The quality of real-world visual content is typically impaired by many factors including image noise and blur. Detecting and analyzing these impairments are important steps for multiple computer vision tasks. This work focuses on perceptual-based locally adaptive noise and blur detection and their application to image restoration.

In the context of noise detection, this work proposes perceptual-based full-reference and no-reference objective image quality metrics by integrating perceptually weighted local noise into a probability summation model. Results are reported on both the LIVE and TID2008 databases. The proposed metrics achieve consistently a good performance across noise types and across databases as compared to many of the best very recent quality metrics. The proposed metrics are able to predict with high accuracy the relative amount of perceived noise in images of different content.

In the context of blur detection, existing approaches are either computationally costly or cannot perform reliably when dealing with the spatially-varying nature of the defocus blur. In addition, many existing approaches do not take human perception into account. This work proposes a blur detection algorithm that is capable of detecting and quantifying the level of spatially-varying blur by integrating directional edge spread calculation, probability of blur detection and local probability summation. The proposed method generates a blur map indicating the relative amount of perceived local blurriness. In order to detect the flat
ear flat regions that do not contribute to perceivable blur, a perceptual model based on the Just Noticeable Difference (JND) is further integrated in the proposed blur detection algorithm to generate perceptually significant blur maps. We compare our proposed method with six other state-of-the-art blur detection methods. Experimental results show that the proposed method performs the best both visually and quantitatively.

This work further investigates the application of the proposed blur detection methods to image deblurring. Two selective perceptual-based image deblurring frameworks are proposed, to improve the image deblurring results and to reduce the restoration artifacts. In addition, an edge-enhanced super resolution algorithm is proposed, and is shown to achieve better reconstructed results for the edge regions.

The power of science lies in its ability to infer and predict the

existence of objects from which no direct information can be obtained

experimentally or observationally. A well known example is to

ascertain the existence of black holes of various masses in different

parts of the universe from indirect evidence, such as X-ray emissions.

In the field of complex networks, the problem of detecting

hidden nodes can be stated, as follows. Consider a network whose

topology is completely unknown but whose nodes consist of two types:

one accessible and another inaccessible from the outside world. The

accessible nodes can be observed or monitored, and it is assumed that time

series are available from each node in this group. The inaccessible

nodes are shielded from the outside and they are essentially

``hidden.'' The question is, based solely on the

available time series from the accessible nodes, can the existence and

locations of the hidden nodes be inferred? A completely data-driven,

compressive-sensing based method is developed to address this issue by utilizing

complex weighted networks of nonlinear oscillators, evolutionary game

and geospatial networks.

Both microbes and multicellular organisms actively regulate their cell

fate determination to cope with changing environments or to ensure

proper development. Here, the synthetic biology approaches are used to

engineer bistable gene networks to demonstrate that stochastic and

permanent cell fate determination can be achieved through initializing

gene regulatory networks (GRNs) at the boundary between dynamic

attractors. This is experimentally realized by linking a synthetic GRN

to a natural output of galactose metabolism regulation in yeast.

Combining mathematical modeling and flow cytometry, the

engineered systems are shown to be bistable and that inherent gene expression

stochasticity does not induce spontaneous state transitioning at

steady state. By interfacing rationally designed synthetic

GRNs with background gene regulation mechanisms, this work

investigates intricate properties of networks that illuminate possible

regulatory mechanisms for cell differentiation and development that

can be initiated from points of instability.

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.

Thousands of high-resolution images are generated each day. Detecting and analyzing variations in these images are key steps in image understanding. This work focuses on spatial and multitemporal

visual change detection and its applications in multi-temporal synthetic aperture radar (SAR) images.

The Canny edge detector is one of the most widely-used edge detection algorithms due to its superior performance in terms of SNR and edge localization and only one response to a single edge. In this work, we propose a mechanism to implement the Canny algorithm at the block level without any loss in edge detection performance as compared to the original frame-level Canny algorithm. The resulting block-based algorithm has significantly reduced memory requirements and can achieve a significantly reduced latency. Furthermore, the proposed algorithm can be easily integrated with other block-based image processing systems. In addition, quantitative evaluations and subjective tests show that the edge detection performance of the proposed algorithm is better than the original frame-based algorithm, especially when noise is present in the images.

