Theses and Dissertations
This collection includes both ASU Theses and Dissertations, submitted by graduate students, and the Barrett, Honors College theses submitted by undergraduate students.
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- Creators: Davulcu, Hasan
- Creators: Turaga, Pavan
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
As the size and scope of valuable datasets has exploded across many industries and fields of research in recent years, an increasingly diverse audience has sought out effective tools for their large-scale data analytics needs. Over this period, machine learning researchers have also been very prolific in designing improved algorithms which are capable of finding the hidden structure within these datasets. As consumers of popular Big Data frameworks have sought to apply and benefit from these improved learning algorithms, the problems encountered with the frameworks have motivated a new generation of Big Data tools to address the shortcomings of the previous generation. One important example of this is the improved performance in the newer tools with the large class of machine learning algorithms which are highly iterative in nature. In this thesis project, I set about to implement a low-rank matrix completion algorithm (as an example of a highly iterative algorithm) within a popular Big Data framework, and to evaluate its performance processing the Netflix Prize dataset. I begin by describing several approaches which I attempted, but which did not perform adequately. These include an implementation of the Singular Value Thresholding (SVT) algorithm within the Apache Mahout framework, which runs on top of the Apache Hadoop MapReduce engine. I then describe an approach which uses the Divide-Factor-Combine (DFC) algorithmic framework to parallelize the state-of-the-art low-rank completion algorithm Orthogoal Rank-One Matrix Pursuit (OR1MP) within the Apache Spark engine. I describe the results of a series of tests running this implementation with the Netflix dataset on clusters of various sizes, with various degrees of parallelism. For these experiments, I utilized the Amazon Elastic Compute Cloud (EC2) web service. In the final analysis, I conclude that the Spark DFC + OR1MP implementation does indeed produce competitive results, in both accuracy and performance. In particular, the Spark implementation performs nearly as well as the MATLAB implementation of OR1MP without any parallelism, and improves performance to a significant degree as the parallelism increases. In addition, the experience demonstrates how Spark's flexible programming model makes it straightforward to implement this parallel and iterative machine learning algorithm.
ContributorsKrouse, Brian (Author) / Ye, Jieping (Thesis advisor) / Liu, Huan (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2014
Description
In contemporary society, sustainability and public well-being have been pressing challenges. Some of the important questions are:how can sustainable practices, such as reducing carbon emission, be encouraged? , How can a healthy lifestyle be maintained?Even though individuals are interested, they are unable to adopt these behaviors due to resource constraints. Developing a framework to enable cooperative behavior adoption and to sustain it for a long period of time is a major challenge. As a part of developing this framework, I am focusing on methods to understand behavior diffusion over time. Facilitating behavior diffusion with resource constraints in a large population is qualitatively different from promoting cooperation in small groups. Previous work in social sciences has derived conditions for sustainable cooperative behavior in small homogeneous groups. However, how groups of individuals having resource constraint co-operate over extended periods of time is not well understood, and is the focus of my thesis. I develop models to analyze behavior diffusion over time through the lens of epidemic models with the condition that individuals have resource constraint. I introduce an epidemic model SVRS ( Susceptible-Volatile-Recovered-Susceptible) to accommodate multiple behavior adoption. I investigate the longitudinal effects of behavior diffusion by varying different properties of an individual such as resources,threshold and cost of behavior adoption. I also consider how behavior adoption of an individual varies with her knowledge of global adoption. I evaluate my models on several synthetic topologies like complete regular graph, preferential attachment and small-world and make some interesting observations. Periodic injection of early adopters can help in boosting the spread of behaviors and sustain it for a longer period of time. Also, behavior propagation for the classical epidemic model SIRS (Susceptible-Infected-Recovered-Susceptible) does not continue for an infinite period of time as per conventional wisdom. One interesting future direction is to investigate how behavior adoption is affected when number of individuals in a network changes. The affects on behavior adoption when availability of behavior changes with time can also be examined.
