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Description
Continuous monitoring in the adequate temporal and spatial scale is necessary for a better understanding of environmental variations. But field deployments of molecular biological analysis platforms in that scale are currently hindered because of issues with power, throughput and automation. Currently, such analysis is performed by the collection of large

Continuous monitoring in the adequate temporal and spatial scale is necessary for a better understanding of environmental variations. But field deployments of molecular biological analysis platforms in that scale are currently hindered because of issues with power, throughput and automation. Currently, such analysis is performed by the collection of large sample volumes from over a wide area and transporting them to laboratory testing facilities, which fail to provide any real-time information. This dissertation evaluates the systems currently utilized for in-situ field analyses and the issues hampering the successful deployment of such bioanalytial instruments for environmental applications. The design and development of high throughput, low power, and autonomous Polymerase Chain Reaction (PCR) instruments, amenable for portable field operations capable of providing quantitative results is presented here as part of this dissertation. A number of novel innovations have been reported here as part of this work in microfluidic design, PCR thermocycler design, optical design and systems integration. Emulsion microfluidics in conjunction with fluorinated oils and Teflon tubing have been used for the fluidic module that reduces cross-contamination eliminating the need for disposable components or constant cleaning. A cylindrical heater has been designed with the tubing wrapped around fixed temperature zones enabling continuous operation. Fluorescence excitation and detection have been achieved by using a light emitting diode (LED) as the excitation source and a photomultiplier tube (PMT) as the detector. Real-time quantitative PCR results were obtained by using multi-channel fluorescence excitation and detection using LED, optical fibers and a 64-channel multi-anode PMT for measuring continuous real-time fluorescence. The instrument was evaluated by comparing the results obtained with those obtained from a commercial instrument and found to be comparable. To further improve the design and enhance its field portability, this dissertation also presents a framework for the instrumentation necessary for a portable digital PCR platform to achieve higher throughputs with lower power. Both systems were designed such that it can easily couple with any upstream platform capable of providing nucleic acid for analysis using standard fluidic connections. Consequently, these instruments can be used not only in environmental applications, but portable diagnostics applications as well.
ContributorsRay, Tathagata (Author) / Youngbull, Cody (Thesis advisor) / Goryll, Michael (Thesis advisor) / Blain Christen, Jennifer (Committee member) / Yu, Hongyu (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Distributed estimation uses many inexpensive sensors to compose an accurate estimate of a given parameter. It is frequently implemented using wireless sensor networks. There have been several studies on optimizing power allocation in wireless sensor networks used for distributed estimation, the vast majority of which assume linear radio-frequency amplifiers. Linear

Distributed estimation uses many inexpensive sensors to compose an accurate estimate of a given parameter. It is frequently implemented using wireless sensor networks. There have been several studies on optimizing power allocation in wireless sensor networks used for distributed estimation, the vast majority of which assume linear radio-frequency amplifiers. Linear amplifiers are inherently inefficient, so in this dissertation nonlinear amplifiers are examined to gain efficiency while operating distributed sensor networks. This research presents a method to boost efficiency by operating the amplifiers in the nonlinear region of operation. Operating amplifiers nonlinearly presents new challenges. First, nonlinear amplifier characteristics change across manufacturing process variation, temperature, operating voltage, and aging. Secondly, the equations conventionally used for estimators and performance expectations in linear amplify-and-forward systems fail. To compensate for the first challenge, predistortion is utilized not to linearize amplifiers but rather to force them to fit a common nonlinear limiting amplifier model close to the inherent amplifier performance. This minimizes the power impact and the training requirements for predistortion. Second, new estimators are required that account for transmitter nonlinearity. This research derives analytically and confirms via simulation new estimators and performance expectation equations for use in nonlinear distributed estimation. An additional complication when operating nonlinear amplifiers in a wireless environment is the influence of varied and potentially unknown channel gains. The impact of these varied gains and both measurement and channel noise sources on estimation performance are analyzed in this paper. Techniques for minimizing the estimate variance are developed. It is shown that optimizing transmitter power allocation to minimize estimate variance for the most-compressed parameter measurement is equivalent to the problem for linear sensors. Finally, a method for operating distributed estimation in a multipath environment is presented that is capable of developing robust estimates for a wide range of Rician K-factors. This dissertation demonstrates that implementing distributed estimation using nonlinear sensors can boost system efficiency and is compatible with existing techniques from the literature for boosting efficiency at the system level via sensor power allocation. Nonlinear transmitters work best when channel gains are known and channel noise and receiver noise levels are low.
