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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.

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
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Description
This dissertation presents the development of structural health monitoring and prognostic health management methodologies for complex structures and systems in the field of mechanical engineering. To overcome various challenges historically associated with complex structures and systems such as complicated sensing mechanisms, noisy information, and large-size datasets, a hybrid monitoring framework

This dissertation presents the development of structural health monitoring and prognostic health management methodologies for complex structures and systems in the field of mechanical engineering. To overcome various challenges historically associated with complex structures and systems such as complicated sensing mechanisms, noisy information, and large-size datasets, a hybrid monitoring framework comprising of solid mechanics concepts and data mining technologies is developed. In such a framework, the solid mechanics simulations provide additional intuitions to data mining techniques reducing the dependence of accuracy on the training set, while the data mining approaches fuse and interpret information from the targeted system enabling the capability for real-time monitoring with efficient computation.

In the case of structural health monitoring, ultrasonic guided waves are utilized for damage identification and localization in complex composite structures. Signal processing and data mining techniques are integrated into the damage localization framework, and the converted wave modes, which are induced by the thickness variation due to the presence of delamination, are used as damage indicators. This framework has been validated through experiments and has shown sufficient accuracy in locating delamination in X-COR sandwich composites without the need of baseline information. Besides the localization of internal damage, the Gaussian process machine learning technique is integrated with finite element method as an online-offline prediction model to predict crack propagation with overloads under biaxial loading conditions; such a probabilistic prognosis model, with limited number of training examples, has shown increased accuracy over state-of-the-art techniques in predicting crack retardation behaviors induced by overloads. In the case of system level management, a monitoring framework built using a multivariate Gaussian model as basis is developed to evaluate the anomalous condition of commercial aircrafts. This method has been validated using commercial airline data and has shown high sensitivity to variations in aircraft dynamics and pilot operations. Moreover, this framework was also tested on simulated aircraft faults and its feasibility for real-time monitoring was demonstrated with sufficient computation efficiency.

This research is expected to serve as a practical addition to the existing literature while possessing the potential to be adopted in realistic engineering applications.
ContributorsLi, Guoyi (Ph.D.) (Author) / Chattopadhyay, Aditi (Thesis advisor) / Mignolet, Marc (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Yekani Fard, Masoud (Committee member) / Jiang, Hanqing (Committee member) / Arizona State University (Publisher)
Created2019
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Description
Biological and biomedical measurements, when adequately analyzed and processed, can be used to impart quantitative diagnosis during primary health care consultation to improve patient adherence to recommended treatments. For example, analyzing neural recordings from neurostimulators implanted in patients with neurological disorders can be used by a physician to adjust detrimental

Biological and biomedical measurements, when adequately analyzed and processed, can be used to impart quantitative diagnosis during primary health care consultation to improve patient adherence to recommended treatments. For example, analyzing neural recordings from neurostimulators implanted in patients with neurological disorders can be used by a physician to adjust detrimental stimulation parameters to improve treatment. As another example, biosequences, such as sequences from peptide microarrays obtained from a biological sample, can potentially provide pre-symptomatic diagnosis for infectious diseases when processed to associate antibodies to specific pathogens or infectious agents. This work proposes advanced statistical signal processing and machine learning methodologies to assess neurostimulation from neural recordings and to extract diagnostic information from biosequences.

For locating specific cognitive and behavioral information in different regions of the brain, neural recordings are processed using sequential Bayesian filtering methods to detect and estimate both the number of neural sources and their corresponding parameters. Time-frequency based feature selection algorithms are combined with adaptive machine learning approaches to suppress physiological and non-physiological artifacts present in neural recordings. Adaptive processing and unsupervised clustering methods applied to neural recordings are also used to suppress neurostimulation artifacts and classify between various behavior tasks to assess the level of neurostimulation in patients.

