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).
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.
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.
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.
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.
36513177
A Bayesian network approach to explaining time series with changing structure
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.
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.
18361624
A new approach to retrieve video by example video clip
The similarity measure between video clips is a key issue in video retrieval. In the developing of our video retrieval system, we propose a new video similarity model. In contrast to existing algorithms, it proposes many influencing factors, such as order factor, speed factor, disturbance factor, etc, based on the subjective visual judgement of human. So this algorithm embodies the degree of similarity completely and systematically. On the other hand, it has resolution adaptation because it can be applied to every level of video structure. In the retrieval system, it can be used to process video query by example clip. This paper introduces it in detail and presents experiment results at the end of the paper.
3266821
A Least Biased Fuzzy Clustering Method
A new operational definition of cluster is proposed, and a fuzzy clustering algorithm with minimal biases is formulated by making use of the maximum entropy principle to maximize the entropy of the centroids with respect to the data points (clustering entropy). The authors make no assumptions on the number of clusters or their initial positions. For each value of an adimensional scale parameter /spl beta/', the clustering algorithm makes each data point iterate towards one of the cluster's centroids, so that both hard and fuzzy partitions are obtained. Since the clustering algorithm can make a multiscale analysis of the given data set one can obtain both hierarchy and partitioning type clustering. The relative stability with respect to /spl beta/' of each cluster structure is defined as the measurement of cluster validity. The authors determine the specific value of /spl beta/' which corresponds to the optimal positions of cluster centroids by minimizing the entropy of the data points with respect to the centroids (clustered entropy). Examples are given to show how this least biased method succeeds in getting perceptually correct clustering results. >
45375926
A Markov chain sequence generator for power macromodeling
In this paper, we present a novel sequence generator based on a Markov chain (MC) model. Specifically, we formulate the problem of generating a sequence of vectors with given average input probability p, average transition density d, and spatial correlation s as a transition matrix computation problem, in which the matrix elements are subject to constraints derived from the specified statistics. We also give a practical heuristic that computes such a matrix and generates a sequence of l n-bit vectors in O(nl+n/sup 2/) time. Derived from a strongly mixing MC, our generator yields binary vector sequences with accurate statistics, high uniformity, and high randomness. Experimental results show that our sequence generator can cover more than 99% of the parameter space. Sequences of 2000 48-bit vectors are generated in less than 0.05 s, with average deviations of the signal statistics p,d, and s equal to 1.6%, 1.8%, and 2.8%, respectively. Our generator enables the detailed study of power macromodeling. Using our tool and the ISCAS'85 benchmark circuits, we have assessed the sensitivity of power dissipation to the three input statistics p,d, and s. Our investigation reveals that power is most sensitive to transition density, while only occasionally exhibiting high sensitivity to signal probability and spatial correlation. Our experiments also show that input signal imbalance can cause estimation errors as high as 100% in extreme cases, although errors are usually within 25%.
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.