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Clustering methods for accurate DNA base-calling

Clustering methods for accurate DNA base-calling

引用

Asilomar Conference on signals, Systems & computers

作者： E.S. Manolakos Communications and Digital Signal Processing (CDSP) Center Electrical and Computer Engineering Department Northeastern University Boston MA USA

Routinely extending the useful read-lengths of DNA chromatograms beyond 1 kps by employing intelligent base-calling algorithms will be extremely useful to genomics research because in many cases the entire coding region of a gene could fit into a single long read. By segmenting the chromatograms into base-call "events" to be labeled in terms of the number of bases they represent, base-calling as a pattern classification problem is formulated. An overview of two unsupervised clustering methods that could be used for its solution is presented.

关键词： Clustering methods DNA Data mining Digital signal processing Clustering algorithms signal processing algorithms Electrokinetics Detectors Sequences signal processing

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Adaptive transmission for Infostations: a MC-CDMA implementation

Adaptive transmission for Infostations: a MC-CDMA implementa...

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Asilomar Conference on signals, Systems & computers

作者： C. Ibars Mizhou Tan Y. Bar-Ness Center for Communications and Signal Processing Research Department of Electrical and Computer Engineering New Jersey Institute of Technology Newark NJ USA

The Infostation concept is proposed for fourth generation cellular communications to provide very low cost data transfer. It provides non-ubiquitous coverage and very high data rates for users within small, isolated coverage areas by means of adaptive transmission. We propose a transmission scheme for infostations based on multi-carrier CDMA (MC-CDMA). The proposed system performs adaptive transmission by changing spreading code allocation and using adaptive modulation. In the receiver we propose to use successive interference cancellation (SIC), which decodes the most reliable symbols first. Approximate analytic and simulated results for bit error rate are given for a Rice Infostation channel. Transmission rates for the two user case under two proposed resource allocation policies are shown.

关键词： Multicarrier code division multiple access Costs Multiaccess communication Adaptive systems Modulation coding Interference cancellation Silicon carbide Decoding Analytical models Bit error rate

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A new space-time differentially coded DS-CDMA transceiver system for reliable communications

A new space-time differentially coded DS-CDMA transceiver sy...

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

作者： Kun Wang Hongya Ge Center for Communications and Signal Processing Research Department of Electrical and Computer Engineering New Jersey Institute of Technology Newark NJ USA

ISBN: (纸本)0780374029

In this work, we present a new space-time differentially coded transceiver system for DS-CDMA applications. The proposed solution allows us to embed transmit diversity into the space-time-frequency (STF) domain in a simple yet effective way. It also enables a simple scheme for differential detection and data separation at the receiver without channel state information (CSI). Simulation results in comparison with other existing approaches demonstrate significant bit-error-rate (BER) performance improvement over a wide range of system parameters, such as signal-to-noise ratio (SNR) and near-far ratio (NFR).

关键词： Argon Transmitters Tin Decoding Antennas

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ASIC implementation architecture for pulse shaping FIR filters in 3G mobile communications

ASIC implementation architecture for pulse shaping FIR filte...

引用

IEEE International Symposium on Circuits and Systems (ISCAS)

作者： W.-P. Zhu M.O. Ahmad M.N.S. Swamy Centre for Signal Processing and Communications Department of Electrical and Computer Engineering Concordia University Montreal QUE Canada

This paper presents two system-on-chip oriented implementation architectures for pulse shaping FIR filters used in 3G mobile communications. One is the look-up-table based distributed arithmetic architecture and the other one a modified multiply and accumulation (MAC) implementation. Both schemes employ the pre-upsampling procedure to minimize the consumption of hardware resources. The proposed architectures have been prototyped with FPGA implementation and can be integrated directly to ASIC products.

关键词： Finite impulse response filter Application specific integrated circuits Pulse shaping methods 3G mobile communication computer architecture signal processing Hardware Multiaccess communication Prototypes Field programmable gate arrays

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Accurate estimation of the signal baseline in DNA chromatograms

Accurate estimation of the signal baseline in DNA chromatogr...

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IEEE Workshop on Neural Networks for signal processing

作者： L. Andrade E.S. Manolakos Communications and Digital Signal Processing (CDSP) Center for Research and Graduate Studies Electrical and Computer Engineering Department Northeastern University Boston MA USA

Estimating accurately the varying baseline level in different parts of a DNA chromatogram is a challenging and important problem for accurate base-calling. We are formulating the problem in a statistical learning framework and propose an Expectation-Maximization algorithm for its solution. In addition we also present a faster, iterative histogram based method for estimating the background of the signal in small size windows. The two methods can be combined with regression techniques to correct the baseline in all regions of the chromatogram and are shown to work well even in areas of low SNR. By improving the separation of clusters, baseline correction actions reduce the classification errors when using the BEM base-caller developed in our group.

关键词： Statistical learning Bayesian methods signal resolution signal to noise ratio Data mining Digital signal processing DNA computing Expectation-maximization algorithms Iterative methods Histograms

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Step-response-based characterization of nonuniform perfect-reconstruction filter banks

Step-response-based characterization of nonuniform perfect-r...

