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- Genre: Doctoral Dissertation
- Creators: Tepedelenlioğlu, Cihan
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
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