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IEEE International Conference on Image Processing

作者： S.D. Booth J.A. Fessler Bioengineering Program and Department of Electrical Engineering and Computer Science University of Michigan MI USA

Iterative methods for tomographic image reconstruction often converge slowly. Preconditioning methods can often accelerate gradient-based iterations. Previous preconditioning methods for PET reconstruction have used either diagonal or Fourier-based preconditioners. Fourier-based preconditioners are well suited to problems with near-circulant Hessian matrices. However, due to the nonuniform Poisson noise variance in PET, the circulant approximation to the Hessian is suboptimal. This paper shows that a particular combined diagonal/Fourier preconditioner yields a more accurate approximation to the Hessian and gives significantly faster convergence rates than does either preconditioner used alone.

关键词： Image reconstruction Tomography Character generation Symmetric matrices Equations Iterative methods Minimization methods Covariance matrix Spatial resolution Yield estimation

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GranatumX:A Community-engaging, Modularized, and Flexible Webtool for Single-cell Data Analysis

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Genomics, Proteomics & Bioinformatics 2021年第3期19卷 452-460页

作者： David G.Garmire Xun Zhu Aravind Mantravadi Qianhui Huang Breck Yunits Yu Liu Thomas Wolfgruber Olivier Poirion Tianying Zhao Cédric Arisdakessian Stefan Stanojevic Lana X.Garmire Department of Electrical Engineering&Computer Science University of MichiganAnn ArborMI 48109USA Epidemiology Program University of Hawaii Cancer CenterHonoluluHI 96813USA Department of Biostatistics University of MichiganAnn ArborMI 48109USA Department of Computational Medicine and Bioinformatics University of MichiganAnn ArborMI 48105USA Molecular Biosciences and Bioengineering Graduate Program University of Hawaii at ManoaHonoluluHI 96822USA

We present GranatumX,a next-generation software environment for single-cell RNA sequencing(scRNA-seq)data *** is inspired by the interactive webtool *** enables biologists to access the latest scRNA-seq bioinformatics methods in a web-based graphical *** also offers software developers the opportunity to rapidly promote their own tools with others in customizable *** architecture of GranatumX allows for easy inclusion of plugin modules,named Gboxes,which wrap around bioinformatics tools written in various programming languages and on various *** can be run on the cloud or private servers and generate reproducible *** is a community-engaging,flexible,and evolving software ecosystem for scRNA-seq analysis,connecting developers with bench *** is freely accessible at http://***/granatumx/app.

关键词： Single-cell RNA sequencing Analysis Pipeline Webtool Module

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Information-Theoretic Design for High-Dimensional Computational Imaging

Information-Theoretic Design for High-Dimensional Computatio...

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Computational Optical Sensing and Imaging, COSI 2024 - Part of Optica Imaging Congress

作者： Markley, Eric Kabuli, Leyla Chien, Tiffany Pinkard, Henry Waller, Laura UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley United States Department of Electrical Engineering and Computer Sciences University of California Berkeley United States

We present a technique for information-theoretic optimization of computational imaging systems demonstrated in snapshot 3D microscopy. By directly evaluating measurement quality and decoupling optimization from downst... 详细信息

关键词： Decoding

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Spectral DefocusCam: hyperspectral imaging using defocus and a spectral filter array

Spectral DefocusCam: hyperspectral imaging using defocus and...

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Computational Optical Sensing and Imaging, COSI 2022

作者： Foley, Christian Monakhova, Kristina Yanny, Kyrollos Waller, Laura Department of Electrical Engineering and Computer Sciences University of California Berkeley United States UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley United States

We propose a compact hyperspectral camera based on a focus-tunable lens and spectral filter array. The camera captures then fuses multiple defocused measurements to obtain a high-resolution hyperspectral volume. ©... 详细信息

ISBN: (纸本)9781557528209

关键词： Hyperspectral imaging

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Modularity detection in protein-protein interaction networks

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BMC Research Notes 2011年第1期4卷 1-6页