In the context of multi-temporal SAR images for earth monitoring applications, one critical issue is the detection of changes occurring after a natural or anthropic disaster. In this work, we propose a novel similarity measure for automatic change detection using a pair of SAR images

acquired at different times and apply it in both the spatial and wavelet domains. This measure is based on the evolution of the local statistics of the image between two dates. The local statistics are modeled as a Gaussian Mixture Model (GMM), which is more suitable and flexible to approximate the local distribution of the SAR image with distinct land-cover typologies. Tests on real datasets show that the proposed detectors outperform existing methods in terms of the quality of the similarity maps, which are assessed using the receiver operating characteristic (ROC) curves, and in terms of the total error rates of the final change detection maps. Furthermore, we proposed a new

similarity measure for automatic change detection based on a divisive normalization transform in order to reduce the computation complexity. Tests show that our proposed DNT-based change detector

exhibits competitive detection performance while achieving lower computational complexity as compared to previously suggested methods.

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.

Neural activity tracking using electroencephalography (EEG) and magnetoencephalography (MEG) brain scanning methods has been widely used in the field of neuroscience to provide insight into the nervous system. However, the tracking accuracy depends on the presence of artifacts in the EEG/MEG recordings. Artifacts include any signals that do not originate from neural activity, including physiological artifacts such as eye movement and non-physiological activity caused by the environment.

This work proposes an integrated method for simultaneously tracking multiple neural sources using the probability hypothesis density particle filter (PPHDF) and reducing the effect of artifacts using feature extraction and stochastic modeling. Unique time-frequency features are first extracted using matching pursuit decomposition for both neural activity and artifact signals.

The features are used to model probability density functions for each signal type using Gaussian mixture modeling for use in the PPHDF neural tracking algorithm. The probability density function of the artifacts provides information to the tracking algorithm that can help reduce the probability of incorrectly estimating the dynamically varying number of current dipole sources and their corresponding neural activity localization parameters. Simulation results demonstrate the effectiveness of the proposed algorithm in increasing the tracking accuracy performance for multiple dipole sources using recordings that have been contaminated by artifacts.

This dissertation introduces stochastic ordering of instantaneous channel powers of fading channels as a general method to compare the performance of a communication system over two different channels, even when a closed-form expression for the metric may not be available. Such a comparison is with respect to a variety of performance metrics such as error rates, outage probability and ergodic capacity, which share common mathematical properties such as monotonicity, convexity or complete monotonicity. Complete monotonicity of a metric, such as the symbol error rate, in conjunction with the stochastic Laplace transform order between two fading channels implies the ordering of the two channels with respect to the metric. While it has been established previously that certain modulation schemes have convex symbol error rates, there is no study of the complete monotonicity of the same, which helps in establishing stronger channel ordering results. Toward this goal, the current research proves for the first time, that all 1-dimensional and 2-dimensional modulations have completely monotone symbol error rates. Furthermore, it is shown that the frequently used parametric fading distributions for modeling line of sight exhibit a monotonicity in the line of sight parameter with respect to the Laplace transform order. While the Laplace transform order can also be used to order fading distributions based on the ergodic capacity, there exist several distributions which are not Laplace transform ordered, although they have ordered ergodic capacities. To address this gap, a new stochastic order called the ergodic capacity order has been proposed herein, which can be used to compare channels based on the ergodic capacity. Using stochastic orders, average performance of systems involving multiple random variables are compared over two different channels. These systems include diversity combining schemes, relay networks, and signal detection over fading channels with non-Gaussian additive noise. This research also addresses the problem of unifying fading distributions. This unification is based on infinite divisibility, which subsumes almost all known fading distributions, and provides simplified expressions for performance metrics, in addition to enabling stochastic ordering.

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.

Doppler radar can be used to measure respiration and heart rate without contact and through obstacles. In this work, a Doppler radar architecture at 2.4 GHz and a new signal processing algorithm to estimate the respiration and heart rate are presented. The received signal is dominated by the transceiver noise, LO phase noise and clutter which reduces the signal-to-noise ratio of the desired signal. The proposed architecture and algorithm are used to mitigate these issues and obtain an accurate estimate of the heart and respiration rate. Quadrature low-IF transceiver architecture is adopted to resolve null point problem as well as avoid 1/f noise and DC offset due to mixer-LO coupling. Adaptive clutter cancellation algorithm is used to enhance receiver sensitivity coupled with a novel Pattern Search in Noise Subspace (PSNS) algorithm is used to estimate respiration and heart rate. PSNS is a modified MUSIC algorithm which uses the phase noise to enhance Doppler shift detection. A prototype system was implemented using off-the-shelf TI and RFMD transceiver and tests were conduct with eight individuals. The measured results shows accurate estimate of the cardio pulmonary signals in low-SNR conditions and have been tested up to a distance of 6 meters.

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.