PML: Toward a High-Level Formal Language for Biological Systems

Documentation of knowledge about biological pathways is often informal and vague, making it difficult to efficiently synthesize the work of others into a holistic understanding of a system. Several researchers have proposed solving this problem by modeling pathways using formal languages, which have a precise and consistent semantics. While precise, many of these languages may be too low-level to model feasibly complex pathways. We have developed the Pathway Modeling Language (PML), a high-level language for modeling pathways. PML is based on a biological metaphor of molecules with binding sites and has special constructs for handling compartment changes in pathways. Our preliminary work has shown that PML's language constructs serve as a promising basis for modeling complex pathways in a readable and composable manner.     

On the Design of a Microcode Compiler for a Machine-Independent High-Level Language

A translator system employing a partial compiler, intermediate language, and three-pass code generator is described that produces compact microcode for a class of horizontal microinstruction machines.     

Evaluating a Computational Model of Emotion

Spurred by a range of potential applications, there has been a growing body of research in computational models of human emotion. To advance the development of these models, it is critical that we evaluate them against the phenomena they purport to model. In this paper, we present one method to evaluate an emotion model that compares the behavior of the model against human behavior using a standard clinical instrument for assessing human emotion and coping. We use this method to evaluate the Emotion and Adaptation (EMA) model of emotion Gratch and Marsella. The evaluation highlights strengths of the approach and identifies where the model needs further development.     

Full Abstraction for a Shared-Variable Parallel Language

We give a new denotational semantics for a shared-variable parallel programming language and prove full abstraction: the semantics gives identical meanings to commands if and only if they induce the same behavior in all program contexts. The meaning of a command is a set of “transition traces,” which record the ways in which a command may interact with and be affected by its environment. We show how to modify the semantics to incorporate new program constructs, to allow for different levels of granularity or atomicity, and to model fair infinite computation, in each case achieving full abstraction with respect to an appropriate notion of program behavior.     

Special Feature Program Measurements on a High-Level Language Computer

Analysis of programs on the Symbol computer helped evaluate its unique architecture and provided insight into the use of programming languages in general.     

Assessing RJSCs In High-Level Language Support

A reduced instruction set computer, RISC I, was compared to five traditional machines. It provided the highest performance with the smallest penalty for using high-level language.     

Interactive High-Level Language Direct-Execution Microprocessor System

It is our habit in writing an English composition that, as we write each word, each phrase, each sentence, and each paragraph, we consciously or unconsciously check the syntax and the semantics of the composition just written. Writing a computer program in a high-level language could be made similar to writing a composition in English. In this case, a highly interactive highlevel language system checks the syntax and the semantics of the highlevel language program as each symbol, each expression, and each statement are being entered at the terminal. When the source program is completely entered, the program could have been debugged and could have run once.     

Flex: A High-Level Language for Specifying Customized Microprocessors

Researchers at Bell Labs have recently developed a silicon compiler, named Plex, that automatically generates VLSI layouts of high performance and area efficient microprocessors. Plex takes as input a specification of the function to be executed and generates a complete mask-level layout of a customized microprocessor to execute that function. The Plex microprocessor interacts with the external world, via input and output wires, and interrupts. The dedicated function performed by a Plex microprocessor typically involves real-time handling of inputs and interrupts-and the real-time generation of output signals.     

A Parallel Computational Model for Heterogeneous Clusters

This paper addresses the maximal lifetime scheduling for sensor surveillance systems with K sensors to 1 target. Given a set of sensors and targets in an Euclidean plane, a sensor can watch only one target at a time and a target should be watched by k, kges1, sensors at any time. Our task is to schedule sensors to watch targets and pass data to the base station, such that the lifetime of the surveillance system is maximized, where the lifetime is the duration up to the time when there exists one target that cannot be watched by k sensors or data cannot be forwarded to the base station due to the depletion of energy of the sensor nodes. We propose an optimal solution to find the target watching schedule for sensors that achieves the maximal lifetime. Our solution consists of three steps: 1) computing the maximal lifetime of the surveillance system and a workload matrix by using linear programming techniques, 2) decomposing the workload matrix into a sequence of schedule matrices that can achieve the maximal lifetime, and 3) determining the sensor surveillance trees based on the above obtained schedule matrices, which specify the active sensors and the routes to pass sensed data to the base station. This is the first time in the literature that this scheduling problem of sensor surveillance systems has been formulated and the optimal solution has been found. We illustrate our optimal method by a numeric example and experiments in the end     

A Transformational Derivation of a Parsing Algorithm in a High-Level Language

This paper presents a detailed algorithm derivation scenario, using correctness preserving source-to-source transfonnations. The algorithm derived is the Cocke-Younger nodal spans parsing algorithm. We describe a high-level SETL-like specification language, and give a partial correctness formalism and a set of transformation rules which enable the combination of algorithms whose partial correctness has already been established.     

High-Level Parallel Ant Colony Optimization with Algorithmic Skeletons

Parallel implementations of swarm intelligence algorithms such as the ant colony optimization (ACO) have been widely used to shorten the execution time when solving complex optimization problems. When aiming for a GPU environment, developing efficient parallel versions of such algorithms using CUDA can be a difficult and error-prone task even for experienced programmers. To overcome this issue, the parallel programming model of Algorithmic Skeletons simplifies parallel programs by abstracting from low-level features. This is realized by defining common programming patterns (e.g. map, fold and zip) that later on will be converted to efficient parallel code. In this paper, we show how algorithmic skeletons formulated in the domain specific language Musket can cope with the development of a parallel implementation of ACO and how that compares to a low-level implementation. Our experimental results show that Musket suits the development of ACO. Besides making it easier for the programmer to deal with the parallelization aspects, Musket generates high performance code with similar execution times when compared to low-level implementations.

     

一种蛋白质点突变计算机预测的并行模型

认识和预测蛋白质天然构象的波动对蛋白质-蛋白质对接和设计等应用是非常重要的.但是许多骨架柔性的方法会导致骨架较大幅度的波动.Backrub模型能够对骨架进行微小的扰动,符合高分辨率晶体结构中观察到的构象的微妙变化.本文提出了一种基于Backrub的并行扰动骨架和侧链的模型,可以对天然构象的等价状态进行模拟.这种并行扰动方式更加接近于真实情况下蛋白质构象的运动方式,更好地模拟了实验数据.通过预测10个点突变实例,相比串行随机扰动模型产生的构象,并行模型不仅从时间上提高了产生构象的速度,更提高了侧链的预测精度.     

Support Facilities for Development of Parallel Computational Algorithms

An approach to the development of parallel programs is described, which is based on algorithmic specification. Functional characteristics and structure of the system that supports the approach and is based on the parallel programming language SuperPascal are suggested. The system is designed for the development of parallel algorithms and for teaching parallel programming.     

一种实用的并行计算模型

对于当前流行的工作站集群环境和各类并行机系统,文中提出了一种实用的并行计算模型,即基于LogGP的非独占异质同步模型NHBL（Nondedicated Heterogeneous Barrier LogGP）,它旨在反映具有异质性和非独占性的NOW计算环境对并行算法设计和分析的影响,然后用NHBL模型分析了PSRS算法在国家高性能计算中心（合肥）的工作站集群NHPCC-Cluster和曙光－1000MPP由的代价,并用实测结果进行了验证。     

Performance Evaluation of a Parallel Pipeline Computational Model for Space-Time Adaptive Processing

This paper presents further results on the design and implementation of various optimizations based on our earlier work of developing a parallel pipelined model for the computational intensive applications that have multiple processing tasks. Performance evaluation of this model was done by using a real-time airborne radar application that employs a Space-Time Adaptive Processing (STAP) algorithm. This paper focuses on the following four issues: (1) The tradeoffs between increasing the throughput and reducing the latency are examined in more detail when allocating processors among different processing tasks. (2) A multi-threaded design is incorporated into the pipeline model and implemented on a massively parallel computer with symmetric multi-processor nodes, which shows enhanced performance. (3) The disk I/O is incorporated into the parallel pipeline to study its effect on performance in which two I/O task designs have been implemented: embedding I/O in the pipeline or having a separate I/O task. By using a double buffering approach together with the asynchronous I/O, the overall pipeline performance scales well as the number of processors increases. (4) From the comparison of the two I/O implementations, it is discovered that the latency may be improved when merging multiple tasks into a single task. The effect of reorganizing the task structure of the pipeline is discussed in detail. All the performance results shown in this work demonstrate the linear scalability the parallel pipeline model can achieve using a production radar application. Although this paper focuses on the implementation of the parallel pipeline model and uses the results from a STAP application to support the claims of the discovered properties for this pipeline, this model is also applicable to many other types of applications with similar computational characteristics.     

FPGA高级语言设计开发环境构建

针对传统FPGA芯片开发流程对开发人员要求高,开发难度大、周期长的难题,基于FPGA芯片高级综合工具CatapultcSynthesis以及配套的设计验证工具,构建了新的FPGA高级语言设计开发环境,支持将C语言算法快速高效地实现到FPGA芯片上。实验表明．该开发环境能有效降低设计人员的开发难度,缩短工程研发周期。