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- Member of: ASU Electronic Theses and Dissertations
Description
The healthcare system in this country is currently unacceptable. New technologies may contribute to reducing cost and improving outcomes. Early diagnosis and treatment represents the least risky option for addressing this issue. Such a technology needs to be inexpensive, highly sensitive, highly specific, and amenable to adoption in a clinic. This thesis explores an immunodiagnostic technology based on highly scalable, non-natural sequence peptide microarrays designed to profile the humoral immune response and address the healthcare problem. The primary aim of this thesis is to explore the ability of these arrays to map continuous (linear) epitopes. I discovered that using a technique termed subsequence analysis where epitopes could be decisively mapped to an eliciting protein with high success rate. This led to the discovery of novel linear epitopes from Plasmodium falciparum (Malaria) and Treponema palladium (Syphilis), as well as validation of previously discovered epitopes in Dengue and monoclonal antibodies. Next, I developed and tested a classification scheme based on Support Vector Machines for development of a Dengue Fever diagnostic, achieving higher sensitivity and specificity than current FDA approved techniques. The software underlying this method is available for download under the BSD license. Following this, I developed a kinetic model for immunosignatures and tested it against existing data driven by previously unexplained phenomena. This model provides a framework and informs ways to optimize the platform for maximum stability and efficiency. I also explored the role of sequence composition in explaining an immunosignature binding profile, determining a strong role for charged residues that seems to have some predictive ability for disease. Finally, I developed a database, software and indexing strategy based on Apache Lucene for searching motif patterns (regular expressions) in large biological databases. These projects as a whole have advanced knowledge of how to approach high throughput immunodiagnostics and provide an example of how technology can be fused with biology in order to affect scientific and health outcomes.
ContributorsRicher, Joshua Amos (Author) / Johnston, Stephen A. (Thesis advisor) / Woodbury, Neal (Committee member) / Stafford, Phillip (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Arizona State University (Publisher)
Created2014
Description
The radar performance of detecting a target and estimating its parameters can deteriorate rapidly in the presence of high clutter. This is because radar measurements due to clutter returns can be falsely detected as if originating from the actual target. Various data association methods and multiple hypothesis filtering approaches have been considered to solve this problem. Such methods, however, can be computationally intensive for real time radar processing. This work proposes a new approach that is based on the unsupervised clustering of target and clutter detections before target tracking using particle filtering. In particular, Gaussian mixture modeling is first used to separate detections into two Gaussian distinct mixtures. Using eigenvector analysis, the eccentricity of the covariance matrices of the Gaussian mixtures are computed and compared to threshold values that are obtained a priori. The thresholding allows only target detections to be used for target tracking. Simulations demonstrate the performance of the new algorithm and compare it with using k-means for clustering instead of Gaussian mixture modeling.
ContributorsFreeman, Matthew Gregory (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Bliss, Daniel (Thesis advisor) / Chakrabarti, Chaitali (Committee member) / Arizona State University (Publisher)
Created2016
Description
Deep learning architectures have been widely explored in computer vision and have
depicted commendable performance in a variety of applications. A fundamental challenge
in training deep networks is the requirement of large amounts of labeled training
data. While gathering large quantities of unlabeled data is cheap and easy, annotating
the data is an expensive process in terms of time, labor and human expertise.
Thus, developing algorithms that minimize the human effort in training deep models
is of immense practical importance. Active learning algorithms automatically identify
salient and exemplar samples from large amounts of unlabeled data and can augment
maximal information to supervised learning models, thereby reducing the human annotation
effort in training machine learning models. The goal of this dissertation is to
fuse ideas from deep learning and active learning and design novel deep active learning
algorithms. The proposed learning methodologies explore diverse label spaces to
solve different computer vision applications. Three major contributions have emerged
from this work; (i) a deep active framework for multi-class image classication, (ii)
a deep active model with and without label correlation for multi-label image classi-
cation and (iii) a deep active paradigm for regression. Extensive empirical studies
on a variety of multi-class, multi-label and regression vision datasets corroborate the
potential of the proposed methods for real-world applications. Additional contributions
include: (i) a multimodal emotion database consisting of recordings of facial
expressions, body gestures, vocal expressions and physiological signals of actors enacting
various emotions, (ii) four multimodal deep belief network models and (iii)
an in-depth analysis of the effect of transfer of multimodal emotion features between
source and target networks on classification accuracy and training time. These related
contributions help comprehend the challenges involved in training deep learning
models and motivate the main goal of this dissertation.