For pathogen detection and identification, random peptide sequences and their properties are first uniquely mapped to highly-localized signals and their corresponding parameters in the time-frequency plane. Time-frequency signal processing methods are then applied to estimate antigenic determinants or epitope candidates for detecting and identifying potential pathogens.
ContributorsMaurer, Alexander Joseph (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Bliss, Daniel (Committee member) / Chakrabarti, Chaitali (Committee member) / Kovvali, Narayan (Committee member) / Arizona State University (Publisher)
Created2016
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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

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
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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

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
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Description
Predicting nonlinear dynamical systems has been a long-standing challenge in science. This field is currently witnessing a revolution with the advent of machine learning methods. Concurrently, the analysis of dynamics in various nonlinear complex systems continues to be crucial. Guided by these directions, I conduct the following studies. Predicting critical

Predicting nonlinear dynamical systems has been a long-standing challenge in science. This field is currently witnessing a revolution with the advent of machine learning methods. Concurrently, the analysis of dynamics in various nonlinear complex systems continues to be crucial. Guided by these directions, I conduct the following studies. Predicting critical transitions and transient states in nonlinear dynamics is a complex problem. I developed a solution called parameter-aware reservoir computing, which uses machine learning to track how system dynamics change with a driving parameter. I show that the transition point can be accurately predicted while trained in a sustained functioning regime before the transition. Notably, it can also predict if the system will enter a transient state, the distribution of transient lifetimes, and their average before a final collapse, which are crucial for management. I introduce a machine-learning-based digital twin for monitoring and predicting the evolution of externally driven nonlinear dynamical systems, where reservoir computing is exploited. Extensive tests on various models, encompassing optics, ecology, and climate, verify the approach’s effectiveness. The digital twins can extrapolate unknown system dynamics, continually forecast and monitor under non-stationary external driving, infer hidden variables, adapt to different driving waveforms, and extrapolate bifurcation behaviors across varying system sizes. Integrating engineered gene circuits into host cells poses a significant challenge in synthetic biology due to circuit-host interactions, such as growth feedback. I conducted systematic studies on hundreds of circuit structures exhibiting various functionalities, and identified a comprehensive categorization of growth-induced failures. I discerned three dynamical mechanisms behind these circuit failures. Moreover, my comprehensive computations reveal a scaling law between the circuit robustness and the intensity of growth feedback. A class of circuits with optimal robustness is also identified. Chimera states, a phenomenon of symmetry-breaking in oscillator networks, traditionally have transient lifetimes that grow exponentially with system size. However, my research on high-dimensional oscillators leads to the discovery of ’short-lived’ chimera states. Their lifetime increases logarithmically with system size and decreases logarithmically with random perturbations, indicating a unique fragility. To understand these states, I use a transverse stability analysis supported by simulations.
ContributorsKong, Lingwei (Author) / Lai, Ying-Cheng (Thesis advisor) / Tian, Xiaojun (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Alkhateeb, Ahmed (Committee member) / Arizona State University (Publisher)
Created2023
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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

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
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Description
Disentangling latent spaces is an important research direction in the interpretability of unsupervised machine learning. Several recent works using deep learning are very effective at producing disentangled representations. However, in the unsupervised setting, there is no way to pre-specify which part of the latent space captures specific factors of

Disentangling latent spaces is an important research direction in the interpretability of unsupervised machine learning. Several recent works using deep learning are very effective at producing disentangled representations. However, in the unsupervised setting, there is no way to pre-specify which part of the latent space captures specific factors of variations. While this is generally a hard problem because of the non-existence of analytical expressions to capture these variations, there are certain factors like geometric

transforms that can be expressed analytically. Furthermore, in existing frameworks, the disentangled values are also not interpretable. The focus of this work is to disentangle these geometric factors of variations (which turn out to be nuisance factors for many applications) from the semantic content of the signal in an interpretable manner which in turn makes the features more discriminative. Experiments are designed to show the modularity of the approach with other disentangling strategies as well as on multiple one-dimensional (1D) and two-dimensional (2D) datasets, clearly indicating the efficacy of the proposed approach.
ContributorsKoneripalli Seetharam, Kaushik (Author) / Turaga, Pavan (Thesis advisor) / Papandreou-Suppappola, Antonia (Committee member) / Jayasuriya, Suren (Committee member) / Arizona State University (Publisher)
Created2019
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Description
Infants born before 37 weeks of pregnancy are considered to be preterm. Typically, preterm infants have to be strictly monitored since they are highly susceptible to health problems like hypoxemia (low blood oxygen level), apnea, respiratory issues, cardiac problems, neurological problems as well as an increased chance of long-term health

