基于平均交互信息量的DNA序列相似性分析

序列相似性分析是生物信息学中一个重要问题,对于研究物种的进化起源有着重要的意义.序列相似性算法包括基于序列比对的方法及非比对方法两种.基于比对的方法对于序列整体的衡量略有欠缺;非比对算法中有DNA曲线化方法以及比较序列各自整体碱基分布间的信息量差异的方法,只是考虑了序列整体信息间的差异,但未考虑序列各个位点间的差异.因此,提出了一种基于信息熵的相似性度量模型,把序列比对与信息量差异结合起来,将两条比对后的序列间的平均交互信息量与其联合熵之比作为两条序列的相似性度量.使用该度量构建了11个物种的相似性矩阵,对各物种间的相似性进行了分析,结果在一定程度上与生物分类学相契合.通过距离矩阵所构建的进化树,也反映了各物种间的进化关系,表明该模型的设计具有合理性.     

基于信息量的DNA序列相似性分析

针对传统方法在分析DNA序列相似性方面的不足, 提出了一种新的基于信息量的DNA序列相似性分析算法, 该方法将DNA序列视为基于符号集{A, C, G, T}的信号序列, 全部待比较的DNA序列组合成一个以字符A、C、G、T为属性值的信息系统。在所得数据库系统中引进DNA序列的信息量、联合信息量、条件信息量、交互信息量等概念, 讨论这些信息量的性质并给出它们之间的一些关系式, 然后在此基础上构建DNA序列相似性分析模型。仿真实验结果表明, 该方法不但能快速、有效地分析DNA序列相似性, 而且较好地克服了DNA碱基数量很大且不同物种的DNA序列长短不同的不足。     

基于整体和局部相似性的序列聚类算法

现有的很多序列聚类算法是基于“局部特征可以表征整个序列”的假设来进行的,即不区分实际应用中序列的整体相似性和局部相似性.这对存在保守子模式的序列,如DNA和蛋白质序列是适用的,但对一些注重整体序列相似性的应用领域,如:在交易数据库中用户购买行为的比较,时间序列数据中全局模式的匹配等,由于难以产生频繁子模式,用基于全局相似性的度量方法进行聚类显得更为合理.此外,在基于局部相似性的序列聚类算法中,选取的局部子模式表征序列的能力也有待进一步提高.由此,针对不同应用领域,分别提出基于整体相似性的序列聚类算法GSClu和基于局部相似性的序列聚类算法LSClu.GSClu和LSClu分别利用带剪枝策略的二分k均值算法和基于有gap约束的强区分度子模式方法对各自领域的序列数据进行聚类.实验采用交易序列数据和蛋白质序列数据,实验结果表明,GSClu和LSClu对各自领域的序列数据具有较快的处理速度和良好的聚类质量.     

一种新的D NA序列图形表达的方法

针对当前DNA序列图形表达模式中存在简并现象的相关问题,提出了一种新的二元符号图形表达方式。将四类碱基的编码过程看成是构成DNA序列的元素在直角坐标平面上的移动过程,以两种不同的标志符号来解决可能出现的元素重叠情况。此方案所标志的图形不存在自交现象,从而在DNA序列和图形表达之间建立了一一对应的关系。通过实例说明该方法在对无向图和有向图表达中均能有效地降低图形简并度,并引入人工代谢系统中的编码模式作为分析工具对DNA序列进行比较分析;以代谢中间物值作为参数,研究不同物种的DNA序列之间的相似性。实例分析表明,该参数能较好地表征不同物种之间的相似性程度高低,是一种简便可行的DNA序列特征的比较方法。     

DnaReSM：一个基于多支持度的DNA重复序列挖掘算法

DNA序列分析研究是生物信息学的重要内容之一。基因组的基因相关区域和基因外区域中含有大量重复序列，尽管目前大多数重复序列的功能还没能肯定，但它们在遗传分析中已起重要作用。挖掘DNA重复序列成为DNA序列分析的关键。自底向上的挖掘算法中间过程产生很多短的、甚至单字符的模式，使得挖掘效率降低；另一方面，目前序列模式挖掘算法在多序列挖掘中表现出高效性，但由于单支持度定义的局限导致无法在挖掘过程中同时找到单条DNA序列中的重复序列，因此不能很好地适用于DNA重复序列挖掘。本文基于新的多支持度序列模式挖掘框架，提出了一种融合自底向上和自顶向下策略挖掘DNA重复序列的新算法DnaReSM，其结果为生物学相关实验提供基础。实验结果表明，DnaReSM探测算法能有效挖掘DNA重复序列。     

