2180147
An experimental evaluation of a loop versus a reference design for two-channel microarrays
MOTIVATION
Despite theoretical arguments that so-called 'loop designs' for two-channel DNA microarray experiments are more efficient, biologists continue to use 'reference designs'. We describe two sets of microarray experiments with RNA from two different biological systems (TPA-stimulated mammalian cells and Streptomyces coelicolor). In each case, both a loop and a reference design were used with the same RNA preparations with the aim of studying their relative efficiency.


RESULTS
The results of these experiments show that (1) the loop design attains a much higher precision than the reference design, (2) multiplicative spot effects are a large source of variability, and if they are not accounted for in the mathematical model, for example, by taking log-ratios or including spot effects, then the model will perform poorly. The first result is reinforced by a simulation study. Practical recommendations are given on how simple loop designs can be extended to more realistic experimental designs and how standard statistical methods allow the experimentalist to use and interpret the results from loop designs in practice.


AVAILABILITY
The data and R code are available at http://exgen.ma.umist.ac.uk


CONTACT
veronica.vinciotti@brunel.ac.uk.
44693659
Global exponential stability of generalized recurrent neural networks with discrete and distributed delays
This paper is concerned with analysis problem for the global exponential stability of a class of recurrent neural networks (RNNs) with mixed discrete and distributed delays. We first prove the existence and uniqueness of the equilibrium point under mild conditions, assuming neither differentiability nor strict monotonicity for the activation function. Then, by employing a new Lyapunov-Krasovskii functional, a linear matrix inequality (LMI) approach is developed to establish sufficient conditions for the RNNs to be globally exponentially stable. Therefore, the global exponential stability of the delayed RNNs can be easily checked by utilizing the numerically efficient Matlab LMI toolbox, and no tuning of parameters is required. A simulation example is exploited to show the usefulness of the derived LMI-based stability conditions.
1087779
A note on the robust stability of uncertain stochastic fuzzy systems with time-delays
Takagi-Sugeno (T-S) fuzzy models are now often used to describe complex nonlinear systems in terms of fuzzy sets and fuzzy reasoning applied to a set of linear submodels. In this note, the T-S fuzzy model approach is exploited to establish stability criteria for a class of nonlinear stochastic systems with time delay. Sufficient conditions are derived in the format of linear matrix inequalities (LMIs), such that for all admissible parameter uncertainties, the overall fuzzy system is stochastically exponentially stable in the mean square, independent of the time delay. Therefore, with the numerically attractive Matlab LMI toolbox, the robust stability of the uncertain stochastic fuzzy systems with time delays can be easily checked.
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.
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.
32095656
Analyzing Outliers Cautiously
Outliers are difficult to handle because some of them can be measurement errors, while others may represent phenomena of interest, something "significant" from the viewpoint of the application domain. Statistical and computational methods have been proposed to detect outliers, but further analysis of outliers requires much relevant domain knowledge. In our previous work (1994), we suggested a knowledge-based method for distinguishing between the measurement errors and phenomena of interest by modeling "real measurements" - how measurements should be distributed in an application domain. In this paper, we make this distinction by modeling measurement errors instead. This is a cautious approach to outlier analysis, which has been successfully applied to a medical problem and may find interesting applications in other domains such as science, engineering, finance, and economics.
206530429
Point representation augmented to surface reconstruction in image-based VR
In this paper we propose a hybrid representation of environment models by a point representation augmented to geometric representation of surface polygons reconstructed from multiple reference images, through which a real time walkthrough of a complex environment can be achieved. By the method, we start from classification of pixels of the source images into two categories, corresponding respectively to the planar and non-planar surfaces in 3D space. For the pixels corresponding to the planar surfaces, the plane coefficients are reconstructed and all their appearances in the reference images are merged to form uniformly sampled texture images by a comparison of sampling rate and resampling. For the pixels corresponding to the non-planar surfaces, a point representation is applied and the redundant pixels are removed again through sampling rate comparison. The remained pixels are organized by OBB-tree according to their space coordinates. At the same time, the holes that are unable to be captured by all the reference images are pre-filled in the preprocessing phase so that the probability of hole appearance in walkthrough is greatly reduced. Under this hybrid representation, texture mapping and point warping are employed to render the novel views, to take full advantages of the acceleration utility of graphics hardware.
17545097
Design of Rotary Clock Based Circuits
Rotary clock technique has been shown to reduce the power dissipation of clock distribution by up to 80%. However, to our knowledge, no practical digital synchronous circuit has been designed that utilizes the rotary technique due to the multi-phase nature of rotary clock signals and the strong coupling between a rotary clock network and the circuit it drives. In this paper, we make the first attempt to design rotary based circuit by proposing a unified clock and circuit design methodology. Given a sequential circuit and a clock frequency, our scheme derives a rotary clock network and a functionally equivalent circuit so that they can be integrated to operate reliably at the target frequency. We have applied our scheme to design several rotary clock based DSP modules. Simulation results show that all designs operate correctly with no timing violation. Compared with designs using conventional clock trees, our designs achieve an average clock power saving of more than 70%.
18685518
A novel 2-DOF parallel mechanism based design of a new 5-axis hybrid machine tool
In this paper, the concept of a new 5-axis hybrid machine tool is proposed. The machine is a tool being with both parallel and serial structures, which is based on a novel 2-DOF parallel platform and serial orientations. The machine tool has advantages in terms of high stiffness, high dexterity, high speed, and being capable of long components manufacturing. The kinematics characteristics, such as inverse and forward kinematics, conditioning indices, of the novel 2-DOF parallel platform are studied. The dimensional synthesis based on the workspace and conditioning indices is presented. The results of the paper are very useful for the design of the hybrid machine tool.