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Identifying underlying factors in breast cancer using independent component analysis

Identifying underlying factors in breast cancer using indepe...

引用

IEEE Workshop on Neural Networks for signal processing

作者： J.A. Berger S. Hautaniemi H. Edgren O. Monni S.K. Mitra O. Yli-Harja J. Astola Department of Electrical and Computer Engineering University of California Santa Barbara CA USA Tampere International Center for Signal Processing Tampere University of Technology Tampere FINLAND VTT Medical Biotechnology Turku FINLAND Biomedicum Biochip Center Helsinki Univ. Hospital Helsinki FINLAND

Independent component analysis is a well-known tool for extracting underlying mechanisms from an observed set of parallel data. Identifying such components in breast cancer cell lines, for both copy number and gene expression, is proposed here with the goal of identifying mechanisms that affect the evolution of breast cancer in humans. This paper illustrates how to utilize independent component analysis on cell line data for achieving this goal. After the components were estimated for the well-studied chromosome 17, and then over the entire genome for a set of 14 different breast cancer cell lines, ontological analysis was performed in order to determine common gene functions that are present in each of the independent components.

关键词： Breast cancer Independent component analysis Data mining Gene expression Humans Biological cells Genomics Bioinformatics Cells (biology) Ontologies

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Support vector machine classifications for microarray expression data set

Support vector machine classifications for microarray expres...

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International Conference on Computational Intelligence and Multimedia Applications

作者： Junying Zhang R. Lee Y.J. Wang Department of Electrical Engineering & Computer Science Catholic University of America Washington D.C. DC USA National Key Laboratory of Radar Signal Processing Xidian University Xi'an China Lombardi Cancer Center George town University Washington D.C. DC USA

ISBN: (纸本)0769519571

Gene selection, cancer classification and functional gene classification are three main concerns and interests by biologists for cancer detection, cancer classification, and understanding the functions of genes from the molecular level of tissues, where the large number of genes and relatively small number of experiments in gene expression data generate a great challenge. After a brief introduction of support vector machine(SVM) for classification, this paper presents recent SVM approaches for gene selection, cancer classification and functional gene classification followed by analysis on the advantages and limitations of SVM on these applications.

关键词： Support vector machines Support vector machine classification Kernel Gene expression signal processing algorithms Cancer detection Cloning Radar signal processing computer science Biology

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Multiple description image coding using pixel interleaving and wavelet transform

Multiple description image coding using pixel interleaving a...

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Midwest Symposium on Circuits and Systems (MWSCAS)

作者： Longji Wang M.N.S. Swamy M.O. Ahmad Center for Signal Processing and Communications Department of Electrical and Computer Engineering Concordia University Canada

Multiple description coding encodes a source image into two or more mutually refinable bitstreams to overcome channel impairments. When one or more channels fail, received bitstream(s) are decoded to provide a lower but acceptable quality of the reconstructed image. This paper proposes a multiple description image coding scheme using pixel interleaving by taking advantage of the intrinsic correlation of the adjacent pixels. We improve substantially the performance of the reconstructed image from multiple descriptions by compromising to some extent the performance of the reconstructed from a single description. This is achieved by incorporating the wavelet transform into the pixel interleaving-based encoder so as to provide the ability to trade off the quantizations of the frequency coefficients and the spatial pixels. Simulations are presented to demonstrate the effectiveness of the proposed schemes.

关键词： Image coding Pixel Interleaved codes Wavelet transforms Image reconstruction Decoding signal processing Quantization Frequency Communication channels

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An efficient pyramid for motion estimation

An efficient pyramid for motion estimation

引用

Midwest Symposium on Circuits and Systems (MWSCAS)

作者： Jinwen Zan M.O. Ahmad M.N.S. Swamy Center for Signal Processing and Communications Department of Electrical and Computer Engineering Concordia University Montreal QUE Canada

It is shown in this paper that by choosing an appropriate value for the parameter a of the generating kernel in constructing Burt and Adelson's pyramid for motion estimation, one can eliminate the operation of floating point multiplication needed in such a construction, and reduce the computational load to the same order as in the case of the mean pyramid. It is further shown through simulation studies that this new kernel does not degrade the performance of motion estimation, as compared to that using kernels giving the best performance.

关键词： Motion estimation Kernel Image resolution Data structures Spatial resolution signal processing signal generators Degradation signal processing algorithms Hardware

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A new architecture of RRNS error-correcting QC encoder/decoder and its FPGA implementation

A new architecture of RRNS error-correcting QC encoder/decod...

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IEEE International Symposium on Circuits and Systems (ISCAS)

作者： Wei Wang M.N.S. Swamy M.O. Ahmad Center for Signal Processing and Communications Department of Electrical and Computer Engineering Concordia University Montreal QUE Canada

In this paper, a new architecture of a redundant residue number system (RRNS) quasi-chaotic (QC) encoder/decoder with an error-correcting ability is proposed for secure communication and is tailored to FPGA implementation. In the proposed architecture, binary subencoders and subdecoders are used so that a number of modulo operations required in the existing design of D. R. Frey (IEEE Trans. Circuits Syst. II, vol. 40, pp. 660-666, Oct. 2000) are replaced by a simple truncation. Furthermore, a size-reduced design of the R/B (residue-to-binary) converter with error-correcting function, which is the crucial part of the system, is proposed. As a case study, the proposed architecture is implemented in FPGA for the case of the 16-bit input and some simulation results obtained.

关键词： Decoding Field programmable gate arrays Chaotic communication computer architecture computer errors Multiaccess communication Filters Application specific integrated circuits Equations signal processing

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An adaptive Viterbi algorithm based on strongly connected trellis decoding

An adaptive Viterbi algorithm based on strongly connected tr...