depicted commendable performance in a variety of applications. A fundamental challenge
in training deep networks is the requirement of large amounts of labeled training
data. While gathering large quantities of unlabeled data is cheap and easy, annotating
the data is an expensive process in terms of time, labor and human expertise.
Thus, developing algorithms that minimize the human effort in training deep models
is of immense practical importance. Active learning algorithms automatically identify
salient and exemplar samples from large amounts of unlabeled data and can augment
maximal information to supervised learning models, thereby reducing the human annotation
effort in training machine learning models. The goal of this dissertation is to
fuse ideas from deep learning and active learning and design novel deep active learning
algorithms. The proposed learning methodologies explore diverse label spaces to
solve different computer vision applications. Three major contributions have emerged
from this work; (i) a deep active framework for multi-class image classication, (ii)
a deep active model with and without label correlation for multi-label image classi-
cation and (iii) a deep active paradigm for regression. Extensive empirical studies
on a variety of multi-class, multi-label and regression vision datasets corroborate the
potential of the proposed methods for real-world applications. Additional contributions
include: (i) a multimodal emotion database consisting of recordings of facial
expressions, body gestures, vocal expressions and physiological signals of actors enacting
various emotions, (ii) four multimodal deep belief network models and (iii)
an in-depth analysis of the effect of transfer of multimodal emotion features between
source and target networks on classification accuracy and training time. These related
contributions help comprehend the challenges involved in training deep learning
models and motivate the main goal of this dissertation.
ContributorsRanganathan, Hiranmayi (Author) / Sethuraman, Panchanathan (Thesis advisor) / Papandreou-Suppappola, Antonia (Committee member) / Li, Baoxin (Committee member) / Chakraborty, Shayok (Committee member) / Arizona State University (Publisher)
Created2018
Description
In the last 15 years, there has been a significant increase in the number of motor neural prostheses used for restoring limb function lost due to neurological disorders or accidents. The aim of this technology is to enable patients to control a motor prosthesis using their residual neural pathways (central or peripheral). Recent studies in non-human primates and humans have shown the possibility of controlling a prosthesis for accomplishing varied tasks such as self-feeding, typing, reaching, grasping, and performing fine dexterous movements. A neural decoding system comprises mainly of three components: (i) sensors to record neural signals, (ii) an algorithm to map neural recordings to upper limb kinematics and (iii) a prosthetic arm actuated by control signals generated by the algorithm. Machine learning algorithms that map input neural activity to the output kinematics (like finger trajectory) form the core of the neural decoding system. The choice of the algorithm is thus, mainly imposed by the neural signal of interest and the output parameter being decoded. The various parts of a neural decoding system are neural data, feature extraction, feature selection, and machine learning algorithm. There have been significant advances in the field of neural prosthetic applications. But there are challenges for translating a neural prosthesis from a laboratory setting to a clinical environment. To achieve a fully functional prosthetic device with maximum user compliance and acceptance, these factors need to be addressed and taken into consideration. Three challenges in developing robust neural decoding systems were addressed by exploring neural variability in the peripheral nervous system for dexterous finger movements, feature selection methods based on clinically relevant metrics and a novel method for decoding dexterous finger movements based on ensemble methods.
