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- All Subjects: Computer Science
- Creators: Tong, Hanghang
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
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
This thesis studies recommendation systems and considers joint sampling and learning. Sampling in recommendation systems is to obtain users' ratings on specific items chosen by the recommendation platform, and learning is to infer the unknown ratings of users to items given the existing data. In this thesis, the problem is formulated as an adaptive matrix completion problem in which sampling is to reveal the unknown entries of a $U\times M$ matrix where $U$ is the number of users, $M$ is the number of items, and each entry of the $U\times M$ matrix represents the rating of a user to an item. In the literature, this matrix completion problem has been studied under a static setting, i.e., recovering the matrix based on a set of partial ratings. This thesis considers both sampling and learning, and proposes an adaptive algorithm. The algorithm adapts its sampling and learning based on the existing data. The idea is to sample items that reveal more information based on the previous sampling results and then learn based on clustering. Performance of the proposed algorithm has been evaluated using simulations.
ContributorsZhu, Lingfang (Author) / Xue, Guoliang (Thesis advisor) / He, Jingrui (Committee member) / Tong, Hanghang (Committee member) / Arizona State University (Publisher)
Created2015
Description
The amount of time series data generated is increasing due to the integration of sensor technologies with everyday applications, such as gesture recognition, energy optimization, health care, video surveillance. The use of multiple sensors simultaneously
for capturing different aspects of the real world attributes has also led to an increase in dimensionality from uni-variate to multi-variate time series. This has facilitated richer data representation but also has necessitated algorithms determining similarity between two multi-variate time series for search and analysis.
Various algorithms have been extended from uni-variate to multi-variate case, such as multi-variate versions of Euclidean distance, edit distance, dynamic time warping. However, it has not been studied how these algorithms account for asynchronous in time series. Human gestures, for example, exhibit asynchrony in their patterns as different subjects perform the same gesture with varying movements in their patterns at different speeds. In this thesis, we propose several algorithms (some of which also leverage metadata describing the relationships among the variates). In particular, we present several techniques that leverage the contextual relationships among the variates when measuring multi-variate time series similarities. Based on the way correlation is leveraged, various weighing mechanisms have been proposed that determine the importance of a dimension for discriminating between the time series as giving the same weight to each dimension can led to misclassification. We next study the robustness of the considered techniques against different temporal asynchronies, including shifts and stretching.
Exhaustive experiments were carried on datasets with multiple types and amounts of temporal asynchronies. It has been observed that accuracy of algorithms that rely on data to discover variate relationships can be low under the presence of temporal asynchrony, whereas in case of algorithms that rely on external metadata, robustness against asynchronous distortions tends to be stronger. Specifically, algorithms using external metadata have better classification accuracy and cluster separation than existing state-of-the-art work, such as EROS, PCA, and naive dynamic time warping.
for capturing different aspects of the real world attributes has also led to an increase in dimensionality from uni-variate to multi-variate time series. This has facilitated richer data representation but also has necessitated algorithms determining similarity between two multi-variate time series for search and analysis.
Various algorithms have been extended from uni-variate to multi-variate case, such as multi-variate versions of Euclidean distance, edit distance, dynamic time warping. However, it has not been studied how these algorithms account for asynchronous in time series. Human gestures, for example, exhibit asynchrony in their patterns as different subjects perform the same gesture with varying movements in their patterns at different speeds. In this thesis, we propose several algorithms (some of which also leverage metadata describing the relationships among the variates). In particular, we present several techniques that leverage the contextual relationships among the variates when measuring multi-variate time series similarities. Based on the way correlation is leveraged, various weighing mechanisms have been proposed that determine the importance of a dimension for discriminating between the time series as giving the same weight to each dimension can led to misclassification. We next study the robustness of the considered techniques against different temporal asynchronies, including shifts and stretching.
Exhaustive experiments were carried on datasets with multiple types and amounts of temporal asynchronies. It has been observed that accuracy of algorithms that rely on data to discover variate relationships can be low under the presence of temporal asynchrony, whereas in case of algorithms that rely on external metadata, robustness against asynchronous distortions tends to be stronger. Specifically, algorithms using external metadata have better classification accuracy and cluster separation than existing state-of-the-art work, such as EROS, PCA, and naive dynamic time warping.
ContributorsGarg, Yash (Author) / Candan, Kasim Selcuk (Thesis advisor) / Chowell-Punete, Gerardo (Committee member) / Tong, Hanghang (Committee member) / Davulcu, Hasan (Committee member) / Sapino, Maria Luisa (Committee member) / Arizona State University (Publisher)
Created2015
Description
Micro-blogging platforms like Twitter have become some of the most popular sites for people to share and express their views and opinions about public events like debates, sports events or other news articles. These social updates by people complement the written news articles or transcripts of events in giving the popular public opinion about these events. So it would be useful to annotate the transcript with tweets. The technical challenge is to align the tweets with the correct segment of the transcript. ET-LDA by Hu et al [9] addresses this issue by modeling the whole process with an LDA-based graphical model. The system segments the transcript into coherent and meaningful parts and also determines if a tweet is a general tweet about the event or it refers to a particular segment of the transcript. One characteristic of the Hu et al’s model is that it expects all the data to be available upfront and uses batch inference procedure. But in many cases we find that data is not available beforehand, and it is often streaming. In such cases it is infeasible to repeatedly run the batch inference algorithm. My thesis presents an online inference algorithm for the ET-LDA model, with a continuous stream of tweet data and compare their runtime and performance to existing algorithms.
