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.
17821282
Clustering with Niching Genetic K-means Algorithm
GA-based clustering algorithms often employ either simple GA, steady state GA or their variants and fail to consistently and efficiently identify high quality solutions (best known optima) of given clustering problems, which involve large data sets with many local optima. To circumvent this problem, we propose Niching Genetic K-means Algorithm (NGKA) that is based on modified deterministic crowding and embeds the computationally attractive k-means. Our experiments show that NGKA can consistently and efficiently identify high quality solutions. Experiments use both simulated and real data with varying size and varying number of local optima. The significance of NGKA is also shown on the experimental data sets by comparing through simulations with Genetically Guided Algorithm (GGA) and Genetic K-means Algorithm (GKA).
14452513
Spatial Operators for Evolving Dynamic Bayesian Networks from Spatio-temporal Data
Learning Bayesian networks from data has been studied extensively in the evolutionary algorithm communities [Larranaga96, Wong99]. We have previously explored extending some of these search methods to temporal Bayesian networks [Tucker01]. A characteristic of many datasets from medical to geographical data is the spatial arrangement of variables. In this paper we investigate a set of operators that have been designed to exploit the spatial nature of such data in order to learn dynamic Bayesian networks more efficiently. We test these operators on synthetic data generated from a Gaussian network where the architecture is based upon a Cartesian coordinate system, and real-world medical data taken from visual field tests of patients suffering from ocular hypertension.
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.
36065326
Learning short multivariate time series models through evolutionary and sparse matrix computation
Multivariate time series (MTS) data are widely available in different fields including medicine, finance, bioinformatics, science and engineering. Modelling MTS data accurately is important for many decision making activities. One area that has been largely overlooked so far is the particular type of time series where the data set consists of a large number of variables but with a small number of observations. In this paper we describe the development of a novel computational method based on Natural Computation and sparse matrices that bypasses the size restrictions of traditional statistical MTS methods, makes no distribution assumptions, and also locates the associated parameters. Extensive results are presented, where the proposed method is compared with both traditional statistical and heuristic search techniques and evaluated on a number of criteria. The results have implications for a wide range of applications involving the learning of short MTS models.
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.
39271056
A hybrid representation of environment models in image-based real time walkthrough
In this paper, a hybrid representation of environment models using a combination of points and polygons is proposed. Through the model, a real time walkthrough of a complex environment can be achieved. We start from multiple depth reference images and classify the pixels of images into two categories, corresponding respectively to planar and non-planar surfaces in 3D space, then all the redundant points are removed by a comparison algorithm of sampling rate. For pixels corresponding to nonplanar surfaces, the point representation is maintained, and a local reconstruction and resampling process is employed to re-sample a set of points that distribute more uniformly on the surfaces. The re-sampled points are organized by an OBB-tree according to their space coordinates and a multiresolution structure is built to improve the rendering efficiency. For pixels corresponding to planar surfaces, the plane coefficients are reconstructed and all their appearances in the reference images are merged to texture maps. Under this hybrid representation, texture mapping and point-based rendering are employed to render the novel views, to take full advantage of the acceleration utility of graphics hardware. The algorithm demonstrates the combined advantages of approaches in traditional computer graphics and PBR/IBR, texture mapping for plane surfaces and point-based rendering for high detail surfaces and shapes.
2422545
Probe-level measurement error improves accuracy in detecting differential gene expression
MOTIVATION
Finding differentially expressed genes is a fundamental objective of a microarray experiment. Numerous methods have been proposed to perform this task. Existing methods are based on point estimates of gene expression level obtained from each microarray experiment. This approach discards potentially useful information about measurement error that can be obtained from an appropriate probe-level analysis. Probabilistic probe-level models can be used to measure gene expression and also provide a level of uncertainty in this measurement. This probe-level measurement error provides useful information which can help in the identification of differentially expressed genes.


RESULTS
We propose a Bayesian method to include probe-level measurement error into the detection of differentially expressed genes from replicated experiments. A variational approximation is used for efficient parameter estimation. We compare this approximation with MAP and MCMC parameter estimation in terms of computational efficiency and accuracy. The method is used to calculate the probability of positive log-ratio (PPLR) of expression levels between conditions. Using the measurements from a recently developed Affymetrix probe-level model, multi-mgMOS, we test PPLR on a spike-in dataset and a mouse time-course dataset. Results show that the inclusion of probe-level measurement error improves accuracy in detecting differential gene expression.


AVAILABILITY
The MAP approximation and variational inference described in this paper have been implemented in an R package pplr. The MCMC method is implemented in Matlab. Both software are available from http://umber.sbs.man.ac.uk/resources/puma.
13088953
A polynomial algorithm for recognizing perfect graphs
We present a polynomial algorithm for recognizing whether a graph is perfect, thus settling a long standing open question. The algorithm uses a decomposition theorem of Conforti, Cornuejols and Vuskovic. Another polynomial algorithm for recognizing perfect graphs, which does not use decomposition, was obtained simultaneously by Chudnovsky and Seymour. Both algorithms need a first phase developed jointly by Chudnovsky, Cornuejols, Liu, Seymour and Vuskovic.
5855159
Skew spreading for peak current reduction
This paper presents a circuit optimization technique called skewspreading. Given an edge-triggered sequential circuit, skew spreadingderives the required clock arrival times for all registers so that theskews are distributed evenly in a preselected time window without changing the operating frequency of the circuit. Skew spreading is ideal for peak current reduction, since it distributes clock activities and the ensuing signal activities widely in time. We have developed a skew spreading algorithm and applied it to a suite of benchmark circuits. Simulation results demonstrate that the variance of the resulting skew from the uniform distribution can be reduced to 4% on the average. In comparison to other gate-level peak current reduction techniques, our scheme achieves an average improvement of 17% with a speedup of up to 13.9 times.