精细神经网络仿真方法研究进展

树突对大脑神经元实现不同的信息处理功能有着重要作用。精细神经元模型是一种对神经元树突以及离子通道的信息处理过程进行精细建模的模型,可以帮助科学家在实验条件的限制之外探索树突信息处理的特性。由精细神经元组成的精细神经网络模型可通过仿真对大脑的信息处理过程进行模拟,对于理解树突的信息处理机制、大脑神经网络功能背后的计算机理具有重要作用。然而,精细神经网络仿真需要进行大量计算,如何对精细神经网络进行高效仿真是一个具有挑战的研究问题。本文对精细神经网络仿真方法进行梳理,介绍了现有主流仿真平台与核心仿真算法,以及可进一步提升仿真效率的高效仿真方法。将具有代表性的高效仿真方法按照发展历程以及核心思路分为网络尺度并行方法、神经元尺度并行方法以及基于GPU(graphics processing unit)的并行仿真方法3类。对各类方法的核心思路进行总结,并对各类方法中代表性工作的细节进行分析介绍。随后对各类方法所具有的优劣势进行分析对比,对一些经典方法进行总结。最后根据高效仿真方法的发展趋势,对未来研究工作进行展望。     

The EM algorithm in a distributed computing environment for modelling environmental space–time data

Statistical models for spatio-temporal data are increasingly used in environmetrics, climate change, epidemiology, remote sensing and dynamical risk mapping. Due to the complexity of the relationships among the involved variables and dimensionality of the parameter set to be estimated, techniques for model definition and estimation which can be worked out stepwise are welcome. In this context, hierarchical models are a suitable solution since they make it possible to define the joint dynamics and the full likelihood starting from simpler conditional submodels. Moreover, for a large class of hierarchical models, the maximum likelihood estimation procedure can be simplified using the Expectation–Maximization (EM) algorithm.In this paper, we define the EM algorithm for a rather general three-stage spatio-temporal hierarchical model, which includes also spatio-temporal covariates. In particular, we show that most of the parameters are updated using closed forms and this guarantees stability of the algorithm unlike the classical optimization techniques of the Newton–Raphson type for maximizing the full likelihood function. Moreover, we illustrate how the EM algorithm can be combined with a spatio-temporal parametric bootstrap for evaluating the parameter accuracy through standard errors and non-Gaussian confidence intervals.To do this a new software library in form of a standard R package has been developed. Moreover, realistic simulations on a distributed computing environment allow us to discuss the algorithm properties and performance also in terms of convergence iterations and computing times.     

A software for simulating steady-state properties of passive dendrites based on the cable theory

In this study, a computer software, CableTeo, is introduced for simulating the steady-state electrical properties of passive dendrite based on the cable theory. The cable theory for dendritic neurons addresses to current-voltage relations in a continuous passive dendritic tree. It is briefly summarized that the cable theory related to passive cables and dendrites, which is a useful approximation and an important reference for excitable cases. The proposed software can be used to construct user-defined dendritic tree model. The user can define the model in detail, display the constructed dendritic tree, and examine the basic electrical properties of the dendritic tree using transfer impedance approach. The software addresses to ones who want to run simple simulations of the cable theory without need to any programming language skills or expensive software. It can also be used for educational purposes.     

A kinematics and dynamics simulation of the IBM-7565 robot using AML

This article presents a kinematics and dynamics simulation of the IBM-7565 robot using its AML programming language. The kinematics and dynamics models are formulated according to the Denavit-Hartenberg convention and a recursive Newton-Euler algorithm, respectively. The simulation is integrated in a CAD software package (CATIA) which is used in robot offline programming and collision/interference analysis. The CAD package software which runs on an IBM 3033 main frame also emulates the AML for automatic programming. The simulation models can be run on the IBM 3033 using the emulator or on the robot's dedicated Series-1 computer to where the programs are downloaded for execution and control of robot motion.     

A heuristic for software evaluation and selection

The proliferation of software packages has created a difficult, complex problem of evaluation and selection for many users. Traditional approaches to the quantification of package performance have relied on compensatory models, such as the linear weighted attribute model, which sums the weighted ratings of software attributes. These approaches define the dimensions of quality too narrowly and, therefore, omit substantial amounts of information from consideration. This paper presents an alternative methodology, previously used in capital rationing and tournament ranking, that expands the opportunity for objective insight into software quality. In particular, it considers three measures of quality, the frequency with which the attribute ratings of one package exceed those of another, the presence of outliers, where very poor performance may exist on a single attribute and be glossed over by compensatory methods, and the cumulative magnitude of attribute ratings on one package that exceed those on others. The proposed methodology is applied to the evaluation of the following software types: word processing, database management systems, spreadsheet/financial planning, integrated software, graphics, data communications and project management.     

Model and software package for studying and optimizing generation characteristics of semiconductor superlattices

A software package for simulating the dynamics of semiconductor superlattices under the influence of an external magnetic field is developed. The analytical and numerical models on which the program package is based are described in detail in the paper. The approbation of the developed package shows that it can be effectively used to study the dynamics of semiconductor superlattices, including the optimization of the generation characteristics of subterahertz and terahertz devices.     