双序列比对的算法研究

双序列比对是生物信息学中最基本的问题之一,其研究方法是设计具有针对性的有效算法对两个DNA或蛋白质序列进行比较,找出两者之间的最大相似性匹配进而判断其是否具有同源性。详尽分析了双序列比对的实际意义,提出最佳比对不一定能反映进化的实际过程并给予分析,重点探讨了最重要的全局比对算法——Smith Waterman算法,同时提出了一种用数组记录比对过程中遍历路径的方法并对比对过程进行递归调用,使之能找出全部具有最大相似性的比对结果。     

一种新的DNA序列3D表示方法及相似分析

提出了一种新的DNA序列的3D图形表示方法,该方法能体现较多的DNA序列的特征,而且避免了信息的丢失。为了进行DNA序列之间的相似性分析,在此方法的基础上对图形进行特征提取并利用高维数据降维算法对提取后的高维数据进行降维,并降到3维,降维后的数据不但保持了原有高维数据的特征而且能很方便地观察它们之间的关系。通过对10个物种的β-球蛋白基因的第一个外显子的相似性分析,得到了较好的结果。     

基于模式匹配的多序列相似性分析

本文提出了一种基于模式匹配的多序列相似性分析方法，该方法将模式匹配应用到序列比对中，采用Kimura双参数模型计算进化矩阵并构造物种进化树，进行相似性分析。实验结果表明该方法的有效性。     

基于数学形态学的时间序列相似性度量研究

时间序列相似性度量在挖掘时间序列模式,提取时间序列关联关系上发挥着重要作用。分析了当前主流的时间序列相似性度量算法,分别指出了各度量算法在度量时序数据相似性时存在的缺陷,并提出了基于数学形态学的时间序列相似性度量算法。通过将归一化的时间序列二值图像化表示,再引入了图像处理领域中的膨胀、腐蚀操作对时序数据进行形态变换分析,提高相似时序数据部分的抗噪性,同时又不降低时序数据非相似部分间的差异度,实现时序数据相似性度量分类精度的提高。在八种时间序列测试数据集合上进行分类实验,实验结果表明提出的基于数学形态学的时间序列相似性度量算法在时间序列分类精度上得到有效改善,相比于DTW相似性度量算法,分类精度平均水平提升了8.74%,最高提升20%。     

一种多搜索策略的多生物序列比对自适应遗传算法

多生物序列比对是用来计算生物序列间相似性的重要工具，本文在引入熵来度量种群多样性的基础上，提出了一种多搜索策略的自适应遗传算法，其交叉和变异概率随着熵的变化进行自动调整，并且综合考虑了利用动态规划算法来设计遗传操作算子．实验结果表明，这个算法具有较强的全局搜索能力和局部搜索能力，并且能有效的克服未成熟收敛问题．     

Only connect: teaching, technology and telesis

Abstract This paper describes an approach to the design of interactive multimedia materials being developed in a European Community project. The developmental process is seen as a dialogue between technologists and teachers. This dialogue is often problematic because of the differences in training, experience and culture between them. Conditions needed for fruitful dialogue are described and the generic model for learning design used in the project is explained.     

European Community policy and the market

Abstract This paper starts with some reflections on the policy considerations and priorities which are shaping European Commission (EC) research programmes. Then it attempts to position the current projects which seek to capitalise on information and communications technologies for learning in relation to these priorities and the apparent realities of the marketplace. It concludes that while there are grounds to be optimistic about the contribution EC programmes can make to the efficiency and standard of education and training, they are still too technology driven.     

一种自适应子融合集成多分类器方法

融合集成方法已经广泛应用在模式识别领域,然而一些基分类器实时性能稳定性较差,导致多分类器融合性能差,针对上述问题本文提出了一种新的基于多分类器的子融合集成分类器系统。该方法考虑在度量层融合层次之上通过对各类基多分类器进行动态选择,票数最多的类别作为融合系统中对特征向量识别的类别,构成一种新的自适应子融合集成分类器方法。实验表明,该方法比传统的分类器以及分类融合方法识别准确率明显更高,具有更好的鲁棒性。     

Avoiding semantic and temporal gaps in developing software intensive systems

Development of software intensive systems (systems) in practice involves a series of self-contained phases for the lifecycle of a system. Semantic and temporal gaps, which occur among phases and among developer disciplines within and across phases, hinder the ongoing development of a system because of the interdependencies among phases and among disciplines. Such gaps are magnified among systems that are developed at different times by different development teams, which may limit reuse of artifacts of systems development and interoperability among the systems. This article discusses such gaps and a systems development process for avoiding them.     

