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Feature extraction for DNA base-calling using NNLS

Feature extraction for DNA base-calling using NNLS

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IEEE/SP Workshop on Statistical signal processing (SSP)

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

We present new algorithms that can be used to extract features from a DNA chromatogram prior to base-calling. The algorithms assume that the inter-base distance has already been equalized using methods such as those presented in L. Andrade-Cetto and E. Manolakos (2005). We show first how a good estimate of the peak diffusion (spread) can be calculated from the raw trace and without having to known the underlying base sequence. Using the estimated inter-peak distance and peak spread parameters a non-negative least squares problem can be formulated in order to find the weight factors of the multiple shapes immersed in broad peaks, typically found towards the end of the chromatogram. The two algorithms combined provide peak hypotheses that are tested by the subsequent base decisions and scoring stage of the base-caller using probabilistic methods

关键词： Feature extraction Sequences signal processing algorithms Electrokinetics Labeling Distortion Digital signal processing DNA computing Least squares approximation Shape

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3D ROC analysis for medical imaging diagnosis

3D ROC analysis for medical imaging diagnosis

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2005 27th Annual International Conference of the engineering in Medicine and Biology Society, IEEE-EMBS 2005

作者： Wang, Su Chang, Chein-I Yang, Sheng-Chih Hsu, Giu-Cheng Hsu, Hsian-He Chung, Pau-Choo Guo, Shu-Mei Lee, San-Kan Remote Sensing Signal and Image Processing Laboratory Department of Computer Science and Electrical Engineering University of Maryland Baltimore County Baltimore MD 21250 Department of Electrical Engineering National Cheng Kung University Taiwan Department of Radiology Tri-Service General Hospital National Defense Medical Center Taipei 114 Taiwan Department of Computer Science and Information Engineering National Cheng Kung University Taiwan Administrative Office Suao Veterans Hospital Yuan County 270 Taiwan

ISBN: (纸本)0780387406

Receiver operating characteristics (ROC) has been widely used as a performance evaluation tool to measure effectiveness of medical modalities. It is derived from a standard detection theory with false alarm and detection power interpreted as false positive (FP) and true positive (TP) respectively in terms of medical diagnosis. The ROC curve is plotted based on TP versus FP via hard decisions. This paper presents a three dimensional (3D) ROC analysis which extends the traditional two-dimensional (2D) ROC analysis by including a threshold parameter in a third dimension resulting from soft decisions, (SD). As a result, a 3D ROC curve can be plotted based on three parameters, TP, FP and SD. By virtue of such a 3D ROC curve three two-dimensional (2D) ROC curves can be derived, one of which is the traditional 2D ROC curve of TP versus FP with SD reduced to hard decision. In order to illustrate its utility in medical diagnosis, its application to magnetic resonance (MR) image classification is demonstrated. © 2005 IEEE.

关键词： Medical imaging

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Data-Hiding Codes

Data-Hiding Codes

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作者： Moulin, Pierre Koetter, Ralf IEEE United States University of Illinois Urbana IL 61801 United States Department of Electrical and Computer Engineering United States Beckman Institute Coordinated Science Laboratory United States Department of Statistics United States Board of Governors IEEE Signal Processing Society United States Coordinated Science Laboratory United States

This tutorial paper reviews the theory and design of codes for hiding or embedding information in signals such as images, video, audio, graphics, and text. Such codes have also been called watermarking codes;they can be used in a variety of applications, including copyright protection for digital media, content authentication, media forensics, data binding, and covert communications. Some of these applications imply the presence of an adversary attempting to disrupt the transmission of information to the receiver;other applications involve a noisy, generally unknown, communication channel. Our focus is on the mathematical models, fundamental principles, and code design techniques that are applicable to data hiding. The approach draws from basic concepts in information theory, coding theory, game theory, and signal processing, and is illustrated with applications to the problem of hiding data in images. © 2005 IEEE.

关键词： Codes (symbols)

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A blind estimation approach for symbol timing and carrier frequency offset

A blind estimation approach for symbol timing and carrier fr...

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IEEE International Workshop on VLSI Design and Video Technology, IWVDVT

作者： Feng Yan Wei-Ping Zhu M.O. Ahmad Centre for Signal Processing and Communications Department of Electrical and Computer Engineering Concordia University Montreal QUE Canada Information Science and Engineering Concordia University Montreal QUE Canada

In this paper, the cyclostationarity of over-sampled signal in orthogonal frequency division multiplexing (OFDM) communication systems is studied. A blind symbol timing and carrier frequency offset estimation algorithm is presented based on the cyclic correlation. The proposed algorithm is computationally efficient, and asymptotically unbiased and consistent. Simulation results show that the proposed algorithm is superior to some of the existing methods in terms of the mean square error (MSE) of the estimate.