ContributorsSantucci, Robert (Author) / Spanias, Andreas (Thesis advisor) / Tepedelenlioðlu, Cihan (Committee member) / Bakkaloglu, Bertan (Committee member) / Tsakalis, Kostas (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Radio frequency (RF) transceivers require a disproportionately high effort in terms of test development time, test equipment cost, and test time. The relatively high test cost stems from two contributing factors. First, RF transceivers require the measurement of a diverse set of specifications, requiring multiple test set-ups and long test

Radio frequency (RF) transceivers require a disproportionately high effort in terms of test development time, test equipment cost, and test time. The relatively high test cost stems from two contributing factors. First, RF transceivers require the measurement of a diverse set of specifications, requiring multiple test set-ups and long test times, which complicates load-board design, debug, and diagnosis. Second, high frequency operation necessitates the use of expensive equipment, resulting in higher per second test time cost compared with mixed-signal or digital circuits. Moreover, in terms of the non-recurring engineering cost, the need to measure complex specfications complicates the test development process and necessitates a long learning process for test engineers. Test time is dominated by changing and settling time for each test set-up. Thus, single set-up test solutions are desirable. Loop-back configuration where the transmitter output is connected to the receiver input are used as the desirable test set- up for RF transceivers, since it eliminates the reliance on expensive instrumentation for RF signal analysis and enables measuring multiple parameters at once. In-phase and Quadrature (IQ) imbalance, non-linearity, DC offset and IQ time skews are some of the most detrimental imperfections in transceiver performance. Measurement of these parameters in the loop-back mode is challenging due to the coupling between the receiver (RX) and transmitter (TX) parameters. Loop-back based solutions are proposed in this work to resolve this issue. A calibration algorithm for a subset of the above mentioned impairments is also presented. Error Vector Magnitude (EVM) is a system-level parameter that is specified for most advanced communication standards. EVM measurement often takes extensive test development efforts, tester resources, and long test times. EVM is analytically related to system impairments, which are typically measured in a production test i environment. Thus, EVM test can be eliminated from the test list if the relations between EVM and system impairments are derived independent of the circuit implementation and manufacturing process. In this work, the focus is on the WLAN standard, and deriving the relations between EVM and three of the most detrimental impairments for QAM/OFDM based systems (IQ imbalance, non-linearity, and noise). Having low cost test techniques for measuring the RF transceivers imperfections and being able to analytically compute EVM from the measured parameters is a complete test solution for RF transceivers. These techniques along with the proposed calibration method can be used in improving the yield by widening the pass/fail boundaries for transceivers imperfections. For all of the proposed methods, simulation and hardware measurements prove that the proposed techniques provide accurate characterization of RF transceivers.
