Matching Items (5)
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- All Subjects: Signal Processing
- Creators: Kovvali, Narayan
- Status: Published
Description
Immunosignaturing is a medical test for assessing the health status of a patient by applying microarrays of random sequence peptides to determine the patient's immune fingerprint by associating antibodies from a biological sample to immune responses. The immunosignature measurements can potentially provide pre-symptomatic diagnosis for infectious diseases or detection of biological threats. Currently, traditional bioinformatics tools, such as data mining classification algorithms, are used to process the large amount of peptide microarray data. However, these methods generally require training data and do not adapt to changing immune conditions or additional patient information. This work proposes advanced processing techniques to improve the classification and identification of single and multiple underlying immune response states embedded in immunosignatures, making it possible to detect both known and previously unknown diseases or biothreat agents. Novel adaptive learning methodologies for un- supervised and semi-supervised clustering integrated with immunosignature feature extraction approaches are proposed. The techniques are based on extracting novel stochastic features from microarray binding intensities and use Dirichlet process Gaussian mixture models to adaptively cluster the immunosignatures in the feature space. This learning-while-clustering approach allows continuous discovery of antibody activity by adaptively detecting new disease states, with limited a priori disease or patient information. A beta process factor analysis model to determine underlying patient immune responses is also proposed to further improve the adaptive clustering performance by formatting new relationships between patients and antibody activity. In order to extend the clustering methods for diagnosing multiple states in a patient, the adaptive hierarchical Dirichlet process is integrated with modified beta process factor analysis latent feature modeling to identify relationships between patients and infectious agents. The use of Bayesian nonparametric adaptive learning techniques allows for further clustering if additional patient data is received. Significant improvements in feature identification and immune response clustering are demonstrated using samples from patients with different diseases.
ContributorsMalin, Anna (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Bliss, Daniel (Committee member) / Chakrabarti, Chaitali (Committee member) / Kovvali, Narayan (Committee member) / Lacroix, Zoé (Committee member) / Arizona State University (Publisher)
Created2013
Description
This work considers the problem of multiple detection and tracking in two complex time-varying environments, urban terrain and underwater. Tracking multiple radar targets in urban environments is rst investigated by exploiting multipath signal returns, wideband underwater acoustic (UWA) communications channels are estimated using adaptive learning methods, and multiple UWA communications users are detected by designing the transmit signal to match the environment. For the urban environment, a multi-target tracking algorithm is proposed that integrates multipath-to-measurement association and the probability hypothesis density method implemented using particle filtering. The algorithm is designed to track an unknown time-varying number of targets by extracting information from multiple measurements due to multipath returns in the urban terrain. The path likelihood probability is calculated by considering associations between measurements and multipath returns, and an adaptive clustering algorithm is used to estimate the number of target and their corresponding parameters. The performance of the proposed algorithm is demonstrated for different multiple target scenarios and evaluated using the optimal subpattern assignment metric. The underwater environment provides a very challenging communication channel due to its highly time-varying nature, resulting in large distortions due to multipath and Doppler-scaling, and frequency-dependent path loss. A model-based wideband UWA channel estimation algorithm is first proposed to estimate the channel support and the wideband spreading function coefficients. A nonlinear frequency modulated signaling scheme is proposed that is matched to the wideband characteristics of the underwater environment. Constraints on the signal parameters are derived to optimally reduce multiple access interference and the UWA channel effects. The signaling scheme is compared to a code division multiple access (CDMA) scheme to demonstrate its improved bit error rate performance. The overall multi-user communication system performance is finally analyzed by first estimating the UWA channel and then designing the signaling scheme for multiple communications users.