ContributorsDey, Anindita (Author) / Sundaram, Hari (Thesis advisor) / Turaga, Pavan (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2013
Description
Continuous monitoring of sensor data from smart phones to identify human activities and gestures, puts a heavy load on the smart phone's power consumption. In this research study, the non-Euclidean geometry of the rich sensor data obtained from the user's smart phone is utilized to perform compressive analysis and efficient classification of human activities by employing machine learning techniques. We are interested in the generalization of classical tools for signal approximation to newer spaces, such as rotation data, which is best studied in a non-Euclidean setting, and its application to activity analysis. Attributing to the non-linear nature of the rotation data space, which involve a heavy overload on the smart phone's processor and memory as opposed to feature extraction on the Euclidean space, indexing and compaction of the acquired sensor data is performed prior to feature extraction, to reduce CPU overhead and thereby increase the lifetime of the battery with a little loss in recognition accuracy of the activities. The sensor data represented as unit quaternions, is a more intrinsic representation of the orientation of smart phone compared to Euler angles (which suffers from Gimbal lock problem) or the computationally intensive rotation matrices. Classification algorithms are employed to classify these manifold sequences in the non-Euclidean space. By performing customized indexing (using K-means algorithm) of the evolved manifold sequences before feature extraction, considerable energy savings is achieved in terms of smart phone's battery life.
ContributorsSivakumar, Aswin (Author) / Turaga, Pavan (Thesis advisor) / Spanias, Andreas (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Arizona State University (Publisher)
Created2014
Description
Software has a great impact on the energy efficiency of any computing system--it can manage the components of a system efficiently or inefficiently. The impact of software is amplified in the context of a wearable computing system used for activity recognition. The design space this platform opens up is immense and encompasses sensors, feature calculations, activity classification algorithms, sleep schedules, and transmission protocols. Design choices in each of these areas impact energy use, overall accuracy, and usefulness of the system. This thesis explores methods software can influence the trade-off between energy consumption and system accuracy. In general the more energy a system consumes the more accurate will be. We explore how finding the transitions between human activities is able to reduce the energy consumption of such systems without reducing much accuracy. We introduce the Log-likelihood Ratio Test as a method to detect transitions, and explore how choices of sensor, feature calculations, and parameters concerning time segmentation affect the accuracy of this method. We discovered an approximate 5X increase in energy efficiency could be achieved with only a 5% decrease in accuracy. We also address how a system's sleep mode, in which the processor enters a low-power state and sensors are turned off, affects a wearable computing platform that does activity recognition. We discuss the energy trade-offs in each stage of the activity recognition process. We find that careful analysis of these parameters can result in great increases in energy efficiency if small compromises in overall accuracy can be tolerated. We call this the ``Great Compromise.'' We found a 6X increase in efficiency with a 7% decrease in accuracy. We then consider how wireless transmission of data affects the overall energy efficiency of a wearable computing platform. We find that design decisions such as feature calculations and grouping size have a great impact on the energy consumption of the system because of the amount of data that is stored and transmitted. For example, storing and transmitting vector-based features such as FFT or DCT do not compress the signal and would use more energy than storing and transmitting the raw signal. The effect of grouping size on energy consumption depends on the feature. For scalar features energy consumption is proportional in the inverse of grouping size, so it's reduced as grouping size goes up. For features that depend on the grouping size, such as FFT, energy increases with the logarithm of grouping size, so energy consumption increases slowly as grouping size increases. We find that compressing data through activity classification and transition detection significantly reduces energy consumption and that the energy consumed for the classification overhead is negligible compared to the energy savings from data compression. We provide mathematical models of energy usage and data generation, and test our ideas using a mobile computing platform, the Texas Instruments Chronos watch.