作者： Narayanan, Tejaswini Gersten, Merril Subramaniam, Shankar Grama, Ananth Department of Electrical and Computer Engineering University of California San Diego United States Graduate Program in Bioinformatics and Systems Biology University of California San Diego United States Department of Bioengineering University of California San Diego United States Department of Computer Science Purdue University West Lafayette IN United States

Background: Many recent studies have investigated modularity in biological networks, and its role in functional and structural characterization of constituent biomolecules. A technique that has shown considerable promise in the domain of modularity detection is the Newman and Girvan (NG) algorithm, which relies on the number of shortest-paths across pairs of vertices in the network traversing a given edge, referred to as the betweenness of that edge. The edge with the highest betweenness is iteratively eliminated from the network, with the betweenness of the remaining edges recalculated in every iteration. This generates a complete dendrogram, from which modules are extracted by applying a quality metric called modularity denoted by Q. This exhaustive computation can be prohibitively expensive for large networks such as Protein-Protein Interaction Networks. In this paper, we present a novel optimization to the modularity detection algorithm, in terms of an efficient termination criterion based on a target edge betweenness value, using which the process of iterative edge removal may be terminated. Results: We validate the robustness of our approach by applying our algorithm on real-world protein-protein interaction networks of Yeast, *** and Drosophila, and demonstrate that our algorithm consistently has significant computational gains in terms of reduced runtime, when compared to the NG algorithm. Furthermore, our algorithm produces modules comparable to those from the NG algorithm, qualitatively and quantitatively. We illustrate this using comparison metrics such as module distribution, module membership cardinality, modularity Q, and Jaccard Similarity Coefficient. Conclusions: We have presented an optimized approach for efficient modularity detection in networks. The intuition driving our approach is the extraction of holistic measures of centrality from graphs, which are representative of inherent modular structure of the underlying network, and the applic

关键词： Biological Network Jaccard Index Input Network High Betweenness Jaccard Similarity Coefficient

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Snapshot hyperspectral imaging using a random phase mask and spectral filter array

Snapshot hyperspectral imaging using a random phase mask and...

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Computational Optical Sensing and Imaging, COSI 2020 - Part of Imaging and Applied Optics Congress 2020

作者： Monakhova, Kristina Yanny, Kyrollos Waller, Laura Department of Electrical Engineering and Computer Sciences University of California Berkeley United States UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley United States

We introduce a snapshot hyperspectral imager that uses a random phase mask, repeated spectral filter array, and compressive recovery to achieve high spatial and spectral resolution in a small form factor. © 2020 ... 详细信息

ISBN: (纸本)9781557528209

关键词： Hyperspectral imaging

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MultiWienerNet: Deep learning for fast shift-varying deconvolution

MultiWienerNet: Deep learning for fast shift-varying deconvo...

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Computational Optical Sensing and Imaging, COSI 2021 - Part of OSA Imaging and Applied Optics Congress 2021

作者： Shuai, Richard W. Yanny, Kyrollos Monakhova, Kristina Waller, Laura Department of Electrical Engineering and Computer Sciences University of California Berkeley United States UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley United States

We present a deep-learning method based on Wiener filters and U-Nets that performs image reconstruction in systems with spatially-varying aberrations. We train on simulated microscopy measurements and test on experime... 详细信息

ISBN: (纸本)9781557528209

关键词： Image reconstruction

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Ultrafast photonic PCR

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Light(science & Applications) 2015年第1期4卷 267-273页

作者： Jun Ho Son Byungrae Cho SoonGweon Hong Sang Hun Lee Ori Hoxha Amanda J Haack Luke P Lee Department of Bioengineering University of CaliforniaBerkeleyCA 94720USA Berkeley Sensor and Actuator Center University of CaliforniaBerkeleyCA 94720USA Department of Electrical Engineering and Computer Sciences University of CaliforniaBerkeleyCA 94720USA Biophysics Graduate Program University of CaliforniaBerkeleyCA 94720USA

