Array CGH data modeling and smoothing in Stationary Wavelet Packet Transform domain

Background: Array-based comparative genomic hybridization (array CGH) is a highly efficient technique, allowing the simultaneous measurement of genomic DNA copy number at hundreds or thousands of loci and the reliable detection of local one-copy-level variations. Characterization of these DNA copy number changes is important for both the basic understanding of cancer and its diagnosis. In order to develop effective methods to identify aberration regions from array CGH data, many recent research work focus on both smoothing-based and segmentation-based data processing. In this paper, we propose stationary packet wavelet transform based approach to smooth array CGH data. Our purpose is to remove CGH noise in whole frequency while keeping true signal by using bivariate model. Results: In both synthetic and real CGH data, Stationary Wavelet Packet Transform (SWPT) is the best wavelet transform to analyze CGH signal in whole frequency. We also introduce a new bivariate shrinkage model which shows the relationship of CGH noisy coefficients of two scales in SWPT. Before smoothing, the symmetric extension is considered as a preprocessing step to save information at the border. Conclusions: We have designed the SWTP and the SWPT-Bi which are using the stationary wavelet packet transform with the hard thresholding and the new bivariate shrinkage estimator respectively to smooth the array CGH data. We demonstrate the effectiveness of our approach through theoretical and experimental exploration of a set of array CGH data, including both synthetic data and real data. The comparison results show that our method outperforms the previous approaches

Wavelet-based noise reduction of cDNA microarray images

The advent of microarray imaging technology has lead to enormous progress in the life sciences by allowing scientists to analyze the expression of thousands of genes at a time. For complementary DNA (cDNA) microarray experiments, the raw data are a pair of red and green channel images corresponding to the treatment and control samples. These images are contaminated by a high level of noise due to the numerous noise sources affecting the image formation. A major challenge of microarray image analysis is the extraction of accurate gene expression measurements from the noisy microarray images. A crucial step in this process is denoising, which consists of reducing the noise in the observed microarray images while preserving the signal information as much as possible. This thesis deals with the problem of developing novel methods for reducing noise in cDNA microarray images for accurate estimation of the gene expression levels. Denoising methods based on the wavelet transform have shown significant success when applied to natural images. However, these methods are not very efficient for reducing noise in cDNA microarray images. An important reason for this is that existing methods are only capable of processing the red and green channel images separately. In doing so. they ignore the signal correlation as well as the noise correlation that exists between the wavelet coefficients of the two channels. The primary objective of this research is to design efficient wavelet-based noise reduction algorithms for cDNA microarray images that take into account these inter-channel dependencies by 'jointly' estimating the noise-free coefficients in both the channels. Denoising algorithms are developed using two types of wavelet transforms, namely, the frequently-used discrete wavelet transform (DWT) and the complex wavelet transform (CWT). The main advantage of using the DWT for denoising is that this transform is computationally very efficient. In order to obtain a better denoising performance for microarray images, however, the CWT is preferred to DWT because the former has good directional selectivity properties that are necessary for better representation of the circular edges of spots. The linear minimum mean squared error and maximum a posteriori estimation techniques are used to develop bivariate estimators for the noise-free coefficients of the two images. These estimators are derived by utilizing appropriate joint probability density functions for the image coefficients as well as the noise coefficients of the two channels. Extensive experimentations are carried out on a large set of cDNA microarray images to evaluate the performance of the proposed denoising methods as compared to the existing ones. Comparisons are made using standard metrics such as the peak signal-to-noise ratio (PSNR) for measuring the amount of noise removed from the pixels of the images, and the mean absolute error for measuring the accuracy of the estimated log-intensity ratios obtained from the denoised version of the images. Results indicate that the proposed denoising methods that are developed specifically for the microarray images do, indeed, lead to more accurate estimation of gene expression levels. Thus, it is expected that the proposed methods will play a significant role in improving the reliability of the results obtained from practical microarray experiments

Intelligent Circuits and Systems

ICICS-2020 is the third conference initiated by the School of Electronics and Electrical Engineering at Lovely Professional University that explored recent innovations of researchers working for the development of smart and green technologies in the fields of Energy, Electronics, Communications, Computers, and Control. ICICS provides innovators to identify new opportunities for the social and economic benefits of society.　 This conference bridges the gap between academics and R&D institutions, social visionaries, and experts from all strata of society to present their ongoing research activities and foster research relations between them. It provides opportunities for the exchange of new ideas, applications, and experiences in the field of smart technologies and finding global partners for future collaboration. The ICICS-2020 was conducted in two broad categories, Intelligent Circuits & Intelligent Systems and Emerging Technologies in Electrical Engineering

Compressive sensing for signal ensembles

Compressive sensing (CS) is a new approach to simultaneous sensing and compression that enables a potentially large reduction in the sampling and computation costs for acquisition of signals having a sparse or compressible representation in some basis. The CS literature has focused almost exclusively on problems involving single signals in one or two dimensions. However, many important applications involve distributed networks or arrays of sensors. In other applications, the signal is inherently multidimensional and sensed progressively along a subset of its dimensions; examples include hyperspectral imaging and video acquisition. Initial work proposed joint sparsity models for signal ensembles that exploit both intra- and inter-signal correlation structures. Joint sparsity models enable a reduction in the total number of compressive measurements required by CS through the use of specially tailored recovery algorithms. This thesis reviews several different models for sparsity and compressibility of signal ensembles and multidimensional signals and proposes practical CS measurement schemes for these settings. For joint sparsity models, we evaluate the minimum number of measurements required under a recovery algorithm with combinatorial complexity. We also propose a framework for CS that uses a union-of-subspaces signal model. This framework leverages the structure present in certain sparse signals and can exploit both intra- and inter-signal correlations in signal ensembles. We formulate signal recovery algorithms that employ these new models to enable a reduction in the number of measurements required. Additionally, we propose the use of Kronecker product matrices as sparsity or compressibility bases for signal ensembles and multidimensional signals to jointly model all types of correlation present in the signal when each type of correlation can be expressed using sparsity. We compare the performance of standard global measurement ensembles, which act on all of the signal samples; partitioned measurements, which act on a partition of the signal with a given measurement depending only on a piece of the signal; and Kronecker product measurements, which can be implemented in distributed measurement settings. The Kronecker product formulation in the sparsity and measurement settings enables the derivation of analytical bounds for transform coding compression of signal ensembles and multidimensional signals. We also provide new theoretical results for performance of CS recovery when Kronecker product matrices are used, which in turn motivates new design criteria for distributed CS measurement schemes

Biomedical Signal and Image Processing

Written for senior-level and first year graduate students in biomedical signal and image processing, this book describes fundamental signal and image processing techniques that are used to process biomedical information. The book also discusses application of these techniques in the processing of some of the main biomedical signals and images, such as EEG, ECG, MRI, and CT. New features of this edition include the technical updating of each chapter along with the addition of many more examples, the majority of which are MATLAB based