Exact and approximate area-proportional circular Venn and Euler diagrams

Scientists conducting microarray and other experiments use circular Venn and Euler diagrams to analyze and illustrate their results. As one solution to this problem, this paper introduces a statistical model for fitting area-proportional Venn and Euler diagrams to observed data. The statistical model outlined in this paper includes a statistical loss function and a minimization procedure that enables formal estimation of the Venn/Euler area-proportional model for the first time. A significance test of the null hypothesis is computed for the solution. Residuals from the model are available for inspection. As a result, this algorithm can be used for both exploration and inference on real data sets. A Java program implementing this algorithm is available under the Mozilla Public License. An R function venneuler() is available as a package in CRAN and a plugin is available in Cytoscape.     

Development of a Windows-based indoor air quality simulation software package

A Microsoft Windows-based indoor air quality (IAQ) simulation software package has been developed and has completed a small-scale beta test and quality assurance review. Tentatively named Simulation Tool Kit for Indoor Air Quality and Inhalation Exposure, or STKi for short, this package complements and supplements existing IAQ simulation packages and is designed mainly for advanced users. STKi Version 1 consists of a general-purpose simulation program and four stand-alone, special-purpose programs. The general-purpose program performs multi-zone, multi-pollutant simulations and allows gas-phase chemical reactions. With a large collection of models for sources, sinks, and air filters/cleaners, it can perform simulations for a wide range of indoor air pollution scenarios. The special-purpose programs implement fundamentally based models, which are often excluded from existing IAQ simulation programs despite their improved performance over statistical models. In addition to performing conventional IAQ simulation, which generates time–concentration profiles, STKi can estimate the adequate ventilation rate when certain air quality criteria are given, a unique feature useful for product stewardship and risk management. STKi will be developed in a cumulative manner. More special-purpose simulation programs will be added to the package. Key numerical methods used in STKi are discussed. Ways to convert the STKi programs into language-independent simulation modules that can be used by multi-pathway exposure models are also being explored.     

Ocean software for modeling dynamics of gravity waves

This work is aimed at describing the Ocean software package developed for modeling the dynamics of nonlinear gravity waves and the process of breaking on the surface of a liquid of infinite depth. The modeling is carried out only for a simply connected domain. The used algorithms of Longuet-Higgins, Cokelet, and Krasil’nikov are described. The structure of the software package, computational methods, and indicative functions are described. Tactics for conducting the experiments are proposed. The results of modeling and their comparison with the experimental data are given.     

Polymer-based microfluidic device for measuring membrane protein activities

Functional assays of membrane proteins are becoming increasingly important, both in research and drug discovery applications. The majority of current assays use the patch-clamp technology to measure the activity of ion channels which are over-expressed in cells. In future, in vitro assay systems will be available, which use reconstituted membrane proteins in free-standing lipid bilayers suspended in nano- or micrometer-sized pores. Such functional assays require (1) expression, purification and reconstitution of the membrane protein of interest, (2) a reliable method for lipid bilayer formation and membrane protein integration, and (3) a sensitive detection system. For practical applications, especially for automation, the reliable and controllable transport of fluids is essential. In order to achieve a stable free-standing lipid bilayer, a pore diameter in the micro- to nanometer range is essential. Novel microfluidic devices were developed by bonding a thick (300 μm) polyether ether ketone foil, bearing a channel structure, to a thin (12 μm) foil with a micropore of about 10 μm diameter and then utilized for the formation of stable, free-standing lipid bilayers within the pore. A bacterial voltage-gated potassium channel is integrated therein by fusion and the ion channel activity detected by voltage clamp.     

Stability of hybrid simulation of dynamic systems

This note analyses the problem of stability of hybrid simulation of dynamic systems. Time delays and sample-and-hold operations do cause serious stability problems, and if frequently happens that considerable time and effort are wasted because instability is not known in advance of programming the simulation on the hybrid computer. However, if the system under investigation can be approximated in its response by an equivalent linear system, then it is possible to define a procedure which will predict in advance whether any proposed computing scheme is stable. The text describes one such procedure, together with its implementation as a software package which can be used to predict the stability of simulations of practical size. In addition, the text contains a number of examples which illustrate the application of the software package.     

Recovery of hidden information through synaptic dynamics

The role of synaptic dynamics in processing neural information is investigated in a neural information channel with realistic model neurons having chaotic intrinsic dynamics. Our neuron models are realized in simple analogue circuits, and our synaptic connections are realized both in analogue circuits and through a dynamic clamp program. The information which is input to the first chaotic neuron in the channel emerges partially absent and partially 'hidden'. Part is absent because of the dynamical effects of the chaotic oscillation that effectively acts as a noisy channel. The 'hidden' part is recoverable. We show that synaptic parameters, most significantly receptor binding time constants, can be tuned to enhance the information transmission by the combination of a neuron plus a synapse. We discuss how the dynamics of the synapse can be used to recover 'hidden' information using average mutual information as a measure of the quality of information transport.     