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IEEE International Symposium on Circuits and Systems (ISCAS)

作者： S. Samadi A. Nishihara M.O. Ahmad M.N.S. Swamy Center for Signal Processing and Communications Department of Electrical and Computer Engineering Concordia University Montreal QUE Canada The Center for Research and Development of Educational Technology Tokyo Institute of Technology Tokyo Japan

An algebraic characterization of nonuniform perfect-reconstruction (PR) filter banks with integer decimation factors is derived. The PR property is formulated in the z domain based on the response of the systems to delayed unit step signals. This leads to derivation of a new class of characterizing formulas in terms of the rate conversion factors and the transfer functions of channel filters. We use the formulas to give a set of analytic necessary and sufficient conditions for a nonuniform delay chain filter bank to be a PR system. These conditions are identical to those that characterize exact covering systems of congruence relations using roots of unity. We introduce important results from the mathematics literature on exact covering systems. These results elucidate the admissible factors of decimation in nonuniform PR delay chain systems with maximally distinct decimation factors.

关键词： Channel bank filters Filter bank Delay systems Educational technology Sufficient conditions signal processing Research and development Transfer functions Books Wavelet transforms

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A bandwidth efficient OFDM transmission scheme

A bandwidth efficient OFDM transmission scheme

引用

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

作者： Jaekwon Kim Joonhyuk Kang Edward J. Powers Department of Electrical and Computer Engineering and Telecommunications and Signal Processing Research Center University of Texas Austin Austin TX USA

In this paper, a new bandwidth efficient OFDM transmission scheme is proposed. A bandwidth efficient iterative scheme for OFDM systems without using cyclic prefix was proposed before [3] which works well when a channel does not have a deep spectral null. But such a frequency domain deep null is common in a wireless channel. A bandwidth efficient scheme proposed in this paper works well regardless of the existence of spectral null. In the proposed scheme, OFDM symbols are recovered in two steps. In the first step, only a small portion of the time domain OFDM symbol is recovered by the frequency domain 1-tap equalizer. In the second step, the recovered small portion and the tail part of the previous symbol are used for the cyclic reconstruction and tail cancellation. Simulation experiments are conducted to validate the proposed scheme.

关键词： Lead Artificial neural networks Computational modeling Bandwidth

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Ergodic capacities for downlink of MC-CDMA system with different detection and resource allocation strategies

Ergodic capacities for downlink of MC-CDMA system with diffe...

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Asilomar Conference on signals, Systems & computers

作者： Jianming Zhu Y. Bar-Ness Center for Communication and Signal Processing Research Department of Electrical and Computer Engineering New Jersey Institute of Technology Newark NJ USA

We considered the ergodic capacity for the downlink of an MC-CDMA system. Peer-to-peer decoding and successive cancellation decoding are considered to obtain the ergodic capacity region. It is assumed that the transmitter does not track the instantaneous channel response of all users, but notices the average received SNR of each user. Three types of resource allocation strategies are considered. Numerical results demonstrate ergodic capacity regions with different combination of decoding and resource allocation strategies under the Rayleigh frequency selective channel.

关键词： Downlink Multicarrier code division multiple access Resource management Transmitters Decoding Broadcasting Multiaccess communication Wireless communication Fading Wireless LAN

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Error analysis of the pruned multi-angle resolution beamformer

Error analysis of the pruned multi-angle resolution beamform...

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IEEE Digital signal processing Workshop

作者： Yeo-Sun Yoon L.M. Kaplan J.H. McClellan Center for Signal and Image Processing School of Electrical and Computer Engineering Georgia Institute of Technology Atlanta GA USA CTSPS Department of Engineering Clark Atlanta University Atlanta GA USA

ISBN: (纸本)0780381165

Recently, we proposed the pruned fast beamformer that is able to detect coherent signals during beamforming. The fast beamformer is a multistage approximation to delay and sum beamforming. Using a coherent signal detector, the pruned fast beamformer is able to reduce the computational load by eliminating processing to resolve steering directions that do not contain a target-like source. This paper analyzes the performance of the detector and discusses how approximation errors in the fast beamformer effects detection performance. The results indicate that the coherence detectors is effective under the approximation errors.

关键词： Error analysis Array signal processing Sensor arrays signal processing Detectors Approximation error signal resolution signal detection Delay Performance analysis

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A study between orthogonal subspace projection and generalized likelihood ratio test in hyperspectral image analysis

A study between orthogonal subspace projection and generaliz...

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IEEE International Symposium on Geoscience and Remote Sensing (IGARSS)

作者： Qian Du Hsuan Ren Chein-I Chang Department of Electrical Engineering and Computer Science Texas A and M University Kingsville TX USA Edgewood Chemical and Biological Center US Army MD USA Remote Sensing Signal and Image Processing Laboratory Department of Computer Science and Electrical Engineering University of Maryland Baltimore MD USA

Orthogonal subspace projection (OSP) and generalized likelihood ratio test (GLRT) have shown success in hyperspectral image classification. The OSP is derived by maximizing signal-to-noise ratio (SNR) resulting from a linear mixture model in which the noise is assumed to be white. On the other hand, the GLRT is formulated based on a signal detection model that can be described by a binary hypothesis testing problem. In order for the GLRT to derive an analytical form, the noise in the signal detection model is generally assumed to be white Gaussian noise. However, Gaussianity is generally not true in remotely sensed imagery. Interestingly, such assumption has not been investigated. This paper presents a comparative study between OSP and GLRT based on their assumptions. In particular, a detailed analysis of assumptions made on these two approaches is conducted through a series of computer simulations. Experimental results show that the OSP does not depend on Gaussian noise. By the contrast, the GLRT is affected by the Gaussian noise assumption. If it is violated, its performance is degraded.

关键词： Testing Hyperspectral imaging Image analysis Gaussian noise signal to noise ratio Hyperspectral sensors signal detection Image classification signal analysis Gaussian processes

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