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- Genre: Academic theses
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
Capturing the information in an image into a natural language sentence is
considered a difficult problem to be solved by computers. Image captioning involves not just detecting objects from images but understanding the interactions between the objects to be translated into relevant captions. So, expertise in the fields of computer vision paired with natural language processing are supposed to be crucial for this purpose. The sequence to sequence modelling strategy of deep neural networks is the traditional approach to generate a sequential list of words which are combined to represent the image. But these models suffer from the problem of high variance by not being able to generalize well on the training data.
The main focus of this thesis is to reduce the variance factor which will help in generating better captions. To achieve this, Ensemble Learning techniques have been explored, which have the reputation of solving the high variance problem that occurs in machine learning algorithms. Three different ensemble techniques namely, k-fold ensemble, bootstrap aggregation ensemble and boosting ensemble have been evaluated in this thesis. For each of these techniques, three output combination approaches have been analyzed. Extensive experiments have been conducted on the Flickr8k dataset which has a collection of 8000 images and 5 different captions for every image. The bleu score performance metric, which is considered to be the standard for evaluating natural language processing (NLP) problems, is used to evaluate the predictions. Based on this metric, the analysis shows that ensemble learning performs significantly better and generates more meaningful captions compared to any of the individual models used.
considered a difficult problem to be solved by computers. Image captioning involves not just detecting objects from images but understanding the interactions between the objects to be translated into relevant captions. So, expertise in the fields of computer vision paired with natural language processing are supposed to be crucial for this purpose. The sequence to sequence modelling strategy of deep neural networks is the traditional approach to generate a sequential list of words which are combined to represent the image. But these models suffer from the problem of high variance by not being able to generalize well on the training data.
The main focus of this thesis is to reduce the variance factor which will help in generating better captions. To achieve this, Ensemble Learning techniques have been explored, which have the reputation of solving the high variance problem that occurs in machine learning algorithms. Three different ensemble techniques namely, k-fold ensemble, bootstrap aggregation ensemble and boosting ensemble have been evaluated in this thesis. For each of these techniques, three output combination approaches have been analyzed. Extensive experiments have been conducted on the Flickr8k dataset which has a collection of 8000 images and 5 different captions for every image. The bleu score performance metric, which is considered to be the standard for evaluating natural language processing (NLP) problems, is used to evaluate the predictions. Based on this metric, the analysis shows that ensemble learning performs significantly better and generates more meaningful captions compared to any of the individual models used.
ContributorsKatpally, Harshitha (Author) / Bansal, Ajay (Thesis advisor) / Acuna, Ruben (Committee member) / Gonzalez-Sanchez, Javier (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
Description
A lot of research can be seen in the field of social robotics that majorly concentrate on various aspects of social robots including design of mechanical parts and their move- ment, cognitive speech and face recognition capabilities. Several robots have been developed with the intention of being social, like humans, without much emphasis on how human-like they actually look, in terms of expressions and behavior. Fur- thermore, a substantial disparity can be seen in the success of results of any research involving ”humanizing” the robots’ behavior, or making it behave more human-like as opposed to research into biped movement, movement of individual body parts like arms, fingers, eyeballs, or human-like appearance itself. The research in this paper in- volves understanding why the research on facial expressions of social humanoid robots fails where it is not accepted completely in the current society owing to the uncanny valley theory. This paper identifies the problem with the current facial expression research as information retrieval problem. This paper identifies the current research method in the design of facial expressions of social robots, followed by using deep learning as similarity evaluation technique to measure the humanness of the facial ex- pressions developed from the current technique and further suggests a novel solution to the facial expression design of humanoids using deep learning.
ContributorsMurthy, Shweta (Author) / Gaffar, Ashraf (Thesis advisor) / Ghazarian, Arbi (Committee member) / Gonzalez-Sanchez, Javier (Committee member) / Arizona State University (Publisher)
Created2017
Description
In today's data-driven world, every datum is connected to a large amount of data. Relational databases have been proving itself a pioneer in the field of data storage and manipulation since 1970s. But more recently they have been challenged by NoSQL graph databases in handling data models which have an inherent graphical representation. Graph databases with the ability to store physical relationships between two nodes and native graph processing technique have been doing exceptionally well in graph data storage and management for applications like recommendation engines, biological modeling, network modeling, social media applications, etc.
