Cryo-EM image alignment based on nonuniform fast Fourier transform

In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis.     

几种典型图像采集和处理系统设计与效率分析

以图像采集和处理系统总体框架为基础,介绍了几种典型设计方案,分析了不同方案中系统的时间效率及影响因素.通过实验测试,验证理论分析的正确性,总结了不同方案的合理使用建议.     

农业古籍断句标点模式研究

农业古籍的整理已经引起了众多学者和专家的注意,但是,对于农业古籍的自动断句、标点模式的研究仍付之阙如。本研究探索并总结出部分农业古籍断句、标点识别模式。首先采用句法特征词断句法、同义语标志词法进行初步断句;进而利用反义复合词、引书标志、时序、数量词、重叠字词、动名结构及比较句法进一步对子句进行断句、标点;最后使用农业用语和禁用模式表进一步提高断句、标点后农业古籍的可读性和准确性。经测试表明,断句、标点的平均准确率分别达到48%和35%,证明本方法具有一定的正确性和可行性。     

Horizontal Voting Ensemble Based Predictive Modeling System for ColonCancer

Colon cancer is the third most commonly diagnosed cancer in the world. Most colon AdenoCArcinoma (ACA) arises from pre-existing benign polyps in the mucosa of the bowel. Thus, detecting benign at the earliest helps reduce the mortality rate. In this work, a Predictive Modeling System (PMS) is developed for the classification of colon cancer using the Horizontal Voting Ensemble (HVE) method. Identifying different patterns in microscopic images is essential to an effective classification system. A twelve-layer deep learning architecture has been developed to extract these patterns. The developed HVE algorithm can increase the system’s performance according to the combined models from the last epochs of the proposed architecture. Ten thousand (10000) microscopic images are taken to test the classification performance of the proposed PMS with the HVE method. The microscopic images obtained from the colon tissues are classified into ACA or benign by the proposed PMS. Results prove that the proposed PMS has ~8% performance improvement over the architecture without using the HVE method. The proposed PMS for colon cancer reduces the misclassification rate and attains 99.2% of sensitivity and 99.4% of specificity. The overall accuracy of the proposed PMS is 99.3%, and without using the HVE method, it is only 91.3%.     

A parallelized eno procedure for direct numerical simulation of compressible turbulence

In this paper, a finite-difference based ENO (essentially nonoscillatory) procedure has been chosen for the direct numerical simulation (DNS) of compressible turbulence. The implementation of the ENO scheme follows the relatively efficient procedure in Shuet al. (1992), but the latter has been modified in the present paper to admit scalar conservation equations and to run on the iPSC/860 Paragon parallel supercomputer. DNS results with our procedure are in excellent agreement with pseudo-spectral and Padé approximation calculations in two and three dimensions. This is the case for a variety of initial conditions for compressible turbulence. The parallel algorithms presented are simple but quite efficient for DNS, with a speedup that approaches the theoretical value. Some of the attractive features include 1) minimum communication whereby a processor only communicates with two neighbors, 2) almost one hundred percent load balancing, 3) a checker-board approach to solve the Poisson equation reduces communication by a factor of approximately 2, and, 4) obtaining turbulence statistics is based on a global collect approach, which is implemented to ensure that a single number, rather than a large matrix of numbers, is communicated between processors. The ENO code presented in this paper should be quite useful in its own right, while the parallel implementation should allow the simulation of fairly realistic problems.     

Parallel algorithms for image enhancement and segmentation by region growing, with an experimental study

This paper presents efficient and portable implementations of a powerful image enhancement process, the Symmetric Neighborhood Filter (SNF), and an image segmentation technique that makes use of the SNF and a variant of the conventional connected components algorithm which we call -Connected Components. We use efficient techniques for distributing and coalescing data as well as efficient combinations of task and data parallelism. The image segmentation algorithm makes use of an efficient connected components algorithm based on a novel approach for parallel merging. The algorithms have been coded in Split-C and run on a variety of platforms, including the Thinking Machines CM-5, IBM SP-1 and SP-2, Cray Research T3D, Meiko Scientific CS-2, Intel Paragon, and workstation clusters. Our experimental results are consistent with the theoretical analysis (and provide the best known execution times for segmentation, even when compared with machine-specific implementations). Our test data include difficult images from the Landsat Thematic Mapper (TM) satellite data.Also affiliated with the Department of Electrical Engineering.Also affiliated with the Department of Computer Science and the Center for Automation Research.     

创新实践教学模式,培养复合型人才

针对目前高校现行实践教学体制存在的弊端,在分析产生原因的基础上,提出一种科学的实践教学模式,该模式与信息与计算科学专业培养的目标以及社会发展的内在需求相结合,在信息处理和软件开发能力培养方面取得一定效果,增强了学生就业竞争力。     

基于CBS模式的档案管理数字化系统的研究

随着我国经济和社会的飞速发展.人民对信息的要求日益提高.档案管理在这种新的形势下.面临巨大的挑战.传统的档案管理已经不能适应新形势的发展,档案管理数字化系统进行研究势在必行.本文主要对档案管理的涵义、数字化系统方案设计.文档图像处理和系统软件部分等进行了相应的阐述.本文的研究对以后指导档案管理工作具有一定的理论意义和现实意义.     

Embedding multi-dimensional meshes into twisted cubes

The twisted cube is an important variant of the most popular hypercube network for parallel processing. In this paper, we consider the problem of embedding multi-dimensional meshes into twisted cubes in a systematic way. We present a recursive method for embedding a family of disjoint multi-dimensional meshes into a twisted cube with dilation 1 and expansion 1. We also prove that a single multi-dimensional mesh can be embedded into a twisted cube with dilation 2 and expansion 1. Our work extends some previously known results.