An Efficient Sort-Based DDM Matching Algorithm for HLA Applications with a Large Spatial Environment
Simulation is a low cost and safe alternative to solve complex problems in various areas. To promote reuse and interoperability of simulation applications and link geographically dispersed simulation components, distributed simulation was introduced. The high level architecture (HLA) is the IEEE standard for distributed simulation. To optimize communication efficiency between simulation components, HLA defines a data distribution management (DDM) service group for filtering out unnecessary data exchange. It relies on the computation of overlap between update and subscription regions, which is called matching. In this paper, we propose an efficient sort-based DDM matching algorithm for HLA applications with a large spatial environment. A theoretical analysis of our algorithm concludes that it should have good storage and computational scalability. The experimental results have verified the theoretical conclusions by showing that our algorithm has much less storage requirement than the original sort-based matching algorithm and generally has the best computational performance when compared with region-based and the original sort-based matching algorithms.

title: A Service Oriented HLA RTI on the Grid
abstract: Modeling and simulation permeate all areas of business, science and engineering. To promote the interoperability and reusability of simulation applications and link geographically dispersed simulation components, distributed simulation was introduced. While the high level architecture (HLA) is the IEEE standard for distributed simulation, a run time infrastructure (RTI) provides the actual implementation of the HLA. With increased size and complexity of simulation applications, large amounts of distributed computational and data resources are required. The Grid provides a flexible, secure and coordinated resource sharing environment which can facilitate distributed simulation execution. In this paper, we propose a service oriented HLA RTI (SOHR) framework which provides the functionalities of an RTI as Grid services and enables large scale distributed simulations to be conducted on a heterogeneous Grid environment. The various services in SOHR can be dynamically deployed, discovered and undeployed, leading to a scalable distributed simulation environment. While the communications between simulators are through Grid service invocations, the standard HLA interface is provided as a library to increase simulator reusability and interoperability. A subset of HLA specifications was implemented in a SOHR prototype based on GT4 and the experimental results have verified the feasibility of SOHR.

title: Scalable streaming for heterogeneous clients
abstract: Periodic broadcast protocols enable the efficient streaming of highly popular media files to large numbers of concurrent clients. Most previous periodic broadcast protocols, however, assume that all clients can receive at the same rate, and also assume that available bandwidth is not time-varying. In this paper, we first develop a new periodic broadcast protocol, Optimized Heterogeneous Periodic Broadcast (OHPB), that can be optimized for a given population of clients with heterogeneous reception bandwidths and quality-of-service requirements. The OHPB protocol utilizes an optimized segment size progression determined by solving a linear optimization model that takes as input the client population characteristics and an objective function such as mean client startup delay. We then propose complementary client protocols employing work-ahead buffering of data during playback, so as to enable more uniform playback quality when the available bandwidth is time-varying.

title: Performance-directed energy management for storage systems
abstract: Energy consumption has become an important issue in the design of battery-operated mobile devices and sophisticated data centers. The storage hierarchy, which includes memory and disks, is a major energy consumer in such systems; especially for high-end servers at data centers. Much work has focused on energy control algorithms for storage systems that transition a device into a low power mode when a certain usage function exceeds a specified threshold. These algorithms are difficult to use in real systems, however, because designers must painstakingly and manually tune threshold values, and even then a performance guarantee is difficult. To address these limitations, we develop three algorithms: 1) a performance guarantee technique that designers can use with any underlying energy-control algorithm 2) a performance-directed control algorithm that periodically assigns a static configuration to different devices by solving an optimization problem 3) another performance-directed control algorithm that dynamically self-tunes according to an optimal set of thresholds

title: Basic Topological Models for Spatial Entities in 3-Dimensional Space
abstract: In recent years, models of spatial relations, especially topological relations, have attracted much attention from the GIS community. In this paper, some basic topologic models for spatial entities in both vector and raster spaces are discussed.It has been suggested that, in vector space, an open set in 1-D space may not be an open set any more in 2-D and 3-D spaces. Similarly, an open set in 2-D vector space may also not be an open set any more in 3-D vector spaces. As a result, fundamental topological concepts such as boundary and interior are not valid any more when a lower dimensional spatial entity is embedded in higher dimensional space. For example, in 2-D, a line has no interior and the line itself (not its two end-points) forms a boundary. Failure to recognize this fundamental topological property will lead to topological paradox. It has also been stated that the topological models for raster entities are different in Z2 and R2. There are different types of possible boundaries depending on the definition of adjacency or connectedness. If connectedness is not carefully defined, topological paradox may also occur. In raster space, the basic topological concept in vector space—connectedness—is implicitly inherited. This is why the topological properties of spatial entities can also be studied in raster space. Study of entities in raster (discrete) space could be a more efficient method than in vector space, as the expression of spatial entities in discrete space is more explicit than that in connected space.

title: Factoring systems of linear PDEs with finite-dimensional solution spaces
abstract: A D-finite system is a finite set of linear homogeneous partial differential equations in several independent and dependent variables, whose solution space is of finite dimension. Let L be a D-finite system with rational function coefficients. We present an algorithm for computing all hyperexponential solutions of L, and an algorithm for computing all D-finite systems whose coefficients are also rational functions, and whose solutions are contained in the solution space of L.

title: Haplotype reconstruction from SNP fragments by minimum error correction
abstract: Haplotype reconstruction based on aligned single nucleotide polymorphism (SNP) fragments is to infer a pair of haplotypes from localized polymorphism data gathered through short genome fragment assembly. An important computational model of this problem is the minimum error correction (MEC) model, which has been mentioned in several literatures. The model retrieves a pair of haplotypes by correcting minimum number of SNPs in given genome fragments coming from an individual's DNA.



In the first part of this paper, an exact algorithm for the MEC model is presented. Owing to the NP-hardness of the MEC model, we also design a genetic algorithm (GA). The designed GA is intended to solve large size problems and has very good performance. The strength and weakness of the MEC model are shown using experimental results on real data and simulation data. In the second part of this paper, to improve the MEC model for haplotype reconstruction, a new computational model is proposed, which simultaneously employs genotype information of an individual in the process of SNP correction, and is called MEC with genotype information (shortly, MEC/GI). Computational results on extensive datasets show that the new model has much higher accuracy in haplotype reconstruction than the pure MEC model.