On denoising and compression of DNA microarray images

We address the problems of noise and huge data sizes in microarray images. First, we propose a mixture model for describing the statistical and structural properties of microarray images. Then, based on the microarray image model, we present methods for denoising and for compressing microarray images. The denoising method is based on a variant of the translation-invariant wavelet transform. The compression method introduces the notion of approximate contexts (rather than traditional exact contexts) in modeling the symbol probabilities in a microarray image. This inexact context modeling approach is important in dealing with the noisy nature of microarray images. Using the proposed denoising and compression methods, we describe a near-lossless compression scheme suitable for microarray images. Results on both denoising and compression are included, which show the performance of the proposed methods. Further experiments using the results of the proposed near-lossless compression scheme in gene clustering using cell-cycle microarray data for S. cerevisiae showed a general improvement in the clustering performance, when compared with using the original data. This provides an indirect validation of the effectiveness of the proposed denoising method.     

Non-redundant data clustering

Data clustering is a popular approach for automatically finding classes, concepts, or groups of patterns. In practice, this discovery process should avoid redundancies with existing knowledge about class structures or groupings, and reveal novel, previously unknown aspects of the data. In order to deal with this problem, we present an extension of the information bottleneck framework, called coordinated conditional information bottleneck, which takes negative relevance information into account by maximizing a conditional mutual information score subject to constraints. Algorithmically, one can apply an alternating optimization scheme that can be used in conjunction with different types of numeric and non-numeric attributes. We discuss extensions of the technique to the tasks of semi-supervised classification and enumeration of successive non-redundant clusterings. We present experimental results for applications in text mining and computer vision.     

Learning Recursive Bayesian Multinets for Data Clustering by Means of Constructive Induction

This paper introduces and evaluates a new class of knowledge model, the recursive Bayesian multinet (RBMN), which encodes the joint probability distribution of a given database. RBMNs extend Bayesian networks (BNs) as well as partitional clustering systems. Briefly, a RBMN is a decision tree with component BNs at the leaves. A RBMN is learnt using a greedy, heuristic approach akin to that used by many supervised decision tree learners, but where BNs are learnt at leaves using constructive induction. A key idea is to treat expected data as real data. This allows us to complete the database and to take advantage of a closed form for the marginal likelihood of the expected complete data that factorizes into separate marginal likelihoods for each family (a node and its parents). Our approach is evaluated on synthetic and real-world databases.     

Question hard, answer simply: A comment on Storms et al. (2003).

It seems clear that, for whatever reasons, the dementia of the Alzheimer type patient group (as well as other patient groups) exhibits behavior that is different from the normal control group. G. Storms, T. Dirikx, J. Saerens, S. Verstraeten, and P. P. De Deyn (2003) rightfully argue that the observed behavior (similarity judgments) does not tell us the source (cause) of the differences between the 2 groups. Rather, the focus of the study should be placed more on finding the ways the 2 groups are different. They also point out various methodological problems in some of the previous attempts to characterize the nature of the differences. Further methodological issues in G. Storms et al.'s study are examined. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

一种应用于二次布局的有效划分方法

提出了一种基于二次布局的结合MFFC结群和hMETIS划分的算法.实验表明:这种方法能得到很好的布局结果,但是运行消耗的时间比较长.为了缩短划分在二次布局中运行的时间,提出了一种改进的结群算法IMFFC,用它在二次布局中做划分.与前者相比较,这种方法虽然布局质量稍差,但速度更快.     

Capacitated Clustering Problems by Hybrid Simulated Annealing and Tabu Search

The capacitated clustering problem (CCP) is the problem in which a given set of weighted objects is to be partitioned into clusters so that the total weight of objects in each cluster is less than a given value (cluster ‘capacity’). The objective is to minimize the total scatter of objects from the ‘centre’ of the cluster to which they have been allocated. A simple constructive heuristic, a R-interchange generation mechanism, a hybrid simulated annealing (SA) and tabu search (TS) algorithm which has computationally desirable features using a new non-monotonic cooling schedule, are developed. A classification of the existing SA cooling schedules is presented. The effects on the final solution quality of the initial solutions, the cooling schedule parameters and the neighbourhood search strategies are investigated. Computational results on randomly generated problems with size ranging from 50 to 100 customers indicate that the hybrid SA/TS algorithm out-performs previous simulated annealing algorithms, a simple tabu search and local descent algorithms.     

模糊聚类在三维地震参数处理中的应用

三维地震参数是一个庞大的三维数据体，能从不同侧面反映储集层的特征。通过对三维地震参数的分析，可以评估油藏表征的参数（沉积相、构造、生长历史、流体饱和度等）。针对传统的聚类方法不能很好地综合考虑各个参数之间的相似程度，提出了用模糊C-均值聚类（fuzzy c-means clustering，简称FCM）对三维地震参数进行处理。从三维地震参数和油藏表征参数之间的关系出发，采用模糊C-均值聚类方法对三维地震参数进行处理，依此评估油藏表征的参数。测试结果表明，模糊C-均值聚类方法能够对三维地震参数进行较为准确的分类，并为储集层的研究提供了很好的依据。     

模糊C-球壳聚类算法及其在血液细胞图像中的应用

文章从经典的模糊C均值算法开始通过改变其中相似性的度量形式，介绍了一种模糊C球壳聚类（FCSS）算法。在将该算法应用于细胞显微图像半径统计时，采用基于形态学的图像预处理措施，可以获得FCSS算法中有关原型模式的知识，加快收敛速度并避免随机初始化造成的局部极小问题。     

Structured document storage and refined declarative and navigational access mechanisms in HyperStorM

The combination of SGML and database technology allows to refine both declarative and navigational access mechanisms for structured document collection: with regard to declarative access, the user can formulate complex information needs without knowing a query language, the respective document type definition (DTD) or the underlying modelling. Navigational access is eased by hyperlink-rendition mechanisms going beyond plain link-integrity checking. With our approach, the database-internal representation of documents is configurable. It allows for an efficient implementation of operations, because DTD knowledge is not needed for document structure recognition. We show how the number of method invocations and the cost of parsing can be significantly reduced. Edited by Y.C. Tay. Received April 22, 1996 / Accepted March 16, 1997