ContributorsBoyd, Jeffrey Michael (Author) / Sundaram, Hari (Thesis advisor) / Li, Baoxin (Thesis advisor) / Shrivastava, Aviral (Committee member) / Turaga, Pavan (Committee member) / Arizona State University (Publisher)
Created2014
Description
Multidimensional data have various representations. Thanks to their simplicity in modeling multidimensional data and the availability of various mathematical tools (such as tensor decompositions) that support multi-aspect analysis of such data, tensors are increasingly being used in many application domains including scientific data management, sensor data management, and social network data analysis. Relational model, on the other hand, enables semantic manipulation of data using relational operators, such as projection, selection, Cartesian-product, and set operators. For many multidimensional data applications, tensor operations as well as relational operations need to be supported throughout the data life cycle. In this thesis, we introduce a tensor-based relational data model (TRM), which enables both tensor- based data analysis and relational manipulations of multidimensional data, and define tensor-relational operations on this model. Then we introduce a tensor-relational data management system, so called, TensorDB. TensorDB is based on TRM, which brings together relational algebraic operations (for data manipulation and integration) and tensor algebraic operations (for data analysis). We develop optimization strategies for tensor-relational operations in both in-memory and in-database TensorDB. The goal of the TRM and TensorDB is to serve as a single environment that supports the entire life cycle of data; that is, data can be manipulated, integrated, processed, and analyzed.
ContributorsKim, Mijung (Author) / Candan, K. Selcuk (Thesis advisor) / Davulcu, Hasan (Committee member) / Sundaram, Hari (Committee member) / Ye, Jieping (Committee member) / Arizona State University (Publisher)
Created2014
Description
Head movement is known to have the benefit of improving the accuracy of sound localization for humans and animals. Marmoset is a small bodied New World monkey species and it has become an emerging model for studying the auditory functions. This thesis aims to detect the horizontal and vertical rotation of head movement in marmoset monkeys.
Experiments were conducted in a sound-attenuated acoustic chamber. Head movement of marmoset monkey was studied under various auditory and visual stimulation conditions. With increasing complexity, these conditions are (1) idle, (2) sound-alone, (3) sound and visual signals, and (4) alert signal by opening and closing of the chamber door. All of these conditions were tested with either house light on or off. Infra-red camera with a frame rate of 90 Hz was used to capture of the head movement of monkeys. To assist the signal detection, two circular markers were attached to the top of monkey head. The data analysis used an image-based marker detection scheme. Images were processed using the Computation Vision Toolbox in Matlab. The markers and their positions were detected using blob detection techniques. Based on the frame-by-frame information of marker positions, the angular position, velocity and acceleration were extracted in horizontal and vertical planes. Adaptive Otsu Thresholding, Kalman filtering and bound setting for marker properties were used to overcome a number of challenges encountered during this analysis, such as finding image segmentation threshold, continuously tracking markers during large head movement, and false alarm detection.
The results show that the blob detection method together with Kalman filtering yielded better performances than other image based techniques like optical flow and SURF features .The median of the maximal head turn in the horizontal plane was in the range of 20 to 70 degrees and the median of the maximal velocity in horizontal plane was in the range of a few hundreds of degrees per second. In comparison, the natural alert signal - door opening and closing - evoked the faster head turns than other stimulus conditions. These results suggest that behaviorally relevant stimulus such as alert signals evoke faster head-turn responses in marmoset monkeys.
Experiments were conducted in a sound-attenuated acoustic chamber. Head movement of marmoset monkey was studied under various auditory and visual stimulation conditions. With increasing complexity, these conditions are (1) idle, (2) sound-alone, (3) sound and visual signals, and (4) alert signal by opening and closing of the chamber door. All of these conditions were tested with either house light on or off. Infra-red camera with a frame rate of 90 Hz was used to capture of the head movement of monkeys. To assist the signal detection, two circular markers were attached to the top of monkey head. The data analysis used an image-based marker detection scheme. Images were processed using the Computation Vision Toolbox in Matlab. The markers and their positions were detected using blob detection techniques. Based on the frame-by-frame information of marker positions, the angular position, velocity and acceleration were extracted in horizontal and vertical planes. Adaptive Otsu Thresholding, Kalman filtering and bound setting for marker properties were used to overcome a number of challenges encountered during this analysis, such as finding image segmentation threshold, continuously tracking markers during large head movement, and false alarm detection.