ContributorsZhou, Meng (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Tepedelenlioğlu, Cihan (Committee member) / Kovvali, Narayan (Committee member) / Berisha, Visar (Committee member) / Arizona State University (Publisher)
Created2014
Description
Peptide microarrays have been used in molecular biology to profile immune responses and develop diagnostic tools. When the microarrays are printed with random peptide sequences, they can be used to identify antigen antibody binding patterns or immunosignatures. In this thesis, an advanced signal processing method is proposed to estimate epitope antigen subsequences as well as identify mimotope antigen subsequences that mimic the structure of epitopes from random-sequence peptide microarrays. The method first maps peptide sequences to linear expansions of highly-localized one-dimensional (1-D) time-varying signals and uses a time-frequency processing technique to detect recurring patterns in subsequences. This technique is matched to the aforementioned mapping scheme, and it allows for an inherent analysis on how substitutions in the subsequences can affect antibody binding strength. The performance of the proposed method is demonstrated by estimating epitopes and identifying potential mimotopes for eight monoclonal antibody samples.
The proposed mapping is generalized to express information on a protein's sequence location, structure and function onto a highly localized three-dimensional (3-D) Gaussian waveform. In particular, as analysis of protein homology has shown that incorporating different kinds of information into an alignment process can yield more robust alignment results, a pairwise protein structure alignment method is proposed based on a joint similarity measure of multiple mapped protein attributes. The 3-D mapping allocates protein properties into distinct regions in the time-frequency plane in order to simplify the alignment process by including all relevant information into a single, highly customizable waveform. Simulations demonstrate the improved performance of the joint alignment approach to infer relationships between proteins, and they provide information on mutations that cause changes to both the sequence and structure of a protein.
In addition to the biology-based signal processing methods, a statistical method is considered that uses a physics-based model to improve processing performance. In particular, an externally developed physics-based model for sea clutter is examined when detecting a low radar cross-section target in heavy sea clutter. This novel model includes a process that generates random dynamic sea clutter based on the governing physics of water gravity and capillary waves and a finite-difference time-domain electromagnetics simulation process based on Maxwell's equations propagating the radar signal. A subspace clutter suppression detector is applied to remove dominant clutter eigenmodes, and its improved performance over matched filtering is demonstrated using simulations.
The proposed mapping is generalized to express information on a protein's sequence location, structure and function onto a highly localized three-dimensional (3-D) Gaussian waveform. In particular, as analysis of protein homology has shown that incorporating different kinds of information into an alignment process can yield more robust alignment results, a pairwise protein structure alignment method is proposed based on a joint similarity measure of multiple mapped protein attributes. The 3-D mapping allocates protein properties into distinct regions in the time-frequency plane in order to simplify the alignment process by including all relevant information into a single, highly customizable waveform. Simulations demonstrate the improved performance of the joint alignment approach to infer relationships between proteins, and they provide information on mutations that cause changes to both the sequence and structure of a protein.
In addition to the biology-based signal processing methods, a statistical method is considered that uses a physics-based model to improve processing performance. In particular, an externally developed physics-based model for sea clutter is examined when detecting a low radar cross-section target in heavy sea clutter. This novel model includes a process that generates random dynamic sea clutter based on the governing physics of water gravity and capillary waves and a finite-difference time-domain electromagnetics simulation process based on Maxwell's equations propagating the radar signal. A subspace clutter suppression detector is applied to remove dominant clutter eigenmodes, and its improved performance over matched filtering is demonstrated using simulations.
ContributorsO'Donnell, Brian (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Bliss, Daniel (Committee member) / Johnston, Stephen A. (Committee member) / Kovvali, Narayan (Committee member) / Tepedelenlioğlu, Cihan (Committee member) / Arizona State University (Publisher)
Created2014
Description
Tracking targets in the presence of clutter is inevitable, and presents many challenges. Additionally, rapid, drastic changes in clutter density between different environments or scenarios can make it even more difficult for tracking algorithms to adapt. A novel approach to target tracking in such dynamic clutter environments is proposed using a particle filter (PF) integrated with Interacting Multiple Models (IMMs) to compensate and adapt to the transition between different clutter densities. This model was implemented for the case of a monostatic sensor tracking a single target moving with constant velocity along a two-dimensional trajectory, which crossed between regions of drastically different clutter densities. Multiple combinations of clutter density transitions were considered, using up to three different clutter densities. It was shown that the integrated IMM PF algorithm outperforms traditional approaches such as the PF in terms of tracking results and performance. The minimal additional computational expense of including the IMM more than warrants the benefits of having it supplement and amplify the advantages of the PF.
