10662727
Power macromodeling of global interconnects considering practical repeater insertion
In this paper, we present a simple yet highly effective power macromodeling technique for global interconnects that considers optimal repeater insertion. Specifically,our model estimates the interconnect power dissipation from the interconnect length, the timing budget, the repeater location flexibility, and the signal activity using an analytical function that is derived for a given repeater library and fabrication technology. In experiments with different standard cell libraries, the average error of our technique is less than 2%.
62445228
Practical repeater insertion for low power: what repeater library do we need?
This paper investigates the problem of repeater insertion for low power under a given timing budget. A novel repeater insertion algorithm is proposed to compute the optimal repeater number and width in the discrete solution space, as defined by a given repeater library. Using the proposed algorithm, two practical and highly important questions are addressed. Given a certain tolerance to the degradation of repeater power dissipation: 1) how coarse could the repeater size granularity be? 2) What range should repeater widths be in? The experimental results provide valuable insights into repeater library design. Specifically, the investigation reveals that coarse repeater size granularities can be used to reduce the library size by more than 87% with merely a 4% power degradation. Moreover, for two-pin interconnects with various wire lengths and timing targets, the range of optimal repeater sizes for low power is limited, indicating that a low-cost small-size repeater library, if well designed, is adequate to provide high-quality repeater insertion solutions. The proposed scheme can be used in early design stages to generate a compact repeater library that is passed on to other repeater insertion algorithms.
13241066
Retiming and clock scheduling for digital circuit optimization
This paper investigates the application of simultaneous retiming and clock scheduling for optimizing synchronous circuits under setup and hold constraints. Two optimization problems are explored: (1) clock period minimization and (2) tolerance maximization to clock-signal delay variations. Exact mixed-integer linear programming formulations and efficient heuristics are given for both problems. When both long and short paths are considered, circuits optimized by the combined application of retiming and clock scheduling can achieve shorter clock periods or demonstrate greater tolerance to clock-signal delay variations than circuits optimized by retiming or clock scheduling. Experiments with benchmark circuits demonstrate the effectiveness of the combined optimization. In comparison with the best result obtained by either of the two optimizations, the joint application of retiming and clock scheduling increased operating speeds by more than 8% on the average. It also increased tolerance to clock delay variations by an average of 12% over a broad range of target clock frequencies. Larger relative improvements were achieved for shorter clock periods, thus suggesting that simultaneous retiming and clock scheduling can play an important role in high-speed design.
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.
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.
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.
10851913
Taming heterogeneity - the Ptolemy approach
Modern embedded computing systems tend to be heterogeneous in the sense of being composed of subsystems with very different characteristics, which communicate and interact in a variety of ways-synchronous or asynchronous, buffered or unbuffered, etc. Obviously, when designing such systems, a modeling language needs to reflect this heterogeneity. Today's modeling environments usually offer a variant of what we call amorphous heterogeneity to address this problem. This paper argues that modeling systems in this manner leads to unexpected and hard-to-analyze interactions between the communication mechanisms and proposes a more structured approach to heterogeneity, called hierarchical heterogeneity, to solve this problem. It proposes a model structure and semantic framework that support this form of heterogeneity, and discusses the issues arising from heterogeneous component interaction and the desire for component reuse. It introduces the notion of domain polymorphism as a way to address these issues.
2696332
A boosting approach for motif modeling using ChIP-chip data
MOTIVATION
Building an accurate binding model for a transcription factor (TF) is essential to differentiate its true binding targets from those spurious ones. This is an important step toward understanding gene regulation.


RESULTS
This paper describes a boosting approach to modeling TF-DNA binding. Different from the widely used weight matrix model, which predicts TF-DNA binding based on a linear combination of position-specific contributions, our approach builds a TF binding classifier by combining a set of weight matrix based classifiers, thus yielding a non-linear binding decision rule. The proposed approach was applied to the ChIP-chip data of Saccharomyces cerevisiae. When compared with the weight matrix method, our new approach showed significant improvements on the specificity in a majority of cases.