ContributorsAcharya, Anirudh (Author) / Kambhampati, Subbarao (Thesis advisor) / Davulcu, Hasan (Committee member) / Tong, Hanghang (Committee member) / Arizona State University (Publisher)
Created2015
Description
Online social media is popular due to its real-time nature, extensive connectivity and a large user base. This motivates users to employ social media for seeking information by reaching out to their large number of social connections. Information seeking can manifest in the form of requests for personal and time-critical information or gathering perspectives on important issues. Social media platforms are not designed for resource seeking and experience large volumes of messages, leading to requests not being fulfilled satisfactorily. Designing frameworks to facilitate efficient information seeking in social media will help users to obtain appropriate assistance for their needs
and help platforms to increase user satisfaction.
Several challenges exist in the way of facilitating information seeking in social media. First, the characteristics affecting the user’s response time for a question are not known, making it hard to identify prompt responders. Second, the social context in which the user has asked the question has to be determined to find personalized responders. Third, users employ rhetorical requests, which are statements having the
syntax of questions, and systems assisting information seeking might be hindered from focusing on genuine questions. Fouth, social media advocates of political campaigns employ nuanced strategies to prevent users from obtaining balanced perspectives on
issues of public importance.
Sociological and linguistic studies on user behavior while making or responding to information seeking requests provides concepts drawing from which we can address these challenges. We propose methods to estimate the response time of the user for a given question to identify prompt responders. We compute the question specific social context an asker shares with his social connections to identify personalized responders. We draw from theories of political mobilization to model the behaviors arising from the strategies of people trying to skew perspectives. We identify rhetorical questions by modeling user motivations to post them.
and help platforms to increase user satisfaction.
Several challenges exist in the way of facilitating information seeking in social media. First, the characteristics affecting the user’s response time for a question are not known, making it hard to identify prompt responders. Second, the social context in which the user has asked the question has to be determined to find personalized responders. Third, users employ rhetorical requests, which are statements having the
syntax of questions, and systems assisting information seeking might be hindered from focusing on genuine questions. Fouth, social media advocates of political campaigns employ nuanced strategies to prevent users from obtaining balanced perspectives on
issues of public importance.
Sociological and linguistic studies on user behavior while making or responding to information seeking requests provides concepts drawing from which we can address these challenges. We propose methods to estimate the response time of the user for a given question to identify prompt responders. We compute the question specific social context an asker shares with his social connections to identify personalized responders. We draw from theories of political mobilization to model the behaviors arising from the strategies of people trying to skew perspectives. We identify rhetorical questions by modeling user motivations to post them.
ContributorsRanganath, Suhas (Author) / Liu, Huan (Thesis advisor) / Lai, Ying-Cheng (Thesis advisor) / Tong, Hanghang (Committee member) / Vaculin, Roman (Committee member) / Arizona State University (Publisher)
Created2017
Description
With the rise of the Big Data Era, an exponential amount of network data is being generated at an unprecedented rate across a wide-range of high impact micro and macro areas of research---from protein interaction to social networks. The critical challenge is translating this large scale network data into actionable information.
A key task in the data translation is the analysis of network connectivity via marked nodes---the primary focus of our research. We have developed a framework for analyzing network connectivity via marked nodes in large scale graphs, utilizing novel algorithms in three interrelated areas: (1) analysis of a single seed node via it’s ego-centric network (AttriPart algorithm); (2) pathway identification between two seed nodes (K-Simple Shortest Paths Multithreaded and Search Reduced (KSSPR) algorithm); and (3) tree detection, defining the interaction between three or more seed nodes (Shortest Path MST algorithm).
In an effort to address both fundamental and applied research issues, we have developed the LocalForcasting algorithm to explore how network connectivity analysis can be applied to local community evolution and recommender systems. The goal is to apply the LocalForecasting algorithm to various domains---e.g., friend suggestions in social networks or future collaboration in co-authorship networks. This algorithm utilizes link prediction in combination with the AttriPart algorithm to predict future connections in local graph partitions.
Results show that our proposed AttriPart algorithm finds up to 1.6x denser local partitions, while running approximately 43x faster than traditional local partitioning techniques (PageRank-Nibble). In addition, our LocalForecasting algorithm demonstrates a significant improvement in the number of nodes and edges correctly predicted over baseline methods. Furthermore, results for the KSSPR algorithm demonstrate a speed-up of up to 2.5x the standard k-simple shortest paths algorithm.
A key task in the data translation is the analysis of network connectivity via marked nodes---the primary focus of our research. We have developed a framework for analyzing network connectivity via marked nodes in large scale graphs, utilizing novel algorithms in three interrelated areas: (1) analysis of a single seed node via it’s ego-centric network (AttriPart algorithm); (2) pathway identification between two seed nodes (K-Simple Shortest Paths Multithreaded and Search Reduced (KSSPR) algorithm); and (3) tree detection, defining the interaction between three or more seed nodes (Shortest Path MST algorithm).
In an effort to address both fundamental and applied research issues, we have developed the LocalForcasting algorithm to explore how network connectivity analysis can be applied to local community evolution and recommender systems. The goal is to apply the LocalForecasting algorithm to various domains---e.g., friend suggestions in social networks or future collaboration in co-authorship networks. This algorithm utilizes link prediction in combination with the AttriPart algorithm to predict future connections in local graph partitions.
Results show that our proposed AttriPart algorithm finds up to 1.6x denser local partitions, while running approximately 43x faster than traditional local partitioning techniques (PageRank-Nibble). In addition, our LocalForecasting algorithm demonstrates a significant improvement in the number of nodes and edges correctly predicted over baseline methods. Furthermore, results for the KSSPR algorithm demonstrate a speed-up of up to 2.5x the standard k-simple shortest paths algorithm.
ContributorsFreitas, Scott (Author) / Tong, Hanghang (Thesis advisor) / Maciejewski, Ross (Committee member) / Yang, Yezhou (Committee member) / Arizona State University (Publisher)
Created2018