21789348
Evolutionary algorithms for grouping high dimensional Email data
Grouping problems arise in many industrial and medical applications; examples include bin packing, workshop layout design, and graph colouring. This type of problem has been successfully handled using Grouping Genetic Algorithms. However in problems where there are perhaps thousands of objects to be grouped, we have found that Genetic Algorithm approaches can run into problems. This paper continues our research into a method we have developed for decomposing a large number of objects into mutually exclusive subsets where within-group dependencies are high and between-group dependencies are low. The method uses an Evolutionary Algorithm approach but where the whole population is a solution to the grouping problem rather than considering many candidate solutions. This reduces the resource overheads during computer implementation and the results are promising when compared with standard statistical methods and a Hill Climbing algorithm, all applied to email log file data.
39184835
Improved Robustness in Time Series Analysis of Gene Expression Data by Polynomial Model Based Clustering
Microarray experiments produce large data sets that often contain noise and considerable missing data. Typical clustering methods such as hierarchical clustering or partitional algorithms can often be adversely affected by such data. This paper introduces a method to overcome such problems associated with noise and missing data by modelling the time series data with polynomials and using these models to cluster the data. Similarity measures for polynomials are given that comply with commonly used standard measures. The polynomial model based clustering is compared with standard clustering methods under different conditions and applied to a real gene expression data set. It shows significantly better results as noise and missing data are increased.
14510898
Evolutionary learning of dynamic probabilistic models with large time lags
In this paper, we explore the automatic explanation of multivariate time series (MTS) through learning dynamic Bayesian networks (DBNs). We have developed an evolutionary algorithm which exploits certain characteristics of MTS in order to generate good networks as quickly as possible. We compare this algorithm to other standard learning algorithms that have traditionally been used for static Bayesian networks but are adapted for DBNs in this paper. These are extensively tested on both synthetic and real-world MTS for various aspects of efficiency and accuracy. By proposing a simple representation scheme, an efficient learning methodology, and several useful heuristics, we have found that the proposed method is more efficient for learning DBNs from MTS with large time lags, especially in time-demanding situations. © 2001 John Wiley & Sons, Inc.
40113853
A Framework for Modelling Short, High-Dimensional Multivariate Time Series: Preliminary Results in Virus Gene Expression Data Analysis
Short, high-dimensional Multivariate Time Series (MTS) data are common in many fields such as medicine, finance and science, and any advance in modelling this kind of data would be beneficial. Nowhere is this more true than functional genomics where effective ways of analysing gene expression data are urgently needed. Progress in this area could help obtain a "global" view of biological processes, and ultimately lead to a great improvement in the quality of human life. We present a computational framework for modelling this type of data, and report preliminary experimental results of applying this framework to the analysis of gene expression data in the virology domain. The framework contains a threestep modelling strategy: correlation search, variable grouping, and short MTS modelling. Novel research is involved in each step which has been individually tested on different real-world datasets in engineering and medicine. This is the first attempt to integrate all these components into a coherent computational framework, and test the framework on a very challenging application area, which has produced promising results.
6104018
A framework for modelling virus gene expression data
Short, high-dimensional, Multivariate Time Series (MTS) data are common in many fields such as medicine, finance and science, and any advance in modelling this kind of data would be beneficial. Nowhere is this truer than functional genomics where effective ways of analysing gene expression data are urgently needed. Progress in this area could help obtain a “global” view of biological processes, and ultimately lead to a great improvement in the quality of human life. We present a computational framework for modelling this type of data, and report experimental results of applying this framework to the analysis of gene expression data in the virology domain. The framework contains a three-step modelling strategy: correlation search, variable grouping, and short MTS modelling. Novel research is involved in each step which has been individually tested on different real-world datasets in engineering and medicine. This is the first attempt to integrate all these components into a coherent computational framework, and test the framework on a very challenging application area, producing promising results.