Infants born before 37 weeks of pregnancy are considered to be preterm. Typically, preterm infants have to be strictly monitored since they are highly susceptible to health problems like hypoxemia (low blood oxygen level), apnea, respiratory issues, cardiac problems, neurological problems as well as an increased chance of long-term health issues such as cerebral palsy, asthma and sudden infant death syndrome. One of the leading health complications in preterm infants is bradycardia - which is defined as the slower than expected heart rate, generally beating lower than 60 beats per minute. Bradycardia is often accompanied by low oxygen levels and can cause additional long term health problems in the premature infant.The implementation of a non-parametric method to predict the onset of brady- cardia is presented. This method assumes no prior knowledge of the data and uses kernel density estimation to predict the future onset of bradycardia events. The data is preprocessed, and then analyzed to detect the peaks in the ECG signals, following which different kernels are implemented to estimate the shared underlying distribu- tion of the data. The performance of the algorithm is evaluated using various metrics and the computational challenges and methods to overcome them are also discussed.
It is observed that the performance of the algorithm with regards to the kernels used are consistent with the theoretical performance of the kernel as presented in a previous work. The theoretical approach has also been automated in this work and the various implementation challenges have been addressed.
ContributorsMitra, Sinjini (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Moraffah, Bahman (Thesis advisor) / Turaga, Pavan (Committee member) / Arizona State University (Publisher)
Created2020
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Description
This research presents advances in time-synchronized phasor (i.e.,synchrophasor) estimation and imaging with very-low-frequency electric fields. Phasor measurement units measure and track dynamic systems, often power systems, using synchrophasor estimation algorithms. Two improvements to subspace-based synchrophasor estimation algorithms are shown. The first improvement is a dynamic thresholding method for accurately determining the signal subspace

This research presents advances in time-synchronized phasor (i.e.,synchrophasor) estimation and imaging with very-low-frequency electric fields. Phasor measurement units measure and track dynamic systems, often power systems, using synchrophasor estimation algorithms. Two improvements to subspace-based synchrophasor estimation algorithms are shown. The first improvement is a dynamic thresholding method for accurately determining the signal subspace when using the estimation of signal parameters via rotational invariance techniques (ESPRIT) algorithm. This improvement facilitates accurate ESPRIT-based frequency estimates of both the nominal system frequency and the frequencies of interfering signals such as harmonics or out-of-band interference signals. Proper frequency estimation of all signals present in measurement data allows for accurate least squares estimates of synchrophasors for the nominal system frequency. By including the effects of clutter signals in the synchrophasor estimate, interference from clutter signals can be excluded. The result is near-flat estimation error during nominal system frequency changes, the presence of harmonic distortion, and out-of-band interference. The second improvement reduces the computational burden of the ESPRIT frequency estimation step by showing that an optimized Eigenvalue decomposition of the measurement data can be used instead of a singular value decomposition. This research also explores a deep-learning-based inversion method for imaging objects with a uniform electric field and a 2D planar D-dot array. Using electric fields as an illumination source has seen multiple applications ranging from medical imaging to mineral deposit detection. It is shown that a planar D-dot array and deep neural network can reconstruct the electrical properties of randomized objects. A 16000-sample dataset of objects comprised of a three-by-three grid of randomized dielectric constants was generated to train a deep neural network for predicting these dielectric constants from measured field distortions. Increasingly complex imaging environments are simulated, ranging from objects in free space to objects placed in a physical cage designed to produce uniform electric fields. Finally, this research relaxes the uniform electric field constraint, showing that the volume of an opaque container can be imaged with a copper tube antenna and a 1x4 array of D-dot sensors. Real world experimental results show that it is possible to image buckets of water (targets) within a plastic shed These experiments explore the detectability of targets as a function of target placement within the shed.
ContributorsDrummond, Zachary (Author) / Allee, David R (Thesis advisor) / Claytor, Kevin E (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Aberle, James (Committee member) / Arizona State University (Publisher)
Created2021