ContributorsPadmanaban, Subash (Author) / Greger, Bradley (Thesis advisor) / Santello, Marco (Committee member) / Helms Tillery, Stephen (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Crook, Sharon (Committee member) / Arizona State University (Publisher)
Created2017
Description
Topological methods for data analysis present opportunities for enforcing certain invariances of broad interest in computer vision: including view-point in activity analysis, articulation in shape analysis, and measurement invariance in non-linear dynamical modeling. The increasing success of these methods is attributed to the complementary information that topology provides, as well as availability of tools for computing topological summaries such as persistence diagrams. However, persistence diagrams are multi-sets of points and hence it is not straightforward to fuse them with features used for contemporary machine learning tools like deep-nets. In this paper theoretically well-grounded approaches to develop novel perturbation robust topological representations are presented, with the long-term view of making them amenable to fusion with contemporary learning architectures. The proposed representation lives on a Grassmann manifold and hence can be efficiently used in machine learning pipelines.
The proposed representation.The efficacy of the proposed descriptor was explored on three applications: view-invariant activity analysis, 3D shape analysis, and non-linear dynamical modeling. Favorable results in both high-level recognition performance and improved performance in reduction of time-complexity when compared to other baseline methods are obtained.
The proposed representation.The efficacy of the proposed descriptor was explored on three applications: view-invariant activity analysis, 3D shape analysis, and non-linear dynamical modeling. Favorable results in both high-level recognition performance and improved performance in reduction of time-complexity when compared to other baseline methods are obtained.
ContributorsThopalli, Kowshik (Author) / Turaga, Pavan Kumar (Thesis advisor) / Papandreou-Suppappola, Antonia (Committee member) / Yang, Yezhou (Committee member) / Arizona State University (Publisher)
Created2017
Description
The marked increase in the inflow of remotely sensed data from satellites have trans- formed the Earth and Space Sciences to a data rich domain creating a rich repository for domain experts to analyze. These observations shed light on a diverse array of disciplines ranging from monitoring Earth system components to planetary explo- ration by highlighting the expected trend and patterns in the data. However, the complexity of these patterns from local to global scales, coupled with the volume of this ever-growing repository necessitates advanced techniques to sequentially process the datasets to determine the underlying trends. Such techniques essentially model the observations to learn characteristic parameters of data-generating processes and highlight anomalous planetary surface observations to help domain scientists for making informed decisions. The primary challenge in defining such models arises due to the spatio-temporal variability of these processes.
This dissertation introduces models of multispectral satellite observations that sequentially learn the expected trend from the data by extracting salient features of planetary surface observations. The main objectives are to learn the temporal variability for modeling dynamic processes and to build representations of features of interest that is learned over the lifespan of an instrument. The estimated model parameters are then exploited in detecting anomalies due to changes in land surface reflectance as well as novelties in planetary surface landforms. A model switching approach is proposed that allows the selection of the best matched representation given the observations that is designed to account for rate of time-variability in land surface. The estimated parameters are exploited to design a change detector, analyze the separability of change events, and form an expert-guided representation of planetary landforms for prioritizing the retrieval of scientifically relevant observations with both onboard and post-downlink applications.
This dissertation introduces models of multispectral satellite observations that sequentially learn the expected trend from the data by extracting salient features of planetary surface observations. The main objectives are to learn the temporal variability for modeling dynamic processes and to build representations of features of interest that is learned over the lifespan of an instrument. The estimated model parameters are then exploited in detecting anomalies due to changes in land surface reflectance as well as novelties in planetary surface landforms. A model switching approach is proposed that allows the selection of the best matched representation given the observations that is designed to account for rate of time-variability in land surface. The estimated parameters are exploited to design a change detector, analyze the separability of change events, and form an expert-guided representation of planetary landforms for prioritizing the retrieval of scientifically relevant observations with both onboard and post-downlink applications.