Designing economic np control charts: A programmed simulation approach

This paper presents control charts models and the necessary simulation software for the location of economic values of the control parameters. The simulation program is written in FORTRAN, requires only 10K of main storage, and can run on most mini and micro computers. Two models are presented - one describes the process when it is operating at full capacity and the other when the process is operating under capacity. The models allow the product quality to deteriorate to a further level before an existing out-of-control state is detected, and they can also be used in situations where no prior knowledge exists of the out-of-control causes and the resulting proportion defectives.     

The development of robot art

Going through a few examples of robot artists who are recognized worldwide, we try to analyze the deepest meaning of what is called “robot art” and the related art field definition. We also try to highlight its well-marked borders, such as kinetic sculptures, kinetic art, cyber art, and cyberpunk. A brief excursion into the importance of the context, the message, and its semiotics is also provided, case by case, together with a few hints on the history of this discipline in the light of an artistic perspective. Therefore, the aim of this article is to try to summarize the main characteristics that might classify robot art as a unique and innovative discipline, and to track down some of the principles by which a robotic artifact can or cannot be considered an art piece in terms of social, cultural, and strictly artistic interest. This work was presented in part at the 13th International Symposium on Artificial Life and Robotics, Oita, Japan, January 31–February 2, 2008     

Explanation and prediction: an architecture for default and abductive reasoning

Although there are many arguments that logic is an appropriate tool for artificial intelligence, there has been a perceived problem with the monotonicity of classical logic. This paper elaborates on the idea that reasoning should be viewed as theory formation where logic tells us the consequences of our assumptions. The two activities of predicting what is expected to be true and explaining observations are considered in a simple theory formation framework. Properties of each activity are discussed, along with a number of proposals as to what should be predicted or accepted as reasonable explanations. An architecture is proposed to combine explanation and prediction into one coherent framework. Algorithms used to implement the system as well as examples from a running implementation are given.     

Three Process Perspectives: Organizations, Teams, and People

This paper provides the author's personal views and perspectives on software process improvement. Starting with his first work on technology assessment in IBM over 20 years ago, Watts Humphrey describes the process improvement work he has been directly involved in. This includes the development of the early process assessment methods, the original design of the CMM, and the introduction of the Personal Software Process (PSP)^SM and Team Software Process (TSP){^SM}. In addition to describing the original motivation for this work, the author also reviews many of the problems he and his associates encountered and why they solved them the way they did. He also comments on the outstanding issues and likely directions for future work. Finally, this work has built on the experiences and contributions of many people. Mr. Humphrey only describes work that he was personally involved in and he names many of the key contributors. However, so many people have been involved in this work that a full list of the important participants would be impractical.     

基于复小波噪声方差显著修正的SAR图像去噪

提出了一种基于复小波域统计建模与噪声方差估计显著性修正相结合的合成孔径雷达(Synthetic Aperture Radar,SAR)图像斑点噪声滤波方法。该方法首先通过对数变换将乘性噪声模型转化为加性噪声模型,然后对变换后的图像进行双树复小波变换(Dualtree Complex Wavelet Transform,DCWT),并对复数小波系数的统计分布进行建模。在此先验分布的基础上,通过运用贝叶斯估计方法从含噪系数中恢复原始系数,达到滤除噪声的目的。实验结果表明该方法在去除噪声的同时保留了图像的细节信息,取得了很好的降噪效果。     

How do children do mathematics with LOGO?

Abstract  This paper considers some results of a study designed to investigate the kinds of mathematical activity undertaken by children (aged between 8 and 11) as they learned to program in LOGO. A model of learning modes is proposed, which attempts to describe the ways in which children used and acquired understanding of the programming/mathematical concepts involved. The remainder of the paper is concerned with discussing the validity and limitations of the model, and its implications for further research and curriculum development.