Numerical simulation of the motion of granular material using object-oriented techniques

The objective of this contribution is to present a numerical simulation method to model the motion of a packed bed on a moving grate or in a rotary kiln using object-oriented techniques. The packed bed can be described as granular material consisting of a large number of particles. The method chosen is the Lagrangian time-driven method and it uses the position, the orientation, the velocity and the angular velocity of particles as independent variables. These are obtained by time integration of the three-dimensional dynamics equations which were derived from the classical Newtonian mechanics approach based on the second law of Newton for the translation and rotation of each particle in the granular material. This includes keeping track of all forces and moments acting on each particle at every time-step. Particles are treated as contacting visco-elastic bodies which can overlap each other. Contact forces depend on the overlap geometry, material properties and dynamics of particles and include normal and tangential components of repulsion force with visco-elastic models for energy dissipation through internal and surface friction. The resulting equations of particle motion are solved by the Gear predictor–corrector scheme of fifth-order accuracy.The simulation method is based on object-oriented methodologies and programmed in the programming language C++. This approach supports objects which can be used for three-dimensional particles of various shapes and sizes and for walls as boundaries. The programming modules are implemented in the TOSCA (tools of object-oriented software for continuum mechanic applications) software package which allows for a high degree of flexibility and for shortening the duration of the software development process. As methods for particle motion may deal with particles of different sizes and materials, the approach allows to describe transport processes in technical applications.     

Single neuron computation: from dynamical system to feature detector

White noise methods are a powerful tool for characterizing the computation performed by neural systems. These methods allow one to identify the feature or features that a neural system extracts from a complex input and to determine how these features are combined to drive the system's spiking response. These methods have also been applied to characterize the input-output relations of single neurons driven by synaptic inputs, simulated by direct current injection. To interpret the results of white noise analysis of single neurons, we would like to understand how the obtained feature space of a single neuron maps onto the biophysical properties of the membrane, in particular, the dynamics of ion channels. Here, through analysis of a simple dynamical model neuron, we draw explicit connections between the output of a white noise analysis and the underlying dynamical system. We find that under certain assumptions, the form of the relevant features is well defined by the parameters of the dynamical system. Further, we show that under some conditions, the feature space is spanned by the spike-triggered average and its successive order time derivatives.     

An open source tool for heart rate variability spectral analysis

In this paper we describe a software package for developing heart rate variability analysis. This package, called RHRV, is a third party extension for the open source statistical environment R, and can be freely downloaded from the R-CRAN repository. We review the state of the art of software related to the analysis of heart rate variability (HRV). Based upon this review, we motivate the development of an open source software platform which can be used for developing new algorithms for studying HRV or for performing clinical experiments. In particular, we show how the RHRV package greatly simplifies and accelerates the work of the computer scientist or medical specialist in the HRV field. We illustrate the utility of our package with practical examples.     

基于柴油机虚拟样机的动力学仿真研究

通过对柴油机部件装配进行机构运动学和动力学仿真,能为柴油机的结构和性能优化提供依据。该文基于虚拟样机技术及其支撵软件VN4D和Pro／E,对12VPA6柴油机的曲轴-连杆-活塞机构进行了运动学、动力学仿真研究。首先,运用三维建模软件Pro／E,建立了12VPA6型柴油机曲轴-连杆-活塞机构的虚拟样机模型,然后将模型导入仿真软件VN4D中,对曲轴-连杆-活塞运动件进行了运动学和动力学仿真。通过计算机对柴油机虚拟样机的仿真运行,获取了仿真模型的运动学、动力学特性数据,得到了与理论分析相吻合的结果,为进一步对该型柴油机曲轴-连杆-活塞机构进行有限元分析奠定了基础。     

软件功能测试规模估算模型的研究及其应用

提出一种基于功能点分析法的软件功能测试规模估算模型。该模型适用于黑盒功能测试,用于系统测试阶段或验收测试阶段工作量的估算,基本估算步骤包括估算软件规模、定义规模因子、计算测试规模,并在项目中进行实践应用。结果表明,该模型可以较好地估算软件功能测试规模,可用于测试计划的制定及实施。     

Dynamics analysis of a 3-RRP spherical parallel manipulator using the natural orthogonal complement

In the present research, application of the Natural Orthogonal Complement (NOC) for the dynamic analysis of a spherical parallel manipulator, referred to as SST, is presented. Both inverse and direct dynamics are considered. The NOC and the SST fully parallel robot are explained. To drive the NOC for the SST manipulator, constraints between joint variables are written using the transformation matrices obtained from three different branches of the robot. The Newton–Euler formulation is used to model the dynamics of each individual body, including moving platform and legs of the manipulator. D’Alembert’s principle is applied and Newton–Euler dynamical equations free from non-working generalized constraint forces are obtained. Finally two examples, one for direct and one for inverse dynamics are presented. The correctness and accuracy of the obtained solution are verified by comparing with the solution of the virtual work method as well as commercial multi-body dynamics software.