ContributorsChakraborty, Srija (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Christensen, Philip R. (Philip Russel) (Thesis advisor) / Richmond, Christ (Committee member) / Maurer, Alexander (Committee member) / Arizona State University (Publisher)
Created2019
Description
Robotic lower limb prostheses provide new opportunities to help transfemoral amputees regain mobility. However, their application is impeded by that the impedance control parameters need to be tuned and optimized manually by prosthetists for each individual user in different task environments. Reinforcement learning (RL) is capable of automatically learning from interacting with the environment. It becomes a natural candidate to replace human prosthetists to customize the control parameters. However, neither traditional RL approaches nor the popular deep RL approaches are readily suitable for learning with limited number of samples and samples with large variations. This dissertation aims to explore new RL based adaptive solutions that are data-efficient for controlling robotic prostheses.
This dissertation begins by proposing a new flexible policy iteration (FPI) framework. To improve sample efficiency, FPI can utilize either on-policy or off-policy learning strategy, can learn from either online or offline data, and can even adopt exiting knowledge of an external critic. Approximate convergence to Bellman optimal solutions are guaranteed under mild conditions. Simulation studies validated that FPI was data efficient compared to several established RL methods. Furthermore, a simplified version of FPI was implemented to learn from offline data, and then the learned policy was successfully tested for tuning the control parameters online on a human subject.
Next, the dissertation discusses RL control with information transfer (RL-IT), or knowledge-guided RL (KG-RL), which is motivated to benefit from transferring knowledge acquired from one subject to another. To explore its feasibility, knowledge was extracted from data measurements of able-bodied (AB) subjects, and transferred to guide Q-learning control for an amputee in OpenSim simulations. This result again demonstrated that data and time efficiency were improved using previous knowledge.
While the present study is new and promising, there are still many open questions to be addressed in future research. To account for human adaption, the learning control objective function may be designed to incorporate human-prosthesis performance feedback such as symmetry, user comfort level and satisfaction, and user energy consumption. To make the RL based control parameter tuning practical in real life, it should be further developed and tested in different use environments, such as from level ground walking to stair ascending or descending, and from walking to running.
This dissertation begins by proposing a new flexible policy iteration (FPI) framework. To improve sample efficiency, FPI can utilize either on-policy or off-policy learning strategy, can learn from either online or offline data, and can even adopt exiting knowledge of an external critic. Approximate convergence to Bellman optimal solutions are guaranteed under mild conditions. Simulation studies validated that FPI was data efficient compared to several established RL methods. Furthermore, a simplified version of FPI was implemented to learn from offline data, and then the learned policy was successfully tested for tuning the control parameters online on a human subject.
Next, the dissertation discusses RL control with information transfer (RL-IT), or knowledge-guided RL (KG-RL), which is motivated to benefit from transferring knowledge acquired from one subject to another. To explore its feasibility, knowledge was extracted from data measurements of able-bodied (AB) subjects, and transferred to guide Q-learning control for an amputee in OpenSim simulations. This result again demonstrated that data and time efficiency were improved using previous knowledge.
While the present study is new and promising, there are still many open questions to be addressed in future research. To account for human adaption, the learning control objective function may be designed to incorporate human-prosthesis performance feedback such as symmetry, user comfort level and satisfaction, and user energy consumption. To make the RL based control parameter tuning practical in real life, it should be further developed and tested in different use environments, such as from level ground walking to stair ascending or descending, and from walking to running.
ContributorsGao, Xiang (Author) / Si, Jennie (Thesis advisor) / Huang, He Helen (Committee member) / Santello, Marco (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Arizona State University (Publisher)
Created2020
Description
The problem of multiple object tracking seeks to jointly estimate the time-varying cardinality and trajectory of each object. There are numerous challenges that are encountered in tracking multiple objects including a time-varying number of measurements, under varying constraints, and environmental conditions. In this thesis, the proposed statistical methods integrate the use of physical-based models with Bayesian nonparametric methods to address the main challenges in a tracking problem. In particular, Bayesian nonparametric methods are exploited to efficiently and robustly infer object identity and learn time-dependent cardinality; together with Bayesian inference methods, they are also used to associate measurements to objects and estimate the trajectory of objects. These methods differ from the current methods to the core as the existing methods are mainly based on random finite set theory.