ContributorsNassery, Afsaneh (Author) / Ozev, Sule (Thesis advisor) / Bakkaloglu, Bertan (Committee member) / Kiaei, Sayfe (Committee member) / Kitchen, Jennifer (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Distributed inference has applications in a wide range of fields such as source localization, target detection, environment monitoring, and healthcare. In this dissertation, distributed inference schemes which use bounded transmit power are considered. The performance of the proposed schemes are studied for a variety of inference problems. In the first

Distributed inference has applications in a wide range of fields such as source localization, target detection, environment monitoring, and healthcare. In this dissertation, distributed inference schemes which use bounded transmit power are considered. The performance of the proposed schemes are studied for a variety of inference problems. In the first part of the dissertation, a distributed detection scheme where the sensors transmit with constant modulus signals over a Gaussian multiple access channel is considered. The deflection coefficient of the proposed scheme is shown to depend on the characteristic function of the sensing noise, and the error exponent for the system is derived using large deviation theory. Optimization of the deflection coefficient and error exponent are considered with respect to a transmission phase parameter for a variety of sensing noise distributions including impulsive ones. The proposed scheme is also favorably compared with existing amplify-and-forward (AF) and detect-and-forward (DF) schemes. The effect of fading is shown to be detrimental to the detection performance and simulations are provided to corroborate the analytical results. The second part of the dissertation studies a distributed inference scheme which uses bounded transmission functions over a Gaussian multiple access channel. The conditions on the transmission functions under which consistent estimation and reliable detection are possible is characterized. For the distributed estimation problem, an estimation scheme that uses bounded transmission functions is proved to be strongly consistent provided that the variance of the noise samples are bounded and that the transmission function is one-to-one. The proposed estimation scheme is compared with the amplify and forward technique and its robustness to impulsive sensing noise distributions is highlighted. It is also shown that bounded transmissions suffer from inconsistent estimates if the sensing noise variance goes to infinity. For the distributed detection problem, similar results are obtained by studying the deflection coefficient. Simulations corroborate our analytical results. In the third part of this dissertation, the problem of estimating the average of samples distributed at the nodes of a sensor network is considered. A distributed average consensus algorithm in which every sensor transmits with bounded peak power is proposed. In the presence of communication noise, it is shown that the nodes reach consensus asymptotically to a finite random variable whose expectation is the desired sample average of the initial observations with a variance that depends on the step size of the algorithm and the variance of the communication noise. The asymptotic performance is characterized by deriving the asymptotic covariance matrix using results from stochastic approximation theory. It is shown that using bounded transmissions results in slower convergence compared to the linear consensus algorithm based on the Laplacian heuristic. Simulations corroborate our analytical findings. Finally, a robust distributed average consensus algorithm in which every sensor performs a nonlinear processing at the receiver is proposed. It is shown that non-linearity at the receiver nodes makes the algorithm robust to a wide range of channel noise distributions including the impulsive ones. It is shown that the nodes reach consensus asymptotically and similar results are obtained as in the case of transmit non-linearity. Simulations corroborate our analytical findings and highlight the robustness of the proposed algorithm.
ContributorsDasarathan, Sivaraman (Author) / Tepedelenlioğlu, Cihan (Thesis advisor) / Papandreou-Suppappola, Antonia (Committee member) / Reisslein, Martin (Committee member) / Goryll, Michael (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Electrical neural activity detection and tracking have many applications in medical research and brain computer interface technologies. In this thesis, we focus on the development of advanced signal processing algorithms to track neural activity and on the mapping of these algorithms onto hardware to enable real-time tracking. At the heart

Electrical neural activity detection and tracking have many applications in medical research and brain computer interface technologies. In this thesis, we focus on the development of advanced signal processing algorithms to track neural activity and on the mapping of these algorithms onto hardware to enable real-time tracking. At the heart of these algorithms is particle filtering (PF), a sequential Monte Carlo technique used to estimate the unknown parameters of dynamic systems. First, we analyze the bottlenecks in existing PF algorithms, and we propose a new parallel PF (PPF) algorithm based on the independent Metropolis-Hastings (IMH) algorithm. We show that the proposed PPF-IMH algorithm improves the root mean-squared error (RMSE) estimation performance, and we demonstrate that a parallel implementation of the algorithm results in significant reduction in inter-processor communication. We apply our implementation on a Xilinx Virtex-5 field programmable gate array (FPGA) platform to demonstrate that, for a one-dimensional problem, the PPF-IMH architecture with four processing elements and 1,000 particles can process input samples at 170 kHz by using less than 5% FPGA resources. We also apply the proposed PPF-IMH to waveform-agile sensing to achieve real-time tracking of dynamic targets with high RMSE tracking performance. We next integrate the PPF-IMH algorithm to track the dynamic parameters in neural sensing when the number of neural dipole sources is known. We analyze the computational complexity of a PF based method and propose the use of multiple particle filtering (MPF) to reduce the complexity. We demonstrate the improved performance of MPF using numerical simulations with both synthetic and real data. We also propose an FPGA implementation of the MPF algorithm and show that the implementation supports real-time tracking. For the more realistic scenario of automatically estimating an unknown number of time-varying neural dipole sources, we propose a new approach based on the probability hypothesis density filtering (PHDF) algorithm. The PHDF is implemented using particle filtering (PF-PHDF), and it is applied in a closed-loop to first estimate the number of dipole sources and then their corresponding amplitude, location and orientation parameters. We demonstrate the improved tracking performance of the proposed PF-PHDF algorithm and map it onto a Xilinx Virtex-5 FPGA platform to show its real-time implementation potential. Finally, we propose the use of sensor scheduling and compressive sensing techniques to reduce the number of active sensors, and thus overall power consumption, of electroencephalography (EEG) systems. We propose an efficient sensor scheduling algorithm which adaptively configures EEG sensors at each measurement time interval to reduce the number of sensors needed for accurate tracking. We combine the sensor scheduling method with PF-PHDF and implement the system on an FPGA platform to achieve real-time tracking. We also investigate the sparsity of EEG signals and integrate compressive sensing with PF to estimate neural activity. Simulation results show that both sensor scheduling and compressive sensing based methods achieve comparable tracking performance with significantly reduced number of sensors.