Instructional Module Development System (IMODS) is a web-based software system that guides STEM instructors through the complex task of curriculum design, ensures tight alignment between various components of a course (i.e., learning objectives, content, assessments), and provides relevant information about research-based pedagogical and assessment strategies. The data model of IMODS is highly connected and has an inherent graphical representation between all its entities with numerous relationships between them. This thesis focuses on developing an algorithm to determine completeness of course design developed using IMODS. As part of this research objective, the study also analyzes the data model for best fit database to run these algorithms. As part of this thesis, two separate applications abstracting the data model of IMODS have been developed - one with Neo4j (graph database) and another with PostgreSQL (relational database). The research objectives of the thesis are as follows: (i) evaluate the performance of Neo4j and PostgreSQL in handling complex queries that will be fired throughout the life cycle of the course design process; (ii) devise an algorithm to determine the completeness of a course design developed using IMODS. This thesis presents the process of creating data model for PostgreSQL and converting it into a graph data model to be abstracted by Neo4j, creating SQL and CYPHER scripts for undertaking experiments on both platforms, testing and elaborate analysis of the results and evaluation of the databases in the context of IMODS.
Instructional Module Development System (IMODS) is a web-based software system that guides STEM instructors through the complex task of curriculum design, ensures tight alignment between various components of a course (i.e., learning objectives, content, assessments), and provides relevant information about research-based pedagogical and assessment strategies. The data model of IMODS is highly connected and has an inherent graphical representation between all its entities with numerous relationships between them. This thesis focuses on developing an algorithm to determine completeness of course design developed using IMODS. As part of this research objective, the study also analyzes the data model for best fit database to run these algorithms. As part of this thesis, two separate applications abstracting the data model of IMODS have been developed - one with Neo4j (graph database) and another with PostgreSQL (relational database). The research objectives of the thesis are as follows: (i) evaluate the performance of Neo4j and PostgreSQL in handling complex queries that will be fired throughout the life cycle of the course design process; (ii) devise an algorithm to determine the completeness of a course design developed using IMODS. This thesis presents the process of creating data model for PostgreSQL and converting it into a graph data model to be abstracted by Neo4j, creating SQL and CYPHER scripts for undertaking experiments on both platforms, testing and elaborate analysis of the results and evaluation of the databases in the context of IMODS.
ContributorsSaha, Abir Lal (Author) / Bansal, Srividya (Thesis advisor) / Bansal, Ajay (Committee member) / Gonzalez-Sanchez, Javier (Committee member) / Arizona State University (Publisher)
Created2017
Description
Today, in a world of automation, the impact of Artificial Intelligence can be seen in every aspect of our lives. Starting from smart homes to self-driving cars everything is run using intelligent, adaptive technologies. In this thesis, an attempt is made to analyze the correlation between driving quality and its impact on the use of car infotainment system and vice versa and hence the driver distraction. Various internal and external driving factors have been identified to understand the dependency and seriousness of driver distraction caused due to the car infotainment system. We have seen a number UI/UX changes, speech recognition advancements in cars to reduce distraction. But reducing the number of casualties on road is still a persisting problem in hand as the cognitive load on the driver is considered to be one of the primary reasons for distractions leading to casualties. In this research, a pathway has been provided to move towards building an artificially intelligent, adaptive and interactive infotainment which is trained to behave differently by analyzing the driving quality without the intervention of the driver. The aim is to not only shift focus of the driver from screen to street view, but to also change the inherent behavior of the infotainment system based on the driving statistics at that point in time without the need for driver intervention.
ContributorsSuresh, Seema (Author) / Gaffar, Ashraf (Thesis advisor) / Sodemann, Angela (Committee member) / Gonzalez-Sanchez, Javier (Committee member) / Arizona State University (Publisher)
Created2017