The first contribution proposes dependent nonparametric models such as the dependent Dirichlet process and the dependent Pitman-Yor process to capture the inherent time-dependency in the problem at hand. These processes are used as priors for object state distributions to learn dependent information between previous and current time steps. Markov chain Monte Carlo sampling methods exploit the learned information to sample from posterior distributions and update the estimated object parameters.
The second contribution proposes a novel, robust, and fast nonparametric approach based on a diffusion process over infinite random trees to infer information on object cardinality and trajectory. This method follows the hierarchy induced by objects entering and leaving a scene and the time-dependency between unknown object parameters. Markov chain Monte Carlo sampling methods integrate the prior distributions over the infinite random trees with time-dependent diffusion processes to update object states.
The third contribution develops the use of hierarchical models to form a prior for statistically dependent measurements in a single object tracking setup. Dependency among the sensor measurements provides extra information which is incorporated to achieve the optimal tracking performance. The hierarchical Dirichlet process as a prior provides the required flexibility to do inference. Bayesian tracker is integrated with the hierarchical Dirichlet process prior to accurately estimate the object trajectory.
The fourth contribution proposes an approach to model both the multiple dependent objects and multiple dependent measurements. This approach integrates the dependent Dirichlet process modeling over the dependent object with the hierarchical Dirichlet process modeling of the measurements to fully capture the dependency among both object and measurements. Bayesian nonparametric models can successfully associate each measurement to the corresponding object and exploit dependency among them to more accurately infer the trajectory of objects. Markov chain Monte Carlo methods amalgamate the dependent Dirichlet process with the hierarchical Dirichlet process to infer the object identity and object cardinality.
Simulations are exploited to demonstrate the improvement in multiple object tracking performance when compared to approaches that are developed based on random finite set theory.
The first contribution proposes dependent nonparametric models such as the dependent Dirichlet process and the dependent Pitman-Yor process to capture the inherent time-dependency in the problem at hand. These processes are used as priors for object state distributions to learn dependent information between previous and current time steps. Markov chain Monte Carlo sampling methods exploit the learned information to sample from posterior distributions and update the estimated object parameters.
The second contribution proposes a novel, robust, and fast nonparametric approach based on a diffusion process over infinite random trees to infer information on object cardinality and trajectory. This method follows the hierarchy induced by objects entering and leaving a scene and the time-dependency between unknown object parameters. Markov chain Monte Carlo sampling methods integrate the prior distributions over the infinite random trees with time-dependent diffusion processes to update object states.
The third contribution develops the use of hierarchical models to form a prior for statistically dependent measurements in a single object tracking setup. Dependency among the sensor measurements provides extra information which is incorporated to achieve the optimal tracking performance. The hierarchical Dirichlet process as a prior provides the required flexibility to do inference. Bayesian tracker is integrated with the hierarchical Dirichlet process prior to accurately estimate the object trajectory.
The fourth contribution proposes an approach to model both the multiple dependent objects and multiple dependent measurements. This approach integrates the dependent Dirichlet process modeling over the dependent object with the hierarchical Dirichlet process modeling of the measurements to fully capture the dependency among both object and measurements. Bayesian nonparametric models can successfully associate each measurement to the corresponding object and exploit dependency among them to more accurately infer the trajectory of objects. Markov chain Monte Carlo methods amalgamate the dependent Dirichlet process with the hierarchical Dirichlet process to infer the object identity and object cardinality.
Simulations are exploited to demonstrate the improvement in multiple object tracking performance when compared to approaches that are developed based on random finite set theory.