关键词： Frequency estimation Timing OFDM signal processing algorithms Fading Interchannel interference Pulse shaping methods Additive noise signal processing Computational modeling

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Cost-effective video filtering solution for real-time vision systems

Cost-effective video filtering solution for real-time vision...

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作者： Fischer, Viktor Lukac, Rastislav Martin, Karl Laboratoire Traitement du Signal et Instrumentation Unité Mixte de Recherche CNRS 5516 Université Jean Monnet 10 rue Barrouin 42000 Saint-Etienne France Multimedia Laboratory Edward S. Rogers Sr. Department of Electrical and Computer Engineering University of Toronto 10 King's College Road Toronto Ont. M5S 3G4 Canada Jean Monnet University of Saint-Etienne France Department of Electronics and Computer Science Micronic Košice Slovakia Edward S. Rogers Sr. Department of Electrical and Computer Engineering University of Toronto Toronto Canada IEEE Circuits and Systems IEEE Consumer Electronics IEEE Signal Processing Societies IEEE Signal Processing Society Communications Society

This paper presents an efficient video filtering scheme and its implementation in a field-programmable logic device (FPLD). Since the proposed nonlinear, spatiotemporal filtering scheme is based on order statistics, its efficient implementation benefits from a bit-serial realization. The utilization of both the spatial and temporal correlation characteristics of the processed video significantly increases the computational demands on this solution, and thus, implementation becomes a significant challenge. Simulation studies reported in this paper indicate that the proposed pipelined bit-serial FPLD filtering solution can achieve speeds of up to 97.6 Mpixels/s and consumes 1700 to 2700 logic cells for the speed-optimized and area-optimized versions, respectively. Thus, the filter area represents only 6.6 to 10.5% of the Altera STRATIX EP1S25 device available on the Altera Stratix DSP evaluation board, which has been used to implement a prototype of the entire real-time vision system. As such, the proposed adaptive video filtering scheme is both practical and attractive for real-time machine vision and surveillance systems as well as conventional video and multimedia applications.

关键词： computer vision

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Design of frequency-invariant beamformers employing multi-dimensional Fourier transforms

Design of frequency-invariant beamformers employing multi-di...

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International Workshop on Multidimensional (nD) Systems

作者： Wei Liu S. Weiss Communications & Signal Processing Group Department of Electrical & Electronic Engineering Imperial College London London UK Communications Research Group School of Electronics & Computer Science University of Southampton UK

The design of a class of broadband arrays with frequency invariant beam patterns is studied and a simplified version of the design method employing multi-dimensional Fourier transforms is proposed with detailed account of each step. In the design examples, we give a mathematical explanation for the failure of this method in the lower frequencies. For a design with main beam pointing to a direction other than the broadside, the frequency invariant property is not good and two solutions for this problem are provided.

关键词： Frequency Fourier transforms Sensor arrays Filters Array signal processing signal design Educational institutions computer science Design methodology Two dimensional displays

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Characterization of a cascade LMS predictor

Characterization of a cascade LMS predictor

引用

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

作者： D.Y. Huang X. Su A. Nallanathan Multimedia Signal Processing Laboratory/Media Division Institute for Infocomm Research Singapore Department of Electrical and Computer Engineering National University of Singapore Singapore

An FIR cascade structure for adaptive linear prediction is studied in which each stage FIR filter is independently adapted using an LMS algorithm. Theoretical analysis shows that the cascade performs a linear prediction in a way of successive refinement and each stage tries to obliterate the dominant mode of its input. Experimental results show that the performance of the cascade LMS predictor are in good agreement with our theoretical analysis.

关键词： Least squares approximation Finite impulse response filter Convergence Performance analysis signal analysis Adaptive signal processing Laboratories signal processing algorithms Speech coding Video coding

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A frequency domain sphericity test based approach for parsimonious rake receivers in CDMA systems

A frequency domain sphericity test based approach for parsim...

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International Symposium on signal processing and Its Applications (ISSPA)

作者： A.A. El-sallam Y.H. Leung A.M. Zoubir Communications & Signal Processing Group Department of Electrical & Computer Engineering Curtin University of Technology Perth WA Australia Signal Theory Group Institute for Communication Technology Darmstadt University of Technology Merckstrasse Germany

A frequency domain approach is presented for parsimonious channel estimation which can result in the implementation of a low complexity DS-CDMA RAKE receiver. We consider frequency selective slowly fading channels. A new approach is proposed to identify and estiamte only significant channel parameters. The approach uses the sphericity test and delay estimation methods based on averaged periodogram techniques. Simulations show that, with short training sequences and low signal to noise ratio, the proposed technique can correctly identify the significant channel parameters. Also the parsimonious RAKE receiver based on these estimates gives improved statistical as well as computational performance over classical methods.