ContributorsDutson, Karl (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Kovvali, Narayan (Committee member) / Bliss, Daniel W (Committee member) / Arizona State University (Publisher)
Created2015
Description
In recent years, there has been an increased interest in sharing available bandwidth to avoid spectrum congestion. With an ever-increasing number wireless users, it is critical to develop signal processing based spectrum sharing algorithms to achieve cooperative use of the allocated spectrum among multiple systems in order to reduce interference between systems. This work studies the radar and communications systems coexistence problem using two main approaches. The first approach develops methodologies to increase radar target tracking performance under low signal-to-interference-plus-noise ratio (SINR) conditions due to the coexistence of strong communications interference. The second approach jointly optimizes the performance of both systems by co-designing a common transmit waveform.
When concentrating on improving radar tracking performance, a pulsed radar that is tracking a single target coexisting with high powered communications interference is considered. Although the Cramer-Rao lower bound (CRLB) on the covariance of an unbiased estimator of deterministic parameters provides a bound on the estimation mean squared error (MSE), there exists an SINR threshold at which estimator covariance rapidly deviates from the CRLB. After demonstrating that different radar waveforms experience different estimation SINR thresholds using the Barankin bound (BB), a new radar waveform design method is proposed based on predicting the waveform-dependent BB SINR threshold under low SINR operating conditions.
A novel method of predicting the SINR threshold value for maximum likelihood estimation (MLE) is proposed. A relationship is shown to exist between the formulation of the BB kernel and the probability of selecting sidelobes for the MLE. This relationship is demonstrated as an accurate means of threshold prediction for the radar target parameter estimation of frequency, time-delay and angle-of-arrival.
For the co-design radar and communications system problem, the use of a common transmit waveform for a pulse-Doppler radar and a multiuser communications system is proposed. The signaling scheme for each system is selected from a class of waveforms with nonlinear phase function by optimizing the waveform parameters to minimize interference between the two systems and interference among communications users. Using multi-objective optimization, a trade-off in system performance is demonstrated when selecting waveforms that minimize both system interference and tracking MSE.
When concentrating on improving radar tracking performance, a pulsed radar that is tracking a single target coexisting with high powered communications interference is considered. Although the Cramer-Rao lower bound (CRLB) on the covariance of an unbiased estimator of deterministic parameters provides a bound on the estimation mean squared error (MSE), there exists an SINR threshold at which estimator covariance rapidly deviates from the CRLB. After demonstrating that different radar waveforms experience different estimation SINR thresholds using the Barankin bound (BB), a new radar waveform design method is proposed based on predicting the waveform-dependent BB SINR threshold under low SINR operating conditions.
A novel method of predicting the SINR threshold value for maximum likelihood estimation (MLE) is proposed. A relationship is shown to exist between the formulation of the BB kernel and the probability of selecting sidelobes for the MLE. This relationship is demonstrated as an accurate means of threshold prediction for the radar target parameter estimation of frequency, time-delay and angle-of-arrival.
For the co-design radar and communications system problem, the use of a common transmit waveform for a pulse-Doppler radar and a multiuser communications system is proposed. The signaling scheme for each system is selected from a class of waveforms with nonlinear phase function by optimizing the waveform parameters to minimize interference between the two systems and interference among communications users. Using multi-objective optimization, a trade-off in system performance is demonstrated when selecting waveforms that minimize both system interference and tracking MSE.
ContributorsKota, John S (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Berisha, Visar (Committee member) / Bliss, Daniel (Committee member) / Kovvali, Narayan (Committee member) / Arizona State University (Publisher)
Created2016