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Molecular epidemiology of viral infections is based on identifying genetic markers to assist in epidemiological investigation. Early molecular technologies were limited in its capacity and were dominated by analytical methodology focusing on the viral agent itself where computational technologies were almost exclusively used for phylogenetic inference. Embracing the approaches and achievements of...
The following topics are dealt with: HLA; distributed virtual environments; optimization methods; systems simulations; network simulation; and load balancing.
This paper discusses about new approaches for protein function identification and ligand screening. To find a robust computational method it develops a ligand homology modeling approach and show that remotely related proteins identified by threading often share a common binding site occupied by chemically similar ligands. Itapply FINDSITELHM to the human kinome and construct structure models that...
We re-examine the problem of load balancing in conservatively synchronized parallel, discrete- event simulations executed on high-performance computing clusters, focusing on simulations where computational and messaging load tend to be spatially clustered. Such domains are frequently characterized by the presence of geographic "hot-spots'' - regions that generate significantly more simulation...
Digital hardware designs are nearly always tested and validated prior to deployment using functional-level simulation. Each component of the design, such as a four-bit adder or an eight-to-one multiplexer, is described and modeled as a set of inputs and a set of outputs that change based on changes in the input. Using traditional discrete event simulation, each change in the input set for a component...
The spatial scale, runtime speed and behavioral detail of epidemic outbreak simulations together require the use of large-scale parallel processing. In this paper, an optimistic parallel discrete event execution of a reaction-diffusion simulation model of epidemic outbreaks is presented, with an implementation over the ??sik simulator. Rollback support is achieved with the development of a novel reversible...
A simulation model composed using reusable components is semantically valid if it produces meaningful results in terms of expressed behaviors and meets the desired objective. This paper focuses on the validation of component-based data-driven simulation. In data-driven simulation applications, it is necessary to model entity behavior at higher resolution. In simulations such as military training scenarios...
Ad hoc distributed simulation is an approach to predict future states of operational systems. It is based on embedding on-line simulations into a sensor network and adding communication and synchronization among the simulators. While prior work focused on this approach in the context of online management of transportation systems, this paper describes a generalization of the method and shows how it...
Multi-core processors are commonly available now, but most traditional computer architectural simulators still use single-thread execution. In this paper we use parallel discrete event simulation (PDES) to speedup a cycle-accurate event-driven many-core processor simulator. Evaluation against the sequential version shows that the parallelized one achieves an average speedup of 10.9x (up to 13.6x)...
Wireless network simulation is used for research because of its simplicity and repeatability. While simple radio propagation models are evaluated quickly and are suitable for simple scenarios, sophisticated models can handle more complex environments and provide better accuracy. However, the cost of higher accuracy is slower execution speed. This paper describes experiments that validate ray-tracing...
Maintaining interactivity is one of the key challenges in distributed virtual environments (DVE) due to the large, heterogeneous Internet latency and the fact that clients in a DVE are usually geographically separated. Previous work in this area have dealt with optimizing interactivity performance given limited server resource. In this paper, we consider a new problem, termed the performance-constrained...
In this paper we present the problem of optimizing a business process model with the objective of finding the most beneficial assignment of tasks to agents, without modifying the structure of the process itself. The task assignment problem for four types of processes are distinguished and algorithms for finding optimal solutions to them are presented: 1) a business process with a predetermined workflow,...
In this paper, we present a dynamic load-balancing algorithm for optimistic gate level simulation making use of a machine learning approach. We first introduce two dynamic load-balancing algorithms oriented towards balancing the computational and communication load respectively in a Time Warp simulator. In addition, we utilize a multi-state Q-learning approach to create an algorithm which is a combination...
We propose a computing technique for efficient parallel simulation of compute-intensive DEVS models on the IBM Cell processor, combining multi-grained parallelism and various optimizations to speed up the event execution. Unlike most existing parallelization strategies, our approach explicitly exploits the massive fine-grained event-level parallelism inherent in the simulation process, while most...
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