Matching Items (5)
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
As the demand for wireless systems increases exponentially, it has become necessary
for different wireless modalities, like radar and communication systems, to share the
available bandwidth. One approach to realize coexistence successfully is for each
system to adopt a transmit waveform with a unique nonlinear time-varying phase
function. At the receiver of the system of interest, the waveform received for process-
ing may still suffer from low signal-to-interference-plus-noise ratio (SINR) due to the
presence of the waveforms that are matched to the other coexisting systems. This
thesis uses a time-frequency based approach to increase the SINR of a system by estimating the unique nonlinear instantaneous frequency (IF) of the waveform matched
to the system. Specifically, the IF is estimated using the synchrosqueezing transform,
a highly localized time-frequency representation that also enables reconstruction of
individual waveform components. As the IF estimate is biased, modified versions of
the transform are investigated to obtain estimators that are both unbiased and also
matched to the unique nonlinear phase function of a given waveform. Simulations
using transmit waveforms of coexisting wireless systems are provided to demonstrate
the performance of the proposed approach using both biased and unbiased IF estimators.
for different wireless modalities, like radar and communication systems, to share the
available bandwidth. One approach to realize coexistence successfully is for each
system to adopt a transmit waveform with a unique nonlinear time-varying phase
function. At the receiver of the system of interest, the waveform received for process-
ing may still suffer from low signal-to-interference-plus-noise ratio (SINR) due to the
presence of the waveforms that are matched to the other coexisting systems. This
thesis uses a time-frequency based approach to increase the SINR of a system by estimating the unique nonlinear instantaneous frequency (IF) of the waveform matched
to the system. Specifically, the IF is estimated using the synchrosqueezing transform,
a highly localized time-frequency representation that also enables reconstruction of
individual waveform components. As the IF estimate is biased, modified versions of
the transform are investigated to obtain estimators that are both unbiased and also
matched to the unique nonlinear phase function of a given waveform. Simulations
using transmit waveforms of coexisting wireless systems are provided to demonstrate
the performance of the proposed approach using both biased and unbiased IF estimators.
ContributorsGattani, Vineet Sunil (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Richmond, Christ (Committee member) / Maurer, Alexander (Committee member) / Arizona State University (Publisher)
Created2018
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
A critical problem for airborne, ship board, and land based radars operating in maritime or littoral environments is the detection, identification and tracking of targets against backscattering caused by the roughness of the sea surface. Statistical models, such as the compound K-distribution (CKD), were shown to accurately describe two separate structures of the sea clutter intensity fluctuations. The first structure is the texture that is associated with long sea waves and exhibits long temporal decorrelation period. The second structure is the speckle that accounts for reflections from multiple scatters and exhibits a short temporal decorrelation period from pulse to pulse. Existing methods for estimating the CKD model parameters do not include the thermal noise power, which is critical for real sea clutter processing. Estimation methods that include the noise power are either computationally intensive or require very large data records.
This work proposes two new approaches for accurately estimating all three CKD model parameters, including noise power. The first method integrates, in an iterative fashion, the noise power estimation, using one-dimensional nonlinear curve fitting,
with the estimation of the shape and scale parameters, using closed-form solutions in terms of the CKD intensity moments. The second method is similar to the first except it replaces integer-based intensity moments with fractional moments which have been shown to achieve more accurate estimates of the shape parameter. These new methods can be implemented in real time without requiring large data records. They can also achieve accurate estimation performance as demonstrated with simulated and real sea clutter observation datasets. The work also investigates the numerically computed Cram\'er-Rao lower bound (CRLB) of the variance of the shape parameter estimate using intensity observations in thermal noise with unknown power. Using the CRLB, the asymptotic estimation performance behavior of the new estimators is studied and compared to that of other estimators.
This work proposes two new approaches for accurately estimating all three CKD model parameters, including noise power. The first method integrates, in an iterative fashion, the noise power estimation, using one-dimensional nonlinear curve fitting,
with the estimation of the shape and scale parameters, using closed-form solutions in terms of the CKD intensity moments. The second method is similar to the first except it replaces integer-based intensity moments with fractional moments which have been shown to achieve more accurate estimates of the shape parameter. These new methods can be implemented in real time without requiring large data records. They can also achieve accurate estimation performance as demonstrated with simulated and real sea clutter observation datasets. The work also investigates the numerically computed Cram\'er-Rao lower bound (CRLB) of the variance of the shape parameter estimate using intensity observations in thermal noise with unknown power. Using the CRLB, the asymptotic estimation performance behavior of the new estimators is studied and compared to that of other estimators.
ContributorsNorthrop, Judith (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Chakrabarti, Chaitali (Committee member) / Tepedelenlioğlu, Cihan (Committee member) / Maurer, Alexander (Committee member) / Arizona State University (Publisher)
Created2019
Description
One of the gravest dangers facing cancer patients is an extended symptom-free lull between tumor initiation and the first diagnosis. Detection of tumors is critical for effective intervention. Using the body’s immune system to detect and amplify tumor-specific signals may enable detection of cancer using an inexpensive immunoassay. Immunosignatures are one such assay: they provide a map of antibody interactions with random-sequence peptides. They enable detection of disease-specific patterns using classic train/test methods. However, to date, very little effort has gone into extracting information from the sequence of peptides that interact with disease-specific antibodies. Because it is difficult to represent all possible antigen peptides in a microarray format, we chose to synthesize only 330,000 peptides on a single immunosignature microarray. The 330,000 random-sequence peptides on the microarray represent 83% of all tetramers and 27% of all pentamers, creating an unbiased but substantial gap in the coverage of total sequence space. We therefore chose to examine many relatively short motifs from these random-sequence peptides. Time-variant analysis of recurrent subsequences provided a means to dissect amino acid sequences from the peptides while simultaneously retaining the antibody–peptide binding intensities. We first used a simple experiment in which monoclonal antibodies with known linear epitopes were exposed to these random-sequence peptides, and their binding intensities were used to create our algorithm. We then demonstrated the performance of the proposed algorithm by examining immunosignatures from patients with Glioblastoma multiformae (GBM), an aggressive form of brain cancer. Eight different frameshift targets were identified from the random-sequence peptides using this technique. If immune-reactive antigens can be identified using a relatively simple immune assay, it might enable a diagnostic test with sufficient sensitivity to detect tumors in a clinically useful way.
ContributorsO'Donnell, Brian (Author) / Maurer, Alexander (Author) / Papandreou-Suppappola, Antonia (Author) / Stafford, Phillip (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2015-06-18