The results show that the blob detection method together with Kalman filtering yielded better performances than other image based techniques like optical flow and SURF features .The median of the maximal head turn in the horizontal plane was in the range of 20 to 70 degrees and the median of the maximal velocity in horizontal plane was in the range of a few hundreds of degrees per second. In comparison, the natural alert signal - door opening and closing - evoked the faster head turns than other stimulus conditions. These results suggest that behaviorally relevant stimulus such as alert signals evoke faster head-turn responses in marmoset monkeys.
ContributorsSimhadri, Sravanthi (Author) / Zhou, Yi (Thesis advisor) / Turaga, Pavan (Thesis advisor) / Berisha, Visar (Committee member) / Arizona State University (Publisher)
Created2014
Description
Twitter is a micro-blogging platform where the users can be social, informational or both. In certain cases, users generate tweets that have no "hashtags" or "@mentions"; we call it an orphaned tweet. The user will be more interested to find more "context" of an orphaned tweet presumably to engage with his/her friend on that topic. Finding context for an Orphaned tweet manually is challenging because of larger social graph of a user , the enormous volume of tweets generated per second, topic diversity, and limited information from tweet length of 140 characters. To help the user to get the context of an orphaned tweet, this thesis aims at building a hashtag recommendation system called TweetSense, to suggest hashtags as a context or metadata for the orphaned tweets. This in turn would increase user's social engagement and impact Twitter to maintain its monthly active online users in its social network. In contrast to other existing systems, this hashtag recommendation system recommends personalized hashtags by exploiting the social signals of users in Twitter. The novelty with this system is that it emphasizes on selecting the suitable candidate set of hashtags from the related tweets of user's social graph (timeline).The system then rank them based on the combination of features scores computed from their tweet and user related features. It is evaluated based on its ability to predict suitable hashtags for a random sample of tweets whose existing hashtags are deliberately removed for evaluation. I present a detailed internal empirical evaluation of TweetSense, as well as an external evaluation in comparison with current state of the art method.
ContributorsVijayakumar, Manikandan (Author) / Kambhampati, Subbarao (Thesis advisor) / Liu, Huan (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2014
Description
Many learning models have been proposed for various tasks in visual computing. Popular examples include hidden Markov models and support vector machines. Recently, sparse-representation-based learning methods have attracted a lot of attention in the computer vision field, largely because of their impressive performance in many applications. In the literature, many of such sparse learning methods focus on designing or application of some learning techniques for certain feature space without much explicit consideration on possible interaction between the underlying semantics of the visual data and the employed learning technique. Rich semantic information in most visual data, if properly incorporated into algorithm design, should help achieving improved performance while delivering intuitive interpretation of the algorithmic outcomes. My study addresses the problem of how to explicitly consider the semantic information of the visual data in the sparse learning algorithms. In this work, we identify four problems which are of great importance and broad interest to the community. Specifically, a novel approach is proposed to incorporate label information to learn a dictionary which is not only reconstructive but also discriminative; considering the formation process of face images, a novel image decomposition approach for an ensemble of correlated images is proposed, where a subspace is built from the decomposition and applied to face recognition; based on the observation that, the foreground (or salient) objects are sparse in input domain and the background is sparse in frequency domain, a novel and efficient spatio-temporal saliency detection algorithm is proposed to identify the salient regions in video; and a novel hidden Markov model learning approach is proposed by utilizing a sparse set of pairwise comparisons among the data, which is easier to obtain and more meaningful, consistent than tradition labels, in many scenarios, e.g., evaluating motion skills in surgical simulations. In those four problems, different types of semantic information are modeled and incorporated in designing sparse learning algorithms for the corresponding visual computing tasks. Several real world applications are selected to demonstrate the effectiveness of the proposed methods, including, face recognition, spatio-temporal saliency detection, abnormality detection, spatio-temporal interest point detection, motion analysis and emotion recognition. In those applications, data of different modalities are involved, ranging from audio signal, image to video. Experiments on large scale real world data with comparisons to state-of-art methods confirm the proposed approaches deliver salient advantages, showing adding those semantic information dramatically improve the performances of the general sparse learning methods.
