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- All Subjects: Signal processing--Digital techniques.
- Creators: Bliss, Daniel
Description
Genomic and proteomic sequences, which are in the form of deoxyribonucleic acid (DNA) and amino acids respectively, play a vital role in the structure, function and diversity of every living cell. As a result, various genomic and proteomic sequence processing methods have been proposed from diverse disciplines, including biology, chemistry, physics, computer science and electrical engineering. In particular, signal processing techniques were applied to the problems of sequence querying and alignment, that compare and classify regions of similarity in the sequences based on their composition. However, although current approaches obtain results that can be attributed to key biological properties, they require pre-processing and lack robustness to sequence repetitions. In addition, these approaches do not provide much support for efficiently querying sub-sequences, a process that is essential for tracking localized database matches. In this work, a query-based alignment method for biological sequences that maps sequences to time-domain waveforms before processing the waveforms for alignment in the time-frequency plane is first proposed. The mapping uses waveforms, such as time-domain Gaussian functions, with unique sequence representations in the time-frequency plane. The proposed alignment method employs a robust querying algorithm that utilizes a time-frequency signal expansion whose basis function is matched to the basic waveform in the mapped sequences. The resulting WAVEQuery approach is demonstrated for both DNA and protein sequences using the matching pursuit decomposition as the signal basis expansion. The alignment localization of WAVEQuery is specifically evaluated over repetitive database segments, and operable in real-time without pre-processing. It is demonstrated that WAVEQuery significantly outperforms the biological sequence alignment method BLAST for queries with repetitive segments for DNA sequences. A generalized version of the WAVEQuery approach with the metaplectic transform is also described for protein sequence structure prediction. For protein alignment, it is often necessary to not only compare the one-dimensional (1-D) primary sequence structure but also the secondary and tertiary three-dimensional (3-D) space structures. This is done after considering the conformations in the 3-D space due to the degrees of freedom of these structures. As a result, a novel directionality based 3-D waveform mapping for the 3-D protein structures is also proposed and it is used to compare protein structures using a matched filter approach. By incorporating a 3-D time axis, a highly-localized Gaussian-windowed chirp waveform is defined, and the amino acid information is mapped to the chirp parameters that are then directly used to obtain directionality in the 3-D space. This mapping is unique in that additional characteristic protein information such as hydrophobicity, that relates the sequence with the structure, can be added as another representation parameter. The additional parameter helps tracking similarities over local segments of the structure, this enabling classification of distantly related proteins which have partial structural similarities. This approach is successfully tested for pairwise alignments over full length structures, alignments over multiple structures to form a phylogenetic trees, and also alignments over local segments. Also, basic classification over protein structural classes using directional descriptors for the protein structure is performed.
ContributorsRavichandran, Lakshminarayan (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Spanias, Andreas S (Thesis advisor) / Chakrabarti, Chaitali (Committee member) / Tepedelenlioğlu, Cihan (Committee member) / Lacroix, Zoé (Committee member) / Arizona State University (Publisher)
Created2011
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 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
Description
Tracking a time-varying number of targets is a challenging
dynamic state estimation problem whose complexity is intensified
under low signal-to-noise ratio (SNR) or high clutter conditions.
This is important, for example, when tracking
multiple, closely spaced targets moving in the same direction such as a
convoy of low observable vehicles moving through a forest or multiple
targets moving in a crisscross pattern. The SNR in
these applications is usually low as the reflected signals from
the targets are weak or the noise level is very high.
An effective approach for detecting and tracking a single target
under low SNR conditions is the track-before-detect filter (TBDF)
that uses unthresholded measurements. However, the TBDF has only been used to
track a small fixed number of targets at low SNR.
This work proposes a new multiple target TBDF approach to track a
dynamically varying number of targets under the recursive Bayesian framework.
For a given maximum number of
targets, the state estimates are obtained by estimating the joint
multiple target posterior probability density function under all possible
target
existence combinations. The estimation of the corresponding target existence
combination probabilities and the target existence probabilities are also
derived. A feasible sequential Monte Carlo (SMC) based implementation
algorithm is proposed. The approximation accuracy of the SMC
method with a reduced number of particles is improved by an efficient
proposal density function that partitions the multiple target space into a
single target space.
The proposed multiple target TBDF method is extended to track targets in sea
clutter using highly time-varying radar measurements. A generalized
likelihood function for closely spaced multiple targets in compound Gaussian
sea clutter is derived together with the maximum likelihood estimate of
the model parameters using an iterative fixed point algorithm.
The TBDF performance is improved by proposing a computationally feasible
method to estimate the space-time covariance matrix of rapidly-varying sea
clutter. The method applies the Kronecker product approximation to the
covariance matrix and uses particle filtering to solve the resulting dynamic
state space model formulation.
dynamic state estimation problem whose complexity is intensified
under low signal-to-noise ratio (SNR) or high clutter conditions.
This is important, for example, when tracking
multiple, closely spaced targets moving in the same direction such as a
convoy of low observable vehicles moving through a forest or multiple
targets moving in a crisscross pattern. The SNR in
these applications is usually low as the reflected signals from
the targets are weak or the noise level is very high.
An effective approach for detecting and tracking a single target
under low SNR conditions is the track-before-detect filter (TBDF)
that uses unthresholded measurements. However, the TBDF has only been used to
track a small fixed number of targets at low SNR.
This work proposes a new multiple target TBDF approach to track a
dynamically varying number of targets under the recursive Bayesian framework.
For a given maximum number of
targets, the state estimates are obtained by estimating the joint
multiple target posterior probability density function under all possible
target
existence combinations. The estimation of the corresponding target existence
combination probabilities and the target existence probabilities are also
derived. A feasible sequential Monte Carlo (SMC) based implementation
algorithm is proposed. The approximation accuracy of the SMC
method with a reduced number of particles is improved by an efficient
proposal density function that partitions the multiple target space into a
single target space.
The proposed multiple target TBDF method is extended to track targets in sea
clutter using highly time-varying radar measurements. A generalized
likelihood function for closely spaced multiple targets in compound Gaussian
sea clutter is derived together with the maximum likelihood estimate of
the model parameters using an iterative fixed point algorithm.
The TBDF performance is improved by proposing a computationally feasible
method to estimate the space-time covariance matrix of rapidly-varying sea
clutter. The method applies the Kronecker product approximation to the
covariance matrix and uses particle filtering to solve the resulting dynamic
state space model formulation.
ContributorsEbenezer, Samuel P (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Chakrabarti, Chaitali (Committee member) / Bliss, Daniel (Committee member) / Kovvali, Narayan (Committee member) / Arizona State University (Publisher)
Created2015