ContributorsMiao, Lifeng (Author) / Chakrabarti, Chaitali (Thesis advisor) / Papandreou-Suppappola, Antonia (Thesis advisor) / Zhang, Junshan (Committee member) / Bliss, Daniel (Committee member) / Kovvali, Narayan (Committee member) / Arizona State University (Publisher)
Created2013
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Description
The fluorescence enhancement by a single Noble metal sphere is separated into excitation/absorption enhancement and the emission quantum yield enhancement. Incorporating the classical model of molecular spontaneous emission into the excitation/absorption transition, the excitation enhancement is calculated rigorously by electrodynamics in the frequency domain. The final formula for the excitation

The fluorescence enhancement by a single Noble metal sphere is separated into excitation/absorption enhancement and the emission quantum yield enhancement. Incorporating the classical model of molecular spontaneous emission into the excitation/absorption transition, the excitation enhancement is calculated rigorously by electrodynamics in the frequency domain. The final formula for the excitation enhancement contains two parts: the primary field enhancement calculated from the Mie theory, and a derating factor due to the backscattering field from the molecule. When compared against a simplified model that only involves the primary Mie theory field calculation, this more rigorous model indicates that the excitation enhancement near the surface of the sphere is quenched severely due to the back-scattering field from the molecule. The degree of quenching depends in part on the bandwidth of the illumination because the presence of the sphere induces a red-shift in the absorption frequency of the molecule and at the same time broadens its spectrum. Monochromatic narrow band illumination at the molecule's original (unperturbed) resonant frequency yields large quenching. For the more realistic broadband illumination scenario, we calculate the final enhancement by integrating over the excitation/absorption spectrum. The numerical results indicate that the resonant illumination scenario overestimates the quenching and therefore would underestimate the total excitation enhancement if the illumination has a broader bandwidth than the molecule. Combining the excitation model with the exact Electrodynamical theory for emission, the complete realistic model demonstrates that there is a potential for significant fluorescence enhancement only for the case of a low quantum yield molecule close to the surface of the sphere. General expressions of the fluorescence enhancement for arbitrarily-shaped metal antennas are derived. The finite difference time domain method is utilized for analyzing these complicated antenna structures. We calculate the total excitation enhancement for the two-sphere dimer. Although the enhancement is greater in this case than for the single sphere, because of the derating effects the total enhancement can never reach the local field enhancement. In general, placing molecules very close to a plasmonic antenna surface yields poor enhancement because the local field is strongly affected by the molecular self-interaction with the metal antenna.