ContributorsZhang, Qiang (Author) / Li, Baoxin (Thesis advisor) / Turaga, Pavan (Committee member) / Wang, Yalin (Committee member) / Ye, Jieping (Committee member) / Arizona State University (Publisher)
Created2014
Description
Audio signals, such as speech and ambient sounds convey rich information pertaining to a user’s activity, mood or intent. Enabling machines to understand this contextual information is necessary to bridge the gap in human-machine interaction. This is challenging due to its subjective nature, hence, requiring sophisticated techniques. This dissertation presents a set of computational methods, that generalize well across different conditions, for speech-based applications involving emotion recognition and keyword detection, and ambient sounds-based applications such as lifelogging.
The expression and perception of emotions varies across speakers and cultures, thus, determining features and classification methods that generalize well to different conditions is strongly desired. A latent topic models-based method is proposed to learn supra-segmental features from low-level acoustic descriptors. The derived features outperform state-of-the-art approaches over multiple databases. Cross-corpus studies are conducted to determine the ability of these features to generalize well across different databases. The proposed method is also applied to derive features from facial expressions; a multi-modal fusion overcomes the deficiencies of a speech only approach and further improves the recognition performance.
Besides affecting the acoustic properties of speech, emotions have a strong influence over speech articulation kinematics. A learning approach, which constrains a classifier trained over acoustic descriptors, to also model articulatory data is proposed here. This method requires articulatory information only during the training stage, thus overcoming the challenges inherent to large-scale data collection, while simultaneously exploiting the correlations between articulation kinematics and acoustic descriptors to improve the accuracy of emotion recognition systems.
Identifying context from ambient sounds in a lifelogging scenario requires feature extraction, segmentation and annotation techniques capable of efficiently handling long duration audio recordings; a complete framework for such applications is presented. The performance is evaluated on real world data and accompanied by a prototypical Android-based user interface.
The proposed methods are also assessed in terms of computation and implementation complexity. Software and field programmable gate array based implementations are considered for emotion recognition, while virtual platforms are used to model the complexities of lifelogging. The derived metrics are used to determine the feasibility of these methods for applications requiring real-time capabilities and low power consumption.
The expression and perception of emotions varies across speakers and cultures, thus, determining features and classification methods that generalize well to different conditions is strongly desired. A latent topic models-based method is proposed to learn supra-segmental features from low-level acoustic descriptors. The derived features outperform state-of-the-art approaches over multiple databases. Cross-corpus studies are conducted to determine the ability of these features to generalize well across different databases. The proposed method is also applied to derive features from facial expressions; a multi-modal fusion overcomes the deficiencies of a speech only approach and further improves the recognition performance.
Besides affecting the acoustic properties of speech, emotions have a strong influence over speech articulation kinematics. A learning approach, which constrains a classifier trained over acoustic descriptors, to also model articulatory data is proposed here. This method requires articulatory information only during the training stage, thus overcoming the challenges inherent to large-scale data collection, while simultaneously exploiting the correlations between articulation kinematics and acoustic descriptors to improve the accuracy of emotion recognition systems.
Identifying context from ambient sounds in a lifelogging scenario requires feature extraction, segmentation and annotation techniques capable of efficiently handling long duration audio recordings; a complete framework for such applications is presented. The performance is evaluated on real world data and accompanied by a prototypical Android-based user interface.
The proposed methods are also assessed in terms of computation and implementation complexity. Software and field programmable gate array based implementations are considered for emotion recognition, while virtual platforms are used to model the complexities of lifelogging. The derived metrics are used to determine the feasibility of these methods for applications requiring real-time capabilities and low power consumption.
ContributorsShah, Mohit (Author) / Spanias, Andreas (Thesis advisor) / Chakrabarti, Chaitali (Thesis advisor) / Berisha, Visar (Committee member) / Turaga, Pavan (Committee member) / Arizona State University (Publisher)
Created2015