Machine recognition of hand-drawn circuit diagrams

An application of image processing techniques to recognition of hand-drawn circuit diagrams is presented. The scanned image of a diagram is pre-processed to remove noise and converted to bilevel. Morphological operations are applied to obtain a clean, connected representation using thinned lines. The diagram comprises of nodes, connections and components. Nodes and components are segmented using appropriate thresholds on a spatially varying object pixel density. Connection paths are traced using a pixel-stack. Nodes are classified using syntactic analysis. Components are classified using a combination of invariant moments, scalar pixel-distribution features, and vector relationships between straight lines in polygonal representations. A node recognition accuracy of 82% and a component recognition accuracy of 86% was achieved on a database comprising 107 nodes and 449 components. This recogniser can be used for layout “beautification” or to generate input code for circuit analysis and simulation packages

Sensitivity of building zones to potential global warming

As global warming entails new conditions for the built environment, the thermal and energy performance of existing buildings, which are designed based on current weather data, may become unclear and remain a great concern. Through building computer simulation and qualitative analysis of the weighted factor for the outdoor temperature impact on building energy and thermal performance, this paper investigates the sensitivity of different office building zoning to the potential global warming. A standard office building type is examined for all eight capital cities in Australia. Results show that comparing the middle and top floors, except for cool climate (i.e. Hobart), the ground floor appears to be the most sensitive to the effect of global warming and has the highest tendency for a overheating problem. From the analysis of the responses of different zone orientations to the outdoor air temperature increase, it is also found that there are widely varied responses between zone orientations, with South zone (in the southern hemisphere) being the most sensitive. With an increased external air temperature, the variation between different floors or zone orientations will become more significant, up to 53 percent increase of overheating hours in Darwin and 47 percent increase of cooling load in Hobart.

Scaffolding techniques : a teacher training for cooperative learning in Thailand primary education

In general, the benefits of using cooperative learning include academic achievement, communication skills, problem-solving, social skills and student motivation. Yet cooperative learning as a Western educational concept may be ineffective in a different learning system. The study aims to investigate scaffolding techniques for cooperative learning in Thailand primary education. The program was designed to foster Thai primary school teachers’ cooperative learning implementation that includes the basic tenets of cooperative learning and socio-cognitive based learning. Two teachers were invited to participate in this experimental teacher training program for one and a half weeks. Then the teachers implemented a cooperative learning in their mathematics class for six weeks. The data from teacher interview and classroom observation indicated that the both teachers are able to utilise questions to scaffold their students’ engagement in cooperative learning. This initiative study showed that difficulty or failure of implementing cooperative learning in Thailand education may not be derived from cultural difference. The paper discussed the techniques the participant teachers applied with proactive scaffolding, reactive scaffolding and scaffolding questions that can be used to facilitate the implementation of cooperative learning in Thai school.

Evaluating effects of eco-driving at traffic intersections based on traffic micro-simulation

Eco-driving is an initiative driving behavior which aims to reduce fuel consumption and emissions from automobiles. Recently, it has attracted increasing interests and has been adopted by many drivers in Australia. Although many of the studies have revealed considerable benefits in terms of fuel consumption and emissions after utilising eco-driving, most of the literature investigated eco-driving effects on individual driver but not traffic flow. The driving behavior of eco-drivers will potentially affect other drivers and thereby affects the entire traffic flow. To comprehensively assess and understand how effectively eco-driving can perform, therefore, measurement on traffic flow is necessary. In this paper, we proposed and demonstrated an evaluation method based on a microscopic traffic simulator (Aimsun). We focus on one particular eco-