ContributorsZhang, Zhe (Author) / Diaz, Rodolfo E (Thesis advisor) / Lim, Derrick (Thesis advisor) / Pan, George (Committee member) / Yu, Hongyu (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Asymptotic and Numerical methods are popular in applied electromagnetism. In this work, the two methods are applied for collimated antennas and calibration targets, respectively. As an asymptotic method, the diffracted Gaussian beam approach (DGBA) is developed for design and simulation of collimated multi-reflector antenna systems, based upon Huygens principle and

Asymptotic and Numerical methods are popular in applied electromagnetism. In this work, the two methods are applied for collimated antennas and calibration targets, respectively. As an asymptotic method, the diffracted Gaussian beam approach (DGBA) is developed for design and simulation of collimated multi-reflector antenna systems, based upon Huygens principle and independent Gaussian beam expansion, referred to as the frames. To simulate a reflector antenna in hundreds to thousands of wavelength, it requires 1E7 - 1E9 independent Gaussian beams. To this end, high performance parallel computing is implemented, based on Message Passing Interface (MPI). The second part of the dissertation includes the plane wave scattering from a target consisting of doubly periodic array of sharp conducting circular cones by the magnetic field integral equation (MFIE) via Coiflet based Galerkin's procedure in conjunction with the Floquet theorem. Owing to the orthogonally, compact support, continuity and smoothness of the Coiflets, well-conditioned impedance matrices are obtained. Majority of the matrix entries are obtained in the spectral domain by one-point quadrature with high precision. For the oscillatory entries, spatial domain computation is applied, bypassing the slow convergence of the spectral summation of the non-damping propagating modes. The simulation results are compared with the solutions from an RWG-MLFMA based commercial software, FEKO, and excellent agreement is observed.
ContributorsWang, Le, 1975- (Author) / Pan, George (Thesis advisor) / Yu, Hongyu (Committee member) / Aberle, James T., 1961- (Committee member) / Diaz, Rodolfo (Committee member) / Kitchen, Jennifer (Committee member) / Arizona State University (Publisher)
Created2012
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Description
Harsh environments have conditions that make collecting scientific data difficult with existing commercial-off-the-shelf technology. Micro Electro Mechanical Systems (MEMS) technology is ideally suited for harsh environment characterization and operation due to the wide range of materials available and an incredible array of different sensing techniques while providing small device size,

Harsh environments have conditions that make collecting scientific data difficult with existing commercial-off-the-shelf technology. Micro Electro Mechanical Systems (MEMS) technology is ideally suited for harsh environment characterization and operation due to the wide range of materials available and an incredible array of different sensing techniques while providing small device size, low power consumption, and robustness. There were two main objectives of the research conducted. The first objective was to design, fabricate, and test novel sensors that measure the amount of exposure to ionizing radiation for a wide range of applications including characterization of harsh environments. Two types of MEMS ionizing radiation dosimeters were developed. The first sensor was a passive radiation-sensitive capacitor-antenna design. The antenna's emitted frequency of peak-intensity changed as exposure time to radiation increased. The second sensor was a film bulk acoustic-wave resonator, whose resonant frequency decreased with increasing ionizing radiation exposure time. The second objective was to develop MEMS sensor systems that could be deployed to gather scientific data and to use that data to address the following research question: do temperature and/or conductivity predict the appearance of photosynthetic organisms in hot springs. To this end, temperature and electrical conductivity sensor arrays were designed and fabricated based on mature MEMS technology. Electronic circuits and the software interface to the electronics were developed for field data collection. The sensor arrays utilized in the hot springs yielded results that support the hypothesis that temperature plays a key role in determining where the photosynthetic organisms occur. Additionally, a cold-film fluidic flow sensor was developed, which is suitable for near-boiling temperature measurement. Future research should focus on (1) developing a MEMS pH sensor array with integrated temperature, conductivity, and flow sensors to provide multi-dimensional data for scientific study and (2) finding solutions to biofouling and self-calibration, which affects sensor performance over long-term deployment.