关键词： Frequency domain analysis System testing Fading Multipath channels Multiaccess communication Baseband signal processing Correlators Fingers Delay

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An embedded system developed for hand held assay used in water monitoring

An embedded system developed for hand held assay used in wat...

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Chemical and Biological Standoff Detection III

作者： Wu, Lin Wang, Jianwei Ramakrishna, Bharath Hsueh, Mingkai Liu, Jonathan Wu, Qufei Wu, Chao-Cheng Cao, Mang Chang, Chein-I. Jensen, Janet L. Jensen, James O. Knapp, Harlan Daniel, Robert Yin, Ray Remote Sensing Signal and Image Processing Laboratory Department of Computer Science and Electrical Engineering University of Maryland Baltimore County Baltimore MD 21250 US Army Edgewood Chemical and Biological Center Aberdeen Proving Ground MD 21010 ANP Technologies Inc. 824 Interchange Boulevard Newark DE 19711

The US Army Joint Service Agent Water Monitor (JSAWM) program is currently interested in an approach that can implement a hardware-designed device in ticket-based hand-held assay (currently being developed) used for chemical/biological agent detection. This paper presents a preliminary investigation of the proof of concept. Three components are envisioned to accomplish the task. One is the ticket development which has been undertaken by the ANP, Inc. Another component is the software development which has been carried out by the Remote Sensing signal and Image processing laboratory (RSSIPL) at the University of Maryland, Baltimore County (UMBC). A third component is an embedded system development which can be used to drive the UMBC-developed software to analyze the ANP-developed HHA tickets on a small pocket-size device like a PDA. The main focus of this paper is to investigate the third component that is viable and is yet to be explored. In order to facilitate to prove the concept, a flatbed scanner is used to replace a ticket reader to serve as an input device. The Stargate processor board is used as the embedded System with Embedded Linux installed. It is connected to an input device such as scanner as well as output devices such as LCD display or laptop etc. It executes the C-Coded processing program developed for this embedded system and outputs its findings on a display device. The embedded system to be developed and investigated in this paper is the core of a future hardware device. Several issues arising in such an embedded system will be addressed. Finally, the proof-of-concept pilot embedded system will be demonstrated.

关键词： Embedded systems

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3D ROC analysis for detection software used in water monitoring

3D ROC analysis for detection software used in water monitor...

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Chemical and Biological Standoff Detection III

作者： Liu, Wei-Min Wang, Su Chang, Chein-I. Jensen, Janet L. Jensen, James O. Knapp, Harlan Daniel, Robert Yin, Ray Remote Sensing Signal and Image Processing Laboratory Department of Computer Science and Electrical Engineering University of Maryland Baltimore County Baltimore MD 21250 US Army Edgewood Chemical and Biological Center Aberdeen Proving Ground MD 21010 ANP Technologies Inc. 824 Interchange Boulevard Newark DE 19711

Under the U.S. Army sponsored Joint Service Agent Water Monitor (JSAWM) program, developing hand-held assays using tickets for chemical/biological agent detection has been of major interest. One of keys to success is to develop detection algorithms that not only can effectively detect the presence of various agents, but also can quantify the detected agents. This paper presents a recent development of detection software that can perform 3-dimensional (3D) receiver operating characteristics (ROC) analysis which is based on quantified agent concentration. The ROC curves have been widely used in communications, signal processing and medical communities to evaluate the effectiveness of a detection technique. It generally formulates a signal detection problem as a binary composite hypothesis testing problem with the null hypothesis and the alternative hypothesis represents the case of no signal and the case of signal presence respectively. The ROC curve is then plotted based on the detection probability (power) PD versus the false alarm probability, P F. Unfortunately, such a two-dimensional (2D) (PD,P F)-based ROC curve does not factor in the concentration detected in an agent signal which is a crucial parameter in chemical/biological agent detection. The proposed 3D ROC analysis is developed from such a need. It includes an additional parameter, referred to as threshold t, which is used to threshold the detected agent signal concentration. Consequently, a different value of t results in a different 2D ROC curve. In order to take into account the thresholding factor t, a 3D ROC curve is derived and plotted based on three parameters, (PD,PF,t). As a result of the 3D ROC curve, three 2D ROC curves can be also derived. One is the conventional 2D (P D,PF)-ROC curve. Another is a 2D (PD,t)-ROC curve which describes the relationship between PD and the threshold value t. A third one is a 2D (PF,t)-ROC curve which shows the effect of the threshold value t on PF. The utility of

关键词： computer software

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