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IEEE International Symposium on Circuits and Systems (ISCAS)

作者： Man Guo M.O. Ahmad M.N.S. Swamy Chunyan Wang Department of Electrical & Computer Engineering Center for Signal Processing and Communications Concordia University Montreal QUE Canada

An adaptive Viterbi algorithm using strongly connected trellis decoding of binary convolutional codes is presented. It is known that the strongly connected trellis decoding method can be used to improve the efficiency of hardware utilization and the throughput of the decoding in a systolic array-based Viterbi decoder. However, this method makes the amount of ACS (addition, comparison, and selection) computations in the decoding process much larger than in the conventional trellis decoding. It is shown that the proposed adaptive Viterbi algorithm can reduce the large amount of ACS computations without a degradation in the performance. Further, this algorithm, unlike the adaptive Viterbi algorithm based on low connectivity trellis, does require a sorting operation to determine the most likely survivor paths among all the possible survivor paths. The simulation results show that the proposed adaptive Viterbi algorithm can reduce up to 70% of the average number of ACS computations per strongly connected stage over that using the conventional Viterbi algorithm, while keeping the same error performance as that of the latter.

关键词： Viterbi algorithm Maximum likelihood decoding Hardware Systolic arrays Sorting signal processing algorithms Throughput Sparse matrices Adaptive signal processing Convolutional codes

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A vector based fast block motion estimation algorithm for implementation on SIMD architectures

A vector based fast block motion estimation algorithm for im...

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IEEE International Symposium on Circuits and Systems (ISCAS)

作者： C. Duanmu M.O. Ahmad M.N.S. Swamy A. Shatnawi Department of Electrical & Computer Engineering Center for Signal Processing and Communications Concordia University Montreal QUE Canada

In this paper, a fast block motion estimation algorithm that not only accelerates the process of the motion estimation but also maintains the same accuracy as that of the full search algorithm is proposed. In modern CPUs, the single instruction multiple data (SIMD) technique is commonly used to provide an execution speedup of up to eight fold. The proposed algorithm satisfies the requirements of (i) the easy computation of the lower bounds of the block matching error, and (ii) their storage in a contiguous memory space for its SIMD implementation. Simulation results show that the proposed algorithm is more than 40 times faster than the full search algorithm while keeping the accuracy of the latter.

关键词： Motion estimation signal processing algorithms computer architecture Acceleration Modems Video coding Maintenance engineering Computational modeling MPEG 4 Standard Parallel processing

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Optimization of the three-step search algorithm by exclusion of stationary macroblocks from the search process

Optimization of the three-step search algorithm by exclusion...

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IEEE International Conference on Electronics, Circuits and Systems (ICECS)

作者： C.J. Duanmu M.O. Ahmad M.N.S. Swamy A. Shatnawi Center for Signal Processing and Communications Department of Electrical & Computer Engineering Concordia University Montreal QUE Canada

A typical video frame contains many macroblocks that experience little motion with respect to the reference frame. These macroblocks are referred to as stationary macroblocks. This paper aims at accelerating the three-step search algorithm for block motion estimation (BME) by excluding these stationary macroblocks from the search process. A method to detect these stationary macroblocks by comparing the mean absolute difference between the current macroblock and the reference macroblock with a given threshold is first proposed. In order to make the algorithm more efficient, a mechanism to adapt the threshold level to the changing statistics of the video sequence is then developed. Simulation results demonstrate that by using the proposed algorithm, a speedup of 20 to 40 percent is achieved for typical video test sequences. The accuracy of the proposed algorithm remains about the same as that of the three-step search algorithm.

关键词： signal processing algorithms Motion estimation Video sequences Video coding Video signal processing Acceleration Statistics Testing MPEG 4 Standard Discrete cosine transforms

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A neighborhood-blocks motion estimation technique using the pyramidal data structure

A neighborhood-blocks motion estimation technique using the ...

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International Conference on Acoustics, Speech, and signal processing (ICASSP)

作者： M. Omair Ahmad Jinwen Zan M.N.S. Swamy Center for Signal Processing and Communications Department of Electrical and Computer Engineering Concordia University Montreal QUE Canada

In this paper, a pyramidal motion estimation technique that makes use of the motion correlation within a pyramidal level is proposed. Instead of scaling the motion vectors from the adjacent lower pyramidal level as motion predictions as is done in the conventional technique, in the proposed technique, the motion vectors from the neighboring motion blocks are taken into consideration as possible candidates. Each of these candidate motion vectors is used for prediction and refined. The motion vector that has the least matching distortion is chosen as the final motion vector. Compared to the conventional pyramidal motion estimation technique, the proposed method effectively overcomes the problem of propagation of false motion vectors. Simulation studies show that a substantial performance improvement is achieved, both in terms of the prediction mean square error and the number of coding bits for the motion vectors.

关键词： Mobile communication

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Wavelet-based multiresolution motion estimation through median filtering

Wavelet-based multiresolution motion estimation through medi...

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International Conference on Acoustics, Speech, and signal processing (ICASSP)

作者： Jinwen Zan M. Omair Ahmad M.N.S. Swamy Center for Signal Processing and Communications Department of Electrical and Computer Engineering Concordia University West Montreal QUE Canada

In this paper, a non-causal median filtering method is proposed to predict the motion vectors across the wavelet subbands of a video frame for multiresolution motion estimation. This median filtering method effectively overcomes the problem of propagation of false motion vectors that exists in the conventional multiresolution motion estimation schemes. A significant feature of the proposed technique is that it imposes no demand for additional bandwidth. Simulation studies show that this median filtering-based multiresolution motion; estimation technique effectively improves the motion prediction performance. It is further shown that this performance improvement is achieved with little increase in the computational complexity.

关键词： Filtering Calendars Fires

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