ContributorsOiler, Jonathon (Author) / Yu, Hongyu (Thesis advisor) / Anbar, Ariel (Committee member) / Hartnett, Hilairy (Committee member) / Scannapieco, Evan (Committee member) / Timmes, Francis (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Although high performance, light-weight composites are increasingly being used in applications ranging from aircraft, rotorcraft, weapon systems and ground vehicles, the assurance of structural reliability remains a critical issue. In composites, damage is absorbed through various fracture processes, including fiber failure, matrix cracking and delamination. An important element in achieving

Although high performance, light-weight composites are increasingly being used in applications ranging from aircraft, rotorcraft, weapon systems and ground vehicles, the assurance of structural reliability remains a critical issue. In composites, damage is absorbed through various fracture processes, including fiber failure, matrix cracking and delamination. An important element in achieving reliable composite systems is a strong capability of assessing and inspecting physical damage of critical structural components. Installation of a robust Structural Health Monitoring (SHM) system would be very valuable in detecting the onset of composite failure. A number of major issues still require serious attention in connection with the research and development aspects of sensor-integrated reliable SHM systems for composite structures. In particular, the sensitivity of currently available sensor systems does not allow detection of micro level damage; this limits the capability of data driven SHM systems. As a fundamental layer in SHM, modeling can provide in-depth information on material and structural behavior for sensing and detection, as well as data for learning algorithms. This dissertation focusses on the development of a multiscale analysis framework, which is used to detect various forms of damage in complex composite structures. A generalized method of cells based micromechanics analysis, as implemented in NASA's MAC/GMC code, is used for the micro-level analysis. First, a baseline study of MAC/GMC is performed to determine the governing failure theories that best capture the damage progression. The deficiencies associated with various layups and loading conditions are addressed. In most micromechanics analysis, a representative unit cell (RUC) with a common fiber packing arrangement is used. The effect of variation in this arrangement within the RUC has been studied and results indicate this variation influences the macro-scale effective material properties and failure stresses. The developed model has been used to simulate impact damage in a composite beam and an airfoil structure. The model data was verified through active interrogation using piezoelectric sensors. The multiscale model was further extended to develop a coupled damage and wave attenuation model, which was used to study different damage states such as fiber-matrix debonding in composite structures with surface bonded piezoelectric sensors.
ContributorsMoncada, Albert (Author) / Chattopadhyay, Aditi (Thesis advisor) / Dai, Lenore (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Rajadas, John (Committee member) / Yekani Fard, Masoud (Committee member) / Arizona State University (Publisher)
Created2012
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Description
Adaptive processing and classification of electrocardiogram (ECG) signals are important in eliminating the strenuous process of manually annotating ECG recordings for clinical use. Such algorithms require robust models whose parameters can adequately describe the ECG signals. Although different dynamic statistical models describing ECG signals currently exist, they depend considerably on

Adaptive processing and classification of electrocardiogram (ECG) signals are important in eliminating the strenuous process of manually annotating ECG recordings for clinical use. Such algorithms require robust models whose parameters can adequately describe the ECG signals. Although different dynamic statistical models describing ECG signals currently exist, they depend considerably on a priori information and user-specified model parameters. Also, ECG beat morphologies, which vary greatly across patients and disease states, cannot be uniquely characterized by a single model. In this work, sequential Bayesian based methods are used to appropriately model and adaptively select the corresponding model parameters of ECG signals. An adaptive framework based on a sequential Bayesian tracking method is proposed to adaptively select the cardiac parameters that minimize the estimation error, thus precluding the need for pre-processing. Simulations using real ECG data from the online Physionet database demonstrate the improvement in performance of the proposed algorithm in accurately estimating critical heart disease parameters. In addition, two new approaches to ECG modeling are presented using the interacting multiple model and the sequential Markov chain Monte Carlo technique with adaptive model selection. Both these methods can adaptively choose between different models for various ECG beat morphologies without requiring prior ECG information, as demonstrated by using real ECG signals. A supervised Bayesian maximum-likelihood (ML) based classifier uses the estimated model parameters to classify different types of cardiac arrhythmias. However, the non-availability of sufficient amounts of representative training data and the large inter-patient variability pose a challenge to the existing supervised learning algorithms, resulting in a poor classification performance. In addition, recently developed unsupervised learning methods require a priori knowledge on the number of diseases to cluster the ECG data, which often evolves over time. In order to address these issues, an adaptive learning ECG classification method that uses Dirichlet process Gaussian mixture models is proposed. This approach does not place any restriction on the number of disease classes, nor does it require any training data. This algorithm is adapted to be patient-specific by labeling or identifying the generated mixtures using the Bayesian ML method, assuming the availability of labeled training data.
ContributorsEdla, Shwetha Reddy (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Chakrabarti, Chaitali (Committee member) / Kovvali, Narayan (Committee member) / Tepedelenlioğlu, Cihan (Committee member) / Arizona State University (Publisher)
Created2012