34468051
Approximation Algorithms for Bi-clustering Problems
One of the main goals in the analysis of microarray data is to identify groups of genes and groups of experimental conditions (including environments, individuals and tissues), that exhibit similar expression patterns. This is the so-called bi-clustering problem. In this paper, we consider two variations of the bi-clustering problem: the Consensus Submatrix Problem and the Bottleneck Submatrix Problem. The input of the problems contains a m×n matrix A and integers l and k. The Consensus Submatrix Problem is to find a l×k submatrix with l<m and k<n and a consensus vector such that the sum of distance between all rows in the submatrix and the vector is minimized. The Bottleneck Submatrix Problem is to find a l×k submatrix with l<m and k<n, an integer d and a center vector such that the distance between every row in the submatrix and the vector is at most d and d is minimized. We show that both problems are NP-hard and give randomized approximation algorithms for special cases of the two problems. Using standard techniques, we can derandomize the algorithms to get polynomial time approximation schemes for the two problems. To our knowledge, this is the first time that approximation algorithms with guaranteed ratio are presented for microarray analysis.
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.
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%.
117969594
Delay-Dependent Robust Hinfinity Control for T-S Fuzzy Systems With Time Delay
2596761
Variance-constrained control for uncertain stochastic systems with missing measurements
In this paper, we are concerned with a new control problem for uncertain discrete-time stochastic systems with missing measurements. The parameter uncertainties are allowed to be norm-bounded and enter into the state matrix. The system measurements may be unavailable (i.e., missing data) at any sample time, and the probability of the occurrence of missing data is assumed to be known. The purpose of this problem is to design an output feedback controller such that, for all admissible parameter uncertainties and all possible incomplete observations, the system state of the closed-loop system is mean square bounded, and the steady-state variance of each state is not more than the individual prescribed upper bound. We show that the addressed problem can be solved by means of algebraic matrix inequalities. The explicit expression of the desired robust controllers is derived in terms of some free parameters, which may be exploited to achieve further performance requirements. An illustrative numerical example is provided to demonstrate the usefulness and flexibility of the proposed design approach.
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.
5117413
Consensus clustering and functional interpretation of gene-expression data
Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus clustering, which provides such an advantage. When coupled with a statistically based gene functional analysis, our method allowed the identification of novel genes regulated by NFκB and the unfolded protein response in certain B-cell lymphomas.