Nucleic acid amplification and quantification via polymerase chain reaction(PCR)is one of the most sensitive and powerful tools for clinical laboratories,precision medicine,personalized medicine,agricultural science,forensic science and environmental *** multiplex PCR,characterized by low power consumption,compact size and simple operation,is ideal for timely diagnosis at the point-of-care(POC).Although several fast/ultrafast PCR methods have been proposed,the use of a simple and robust PCR thermal cycler remains challenging for POC ***,we present an ultrafast photonic PCR method using plasmonic photothermal light-to-heat conversion via photon–electron–phonon *** demonstrate an efficient photonic heat converter using a thin gold(Au)film due to its plasmon-assisted high optical absorption(approximately 65%at 450 nm,the peak wavelength of heat source light-emitting diodes(LEDs)).The plasmon-excited Au film is capable of rapidly heating the surrounding solution to over 150℃ within 3 *** this method,ultrafast thermal cycling(30 cycles;heating and cooling rate of 12.7960.93℃ s^(-1) and 6.660.29℃ s^(-1),respectively)from 55℃(temperature of annealing)to 95℃(temperature of denaturation)is accomplished within 5 *** photonic PCR thermal cycles,we demonstrate here successful nucleic acid(λ-DNA)*** simple,robust and low cost approach to ultrafast PCR using an efficient photonic-based heating procedure could be generally integrated into a variety of devices or procedures,including on-chip thermal lysis and heating for isothermal amplifications.

关键词： genomics light-emitting diodes(LEDs) molecular diagnostics personalized medicine plasmonics point-of-care(POC)diagnostics polymerase chain reaction(PCR)

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An efficient decryption method for RSA cryptosystem

An efficient decryption method for RSA cryptosystem

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19th International Conference on Advanced Information Networking and Applications, AINA 2005

作者： Hwang, Ren-Junn Su, Feng-Fu Yeh, Yi-Shiung Chen, Chia-Yao Department of Computer Science and Information Engineering TamKang University Tamsui Taipei 251 Taiwan Degree Program of Electrical Engineering and Computer Science National Chiao Tung University Hsinchu 300 Taiwan

ISBN: (纸本)0769522491

This paper proposes an efficient method to implement RSA decryption algorithm. RSA cryptosystem is the most attractive and popular security technique for many applications, such as electronic commerce and secure internet access. It has to perform modular exponentiation with large exponent and modulus for security consideration. The RSA cryptosystem takes great computational cost. In many RSA applications, user uses a small public key to speed up the encryption operation. However, the decryption operation has to take more computational cost to perform modular exponentiation by this case. This paper proposes an efficient decryption method not only based on Chinese Remainder Theorem (CRT) but also the strong prime of RSA criterion. The proposed decryption method only takes 10% computational costs of the traditional decryption method. It also reduces 66% computational costs than that of decryption methods based on CRT only. In a word, the speed of our proposed method is almost 2.9 times faster than the decryption method based on CRT only. The proposed method enhances the performance of the RSA decryption operation. © 2005 IEEE.

关键词： Cryptography

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Bubble-pen lithography:Fundamentals and applications

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Aggregate 2022年第4期3卷 85-100页

作者： Pavana Siddhartha Kollipara Ritvik Mahendra Jingang Li Yuebing Zheng Walker Department of Mechanical Engineering The University of Texas at AustinAustinTexasUSA Department of Electrical and Computer Engineering The University of Texas at AustinAustinTexasUSA Material Science and Engineering Program Texas Materials InstituteThe University of Texas at AustinAustinTexasUSA

Developing on-chip functional devices requires reliable fabrication methods with high resolution for miniaturization,desired components for enhanced performance,and high throughput for fast prototyping and mass ***,laser-based bubble-pen lithography(BPL)has been developed to enable sub-micron linewidths,in situ synthesis of custom materials,and on-demand patterning for various functional components and *** exploits Marangoni convection induced by a laser-controlled microbubble to attract,accumulate,and immobilize particles,ions,and molecules onto different *** years have witnessed tremendous progress in theory,engineering,and application of BPL,which motivated us to write this ***,an overview of experimental demonstrations and theoretical understandings of BPL is ***,we discuss the advantages of BPL and its diverse applications in quantum dot displays,biological and chemical sensing,clinical diagnosis,nanoalloy synthesis,and *** conclude this review with our perspective on the challenges and future directions of BPL.

关键词： additive manufacturing capillary flow lithography marangoni convection microbubbles sensing

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