16058917
Learning Dynamic Bayesian Networks from Multivariate Time Series with Changing Dependencies
Many examples exist of multivariate time series where dependencies between variables change over time. If these changing dependencies are not taken into account, any model that is learnt from the data will average over the different dependency structures. Paradigms that try to explain underlying processes and observed events in multivariate time series must explicitly model these changes in order to allow non-experts to analyse and understand such data. In this paper we have developed a method for generating explanations in multivariate time series that takes into account changing dependency structure. We make use of a dynamic Bayesian network model with hidden nodes. We introduce a representation and search technique for learning such models from data and test it on synthetic time series and real-world data from an oil refinery, both of which contain changing underlying structure. We compare our method to an existing EM-based method for learning structure. Results are very promising for our method and we include sample explanations, generated from models learnt from the refinery dataset.
790904
A new three-degree-of-freedom parallel manipulator
In this paper, a novel spatial three degree-of-freedom, that are two degrees of translational freedom and one degree of orientational freedom, parallel manipulator is proposed. The parallel manipulator consists of a base plate, a movable platform, and three non-identical connecting legs. The kinematics problems and velocity equation of the new parallel manipulator are given. Three kinds of singularities are presented. The parallel manipulator has wide application in the fields of industrial robots, motion simulators, and parallel kinematics machines.
29682871
A Middleware Based Mobile Scientific Computing System - MobileLab
In this paper we present a scientific computing system named MobileLab which is designed for pervasive computing on the Internet. A middleware named TOM (stands for Tsinghua Operation Middleware) is designed and employed in MobileLab as a key to access the grid. Based on TOM, MobileLab can access the computational resource transparently; distribute the components to optimize the computation procedure and computation can be moved from one node to another. To use a middleware model in the architecture of scientific computing system is our new approach corresponding to the grid computing and mobile computing.
10306588
Word Graphs: The Second Set
In continuation of the paper of Hoede and Li on word graphs for a set of prepositions, word graphs are given for adjectives, adverbs and Chinese classifier words. It is argued that these three classes of words belong to a general class of words that may be called adwords. These words express the fact that certain graphs may be brought into connection with graphs that describe the important classes of nouns and verbs. Some subclasses of adwords are discussed as well as some subclasses of Chinese classifier words.
8835059
Computing the maximum similarity bi-clusters of gene expression data
MOTIVATIONS
Bi-clustering is an important approach in microarray data analysis. The underlying bases for using bi-clustering in the analysis of gene expression data are (1) similar genes may exhibit similar behaviors only under a subset of conditions, not all conditions, (2) genes may participate in more than one function, resulting in one regulation pattern in one context and a different pattern in another. Using bi-clustering algorithms, one can obtain sets of genes that are co-regulated under subsets of conditions.


RESULTS
We develop a polynomial time algorithm to find an optimal bi-cluster with the maximum similarity score. To our knowledge, this is the first formulation for bi-cluster problems that admits a polynomial time algorithm for optimal solutions. The algorithm works for a special case, where the bi-clusters are approximately squares. We then extend the algorithm to handle various kinds of other cases. Experiments on simulation data and real data show that the new algorithms outperform most of the existing methods in many cases. Our new algorithms have the following advantages: (1) no discretization procedure is required, (2) performs well for overlapping bi-clusters and (3) works well for additive bi-clusters.


AVAILABILITY
The software is available at http://www.cs.cityu.edu.hk/~liuxw/msbe/help.html.
893749
A Distributed and Efficient Flooding Scheme Using 1-Hop Information in Mobile Ad Hoc Networks
Flooding is one of the most fundamental operations in mobile ad hoc networks. Traditional implementation of flooding suffers from the problems of excessive redundancy of messages, resource contention, and signal collision. This causes high protocol overhead and interference with the existing traffic in the networks. Some efficient flooding algorithms were proposed to avoid these problems. However, these algorithms either perform poorly in reducing redundant transmissions or require each node to maintain 2-hop (or more) neighbors information. In the paper, we study the sufficient and necessary condition of 100 percent deliverability for flooding schemes that are based on only 1-hop neighbors information. We further propose an efficient flooding algorithm that achieves the local optimality in two senses: 1) the number of forwarding nodes in each step is minimal and 2) the time complexity for computing forwarding nodes is the lowest, which is O(nlogn), where n is the number of neighbors of a node. Extensive simulations have been conducted and simulation results have shown the excellent performance of our algorithm