ContributorsMoraffah, Bahman (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Bliss, Daniel W. (Committee member) / Richmond, Christ D. (Committee member) / Dasarathy, Gautam (Committee member) / Arizona State University (Publisher)
Created2019
Description
The human brain controls a person's actions and reactions. In this study, the main objective is to quantify reaction time towards a change of visual event and figuring out the inherent relationship between response time and corresponding brain activities. Furthermore, which parts of the human brain are responsible for the reaction time is also of interest. As electroencephalogram (EEG) signals are proportional to the change of brain functionalities with time, EEG signals from different locations of the brain are used as indicators of brain activities. As the different channels are from different parts of our brain, identifying most relevant channels can provide the idea of responsible brain locations. In this study, response time is estimated using EEG signal features from time, frequency and time-frequency domain. Regression-based estimation using the full data-set results in RMSE (Root Mean Square Error) of 99.5 milliseconds and a correlation value of 0.57. However, the addition of non-EEG features with the existing features gives RMSE of 101.7 ms and a correlation value of 0.58. Using the same analysis with a custom data-set provides RMSE of 135.7 milliseconds and a correlation value of 0.69. Classification-based estimation provides 79% & 72% of accuracy for binary and 3-class classication respectively. Classification of extremes (high-low) results in 95% of accuracy. Combining recursive feature elimination, tree-based feature importance, and mutual feature information method, important channels, and features are isolated based on the best result. As human response time is not solely dependent on brain activities, it requires additional information about the subject to improve the reaction time estimation.
ContributorsChowdhury, Mohammad Samin Nur (Author) / Bliss, Daniel W (Thesis advisor) / Papandreou-Suppappola, Antonia (Committee member) / Brewer, Gene (Committee member) / Arizona State University (Publisher)
Created2019
Description
Signal compressed using classical compression methods can be acquired using brute force (i.e. searching for non-zero entries in component-wise). However, sparse solutions require combinatorial searches of high computations. In this thesis, instead, two Bayesian approaches are considered to recover a sparse vector from underdetermined noisy measurements. The first is constructed using a Bernoulli-Gaussian (BG) prior distribution and is assumed to be the true generative model. The second is constructed using a Gamma-Normal (GN) prior distribution and is, therefore, a different (i.e. misspecified) model. To estimate the posterior distribution for the correctly specified scenario, an algorithm based on generalized approximated message passing (GAMP) is constructed, while an algorithm based on sparse Bayesian learning (SBL) is used for the misspecified scenario. Recovering sparse signal using Bayesian framework is one class of algorithms to solve the sparse problem. All classes of algorithms aim to get around the high computations associated with the combinatorial searches. Compressive sensing (CS) is a widely-used terminology attributed to optimize the sparse problem and its applications. Applications such as magnetic resonance imaging (MRI), image acquisition in radar imaging, and facial recognition. In CS literature, the target vector can be recovered either by optimizing an objective function using point estimation, or recovering a distribution of the sparse vector using Bayesian estimation. Although Bayesian framework provides an extra degree of freedom to assume a distribution that is directly applicable to the problem of interest, it is hard to find a theoretical guarantee of convergence. This limitation has shifted some of researches to use a non-Bayesian framework. This thesis tries to close this gab by proposing a Bayesian framework with a suggested theoretical bound for the assumed, not necessarily correct, distribution. In the simulation study, a general lower Bayesian Cram\'er-Rao bound (BCRB) bound is extracted along with misspecified Bayesian Cram\'er-Rao bound (MBCRB) for GN model. Both bounds are validated using mean square error (MSE) performances of the aforementioned algorithms. Also, a quantification of the performance in terms of gains versus losses is introduced as one main finding of this report.
ContributorsAlhowaish, Abdulhakim (Author) / Richmond, Christ D (Thesis advisor) / Papandreou-Suppappola, Antonia (Committee member) / Sankar, Lalitha (Committee member) / Arizona State University (Publisher)
Created2019