design and problem solving. Through this investigation students' profiles were categorized based on their scores and based on their mistakes categorized into instances of five computational thinking concepts: abstraction, algorithm, scalability, linguistics, and reasoning. It was shown that even though the notion of computational thinking is not explicit in the curriculum, participants possessed and/or developed this skill through the learning and application of the CS1 core concepts. Furthermore, problem-solving experiences had a direct impact on participants' knowledge skills, explanation skills, and confidence. Implications for teaching CS1 and for future research are also considered.
ContributorsBillionniere, Elodie V (Author) / Collofello, James (Thesis advisor) / Ganesh, Tirupalavanam G. (Thesis advisor) / VanLehn, Kurt (Committee member) / Burleson, Winslow (Committee member) / Arizona State University (Publisher)
Created2011
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
Description
Rapid growth of internet and connected devices ranging from cloud systems to internet of things have raised critical concerns for securing these systems. In the recent past, security attacks on different kinds of devices have evolved in terms of complexity and diversity. One of the challenges is establishing secure communication in the network among various devices and systems. Despite being protected with authentication and encryption, the network still needs to be protected against cyber-attacks. For this, the network traffic has to be closely monitored and should detect anomalies and intrusions. Intrusion detection can be categorized as a network traffic classification problem in machine learning. Existing network traffic classification methods require a lot of training and data preprocessing, and this problem is more serious if the dataset size is huge. In addition, the machine learning and deep learning methods that have been used so far were trained on datasets that contain obsolete attacks. In this thesis, these problems are addressed by using ensemble methods applied on an up to date network attacks dataset. Ensemble methods use multiple learning algorithms to get better classification accuracy that could be obtained when the corresponding learning algorithm is applied alone. This dataset for network traffic classification has recent attack scenarios and contains over fifteen attacks. This approach shows that ensemble methods can be used to classify network traffic and detect intrusions with less training times of the model, and lesser pre-processing without feature selection. In addition, this thesis also shows that only with less than ten percent of the total features of input dataset will lead to similar accuracy that is achieved on whole dataset. This can heavily reduce the training times and classification duration in real-time scenarios.
ContributorsPonneganti, Ramu (Author) / Yau, Stephen (Thesis advisor) / Richa, Andrea (Committee member) / Yang, Yezhou (Committee member) / Arizona State University (Publisher)
Created2019
Description
Machine learning tutorials often employ an application and runtime specific solution for a given problem in which users are expected to have a broad understanding of data analysis and software programming. This thesis focuses on designing and implementing a new, hands-on approach to teaching machine learning by streamlining the process of generating Inertial Movement Unit (IMU) data from multirotor flight sessions, training a linear classifier, and applying said classifier to solve Multi-rotor Activity Recognition (MAR) problems in an online lab setting. MAR labs leverage cloud computing and data storage technologies to host a versatile environment capable of logging, orchestrating, and visualizing the solution for an MAR problem through a user interface. MAR labs extends Arizona State University’s Visual IoT/Robotics Programming Language Environment (VIPLE) as a control platform for multi-rotors used in data collection. VIPLE is a platform developed for teaching computational thinking, visual programming, Internet of Things (IoT) and robotics application development. As a part of this education platform, this work also develops a 3D simulator capable of simulating the programmable behaviors of a robot within a maze environment and builds a physical quadrotor for use in MAR lab experiments.
ContributorsDe La Rosa, Matthew Lee (Author) / Chen, Yinong (Thesis advisor) / Collofello, James (Committee member) / Huang, Dijiang (Committee member) / Arizona State University (Publisher)
Created2018