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.     

一个针对并行模拟引擎的性能评测实例

SimK是由中科院计算所体系结构国家重点实验室开发的一个并行离散时间模拟引擎。基于已经发布的SimKl.0版本,对任务划分及同步推进阻塞控制进行了功能扩展,开发了SimK的1.1版本。同时由于缺乏一个专门对SimK模拟性能评测的Benchmark以及全面的评测结果,首先讨论了并行模拟引擎Benchmark的设计准则,之后介 绍了开发的Benchmark-PassBa11,并且使用它对SimK的强弱扩展性、组件负载不均衡情况下的强扩展性进行了评测,同时对比了组件负载不均衡和均衡情况下的加速比,探讨了模拟计算量的变化对模拟加速比的影响,并讨论了Benchmark的适用性。通过实验讨论得出:a) PassBa11可以作为并行模拟引擎SimK性能评测Benchmark,亦可用于其他并行模拟引擎性能的评测;b) SimK具有良好的强弱扩展性;c)负载平衡和模拟计算量都会对并行模拟加速比产生影响。     

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.     

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.     

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.     

Canis: A High-Level Language for Data-Driven Chart Animations

In this paper, we introduce Canis, a high-level domain-specific language that enables declarative specifications of data-driven chart animations. By leveraging data-enriched SVG charts, its grammar of animations can be applied to the charts created by existing chart construction tools. With Canis, designers can select marks from the charts, partition the selected marks into mark units based on data attributes, and apply animation effects to the mark units, with the control of when the effects start. The Canis compiler automatically synthesizes the Lottie animation JSON files [Aira], which can be rendered natively across multiple platforms. To demonstrate Canis’ expressiveness, we present a wide range of chart animations. We also evaluate its scalability by showing the effectiveness of our compiler in reducing the output specification size and comparing its performance on different platforms against D3.     

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 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.     

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     

Reflections on the High-Level Language Symbol Computer System

A radical computer architecture implementing a programming language and a timeshared operating system directly in hardware, Symbol remains a valuable lesson in building complex systems.     

A Survey of High-Level Language Machines in Japan

Japanese universities and laboratories have developed a number of experimental HLL machines. The appearance of commercial machines—and confirmation of their effectiveness—is expected soon.     

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.     

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。     

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.