15507709
Data-Layout Optimization Using Reuse Distance Distribution
As the ever-increasing gap between the speed of processor and the speed of memory has become the cause of one of primary bottlenecks of computer systems, modern architecture systems use cache to solve this problem, whose utility heavily depends on program data locality. This paper introduces a platform independent data-layout optimization framework to improve program data locality. This framework uses a variable relation model based on variables’ reuse distance distribution to quantitate the relation of variables and accordingly assigns variables which are often accessed together in one group. At the same time this framework introduces a dynamic array regrouping method to group dynamic arrays assigned in a group. Experiments show that this data-layout optimization framework can effectively improve program data locality and program performance.
15870104
Homomorphism Resolving of XPath Trees Based on Automata
As a query language for navigating XML trees and selecting a set of element nodes, XPath is ubiquitous in XML applications. One important issue of XPath queries is containment checking, which is known as a co-NP complete. The homomorphism relationship between two XPath trees, which is a PTIME problem, is a sufficient but not necessary condition for the containment relationship. We propose a new tree structure to depict XPath based on the level of the tree node and adopt a method of sharing the prefixes of multi-trees to construct incrementally the most effective automata, named XTHC (XPath Trees Homomorphism Checker). XTHC takes an XPath tree and produces the result of checking homomorphism relationship between an arbitrary tree in multi-trees and the input tree, thereinto the input tree is transformed into events which force the automata to run. Moreover, we consider and narrow the discrepancy between homomorphism relationship and containment relationship as possible as we can.
8620934
Certifying Concurrent Programs Using Transactional Memory
Transactional memory (TM) is a new promising concurrency-control mechanism that can avoid many of the pitfalls of the traditional lock-based techniques. TM systems handle data races between threads automatically so that programmers do not have to reason about the interaction of threads manually. TM provides a programming model that may make the development of multi-threaded programs easier. Much work has been done to explore the various implementation strategies of TM systems and to achieve better performance, but little has been done on how to formally reason about programs using TM and how to make sure that such reasoning is sound. In this paper, we focus on the semantics of transactional memory and present a proof-carrying code (PCC) system for reasoning about programs using TM. We formalize our reasoning with respect to the TM semantics, prove its soundness, and use examples to demonstrate its effectiveness.
18862565
Inferring Gene Regulatory Networks from Multiple Data Sources Via a Dynamic Bayesian Network with Structural EM
Using our dynamic Bayesian network with structural Expectation Maximization (SEM-DBN), we develop a new framework to model gene regulatory network from both gene expression data and transcriptional factor binding site data. Only based on mRNA expression data, it is not enough to accurately estimate a gene network. It is difficult for us to estimate a gene network accurately only with the mRNA expression data. In this paper, we use the transcription factor binding location data in order to introduce the prior knowledge to SEM-DBN model. Gene expression data are also exploited specifically for likelihood. Meanwhile, we incorporate the prior knowledge into every learning step by SEM rather than only learning from the very beginning, which can compensate the attenuation of the effect with location data. The effectiveness of our proposed method is demonstrated through the analysis of Saccharomyces cerevisiae cell cycle data. The combination of heterogeneous data from multiple sources ensures that our results are more accurate than those recovered from only gene expression data alone.
39739560
Optimal Motion Generation of Flexible Macro-micro Manipulator Systems Using Estimation of Distribution Algorithm
In this paper, a new approach for motion generation and optimization of the flexible macro-micro manipulator system is proposed based on Estimation of Distribution Algorithm (EDA). The macro-micro manipulator system is a redundant system, of which inverse kinematics remains challenging, with no generic solution to date. Here, the manipulator system configurations, or the optimal joint motions, are generated using the EDA algorithm base on Gaussian probability model. Compared with simple genetic algorithms (SGA), this approach uses fewer parameters and the time for motion optimization is remarkably reduced. The proposed approach shows excellent performance on motion generation and optimization of a flexible macro-micro manipulator system, as demonstrated by the simulation results.
2554459
Refinement of optical map assemblies
MOTIVATION
Genomic mutations and variations provide insightful information about the functionality of sequence elements and their association with human diseases. Traditionally, variations are identified through analysis of short DNA sequences, usually shorter than 1000 bp per fragment. Optical maps provide both faster and more cost-efficient means for detecting such differences, because a single map can span over 1 million bp. Optical maps are assembled to cover the whole genome, and the accuracy of assembly is critical.


RESULTS
We present a computationally efficient model-based method for improving quality of such assemblies. Our method provides very high accuracy even with moderate coverage (<20 x). We utilize a hidden Markov model to represent the consensus map and use the expectation-Maximization algorithm to drive the refinement process. We also provide quality scores to assess the quality of the finished map.


AVAILABILITY
Code is available from www.cmb.usc.edu/people/valouev/
4832713
Heteroscedastic Probabilistic Linear Discriminant Analysis with Semi-supervised Extension
Linear discriminant analysis (LDA) is a commonly used method for dimensionality reduction. Despite its successes, it has limitations under some situations, including the small sample size problem, the homoscedasticity assumption that different classes have the same Gaussian distribution, and its inability to produce probabilistic output and handle missing data. In this paper, we propose a semi-supervised and heteroscedastic extension of probabilistic LDA, called S2HPLDA, which aims at overcoming all these limitations under a common principled framework. Moreover, we apply automatic relevance determination to determine the required dimensionality of the low-dimensional space for dimensionality reduction. We empirically compare our method with several related probabilistic subspace methods on some face and object databases. Very promising results are obtained from the experiments showing the effectiveness of our proposed method.
14581660
An Improved Physically-Based Method for Geometric Restoration of Distorted Document Images
In document digitization through camera-based systems, simple imaging setups often produce geometric distortions in the resultant 2D images because of the nonplanar geometric shapes of certain documents such as thick bound books, rolled, folded, or crumpled materials, etc. Previous work [1], [2], [3], [4] has demonstrated that arbitrary warped documents can be successfully restored by flattening a 3D scan of the document. These approaches use physically-based or relaxation-based techniques in their flattening process. While this has been demonstrated to be effective in rectifying the image content and improving OCR, these previous approaches have several limitations in terms of speed and stability. In this paper, we propose a distance-based penalty metric to replace the mass- spring model and introduce additional bending resistance and drag forces to improve the efficiency of the existing approaches. The use of Verlet integration and special plane collision handling schemes also help to achieve better stability without sacrificing efficiency. Experiments on various document images captured from books, brochures, and historical documents with arbitrary warpings have demonstrated large improvements over the existing approaches in terms of stability and efficiency.