27561759
Splice site prediction using support vector machines with a Bayes kernel
One of the most important tasks in correctly annotating genes in higher organisms is to accurately locate the DNA splice sites. Although relatively high accuracy has been achieved by existing methods, most of these prediction methods are computationally extensive. Due to the enormous amount of DNA sequences to be processed, the computational speed is an important issue to consider. In this paper, we present a new machine learning method for predicting DNA splice sites, which first applies a Bayes feature mapping (kernel) to project the data into a new feature space and then uses a linear Support Vector Machine (SVM) as a classifier to recognize the true splice sites. The computation time is linear to the number of sequences tested, while the performance is notably improved compared with the Naive Bayes classifier in terms of classification accuracy, precision, and recall. Our classification results are also comparable to the solution quality obtained by the SVMs with polynomial kernels, while the speed of our proposed method is significantly faster. This is a notable improvement in computational modeling considering the huge amount of DNA sequences to be processed.
10162254
In-broker access control: towards efficient end-to-end performance of information brokerage systems
An XML brokerage system is a distributed XML database system that comprises data sources and brokers which, respectively, hold XML documents and document distribution information. However, all existing information brokerage systems view or handle query brokering and access control as two orthogonal issues: query brokering is a system issue that concerns costs and performance, while access control is a security issue that concerns information confidentiality. As a result, access control deployment strategies (in terms of where and when to do access control) and the impact of such strategies on end-to-end system performance are neglected by existing information brokerage systems. In addition, data source side access control deployment is taken-for-granted as the "right" thing to do. In this paper, we challenge this traditional, taken-for-granted access control deployment methodology, and argue that query brokering and access control are not two orthogonal issues because access control deployment strategies can have a significant impact on the "whole" system's end-to-end performance. We propose the first in-broker access control deployment strategy where access control is "pushed" from the boundary into the "heart" of the information brokerage system
776801
Optimizing SOC Test Resources using Dual Sequences
In this paper, we propose a new data structure called dual sequences to represent SOC test schedules. Dual sequences are used together with a simulated annealing based procedure to optimize the SOC test application time and tester resources. The problems we consider are generation of optimal test schedules for SOCs and minimizing tester memory and test channels. Results of experiments conducted on ITC’02 benchmark SOCs show the effectiveness of the proposed method.
37782928
A multi-dimensional version of the I test
Abstract Two-dimensional arrays with linear subscripts occur quite frequently in real programs. In general, for multi-dimensional linear arrays under constant bounds the Lambda test is an efficient data dependence method to check whether there exist real solutions. In this paper, we propose a multi-dimensional version of the I test, the multi-dimensional I test, that can be applied to testing whether there are integer solutions for multi-dimensional linear arrays under constant limits. Experiments with benchmark showing the effects of the multi-dimensional I test on testing precision and testing efficiency are also presented.
9232977
Placement constraints in floorplan design
In floorplan design, it is common that a designer will want to control the positions of some modules in the final packing for various purposes like datapath alignment and I/O connection. There are several previous works focusing on some particular kinds of placement constraints. In this paper, we will present a unified method to handle all of them simultaneously, including preplace constraint, range constraint, boundary constraint, alignment, abutment, and clustering, etc., in general, nonslicing floorplans. We have used incremental updates and an interesting idea of reduced graph to improve the runtime of the method. We tested our method using some benchmark data with about 1/8 of the modules having placement constraints and the results are very promising. Good packings with all the constraints satisfied can be obtained efficiently.
34361185
Dilation-5 embedding of 3-dimensional grids into hypercubes
We present an algorithm to map the nodes of a 3-dimensional grid to the nodes of its optimal hypercube on a one-to-one basis with dilation at most 5.<<ETX>>
666927
Greedy wire-sizing is linear time
In interconnect optimization by wire-sizing, minimizing weighted sink delay has been shown to be the key problem. Wire-sizing with many important objectives such as minimizing total area subject to delay bounds or minimizing maximum delay can all be reduced to solving a sequence of weighted sink delay problems by Lagrangian relaxation [1, 3]. GWSA, first introduced in [10] for discrete wire-sizing and later extended in [2] to continuous wire-sizing, is a greedy wire-sizing algorithm for the weighted sink delay problem. Although GWSA has been experimentally shown to be very efficient, no mathematical analysis on its convergence rate has ever been reported. In this paper, we consider GWSA for continuous wire sizing. We prove that GWSA converges linearly to the optimal solution, which implies that the run time of GWSA is linear with respect to the number of wire segments for any fixed precision of the solution. Moreover, we also prove that this is true for any starting solution. This is a surprising result because previously it was believed that in order to guarantee convergence, GWSA had to start from a solution in which every wire segment is set to the minimum (or maximum) possible width. Our result implies that GWSA can use a good starting solution to achieve faster convergence. We demonstrate this point by showing that the minimization of maximum delay using Lagrangian relaxation can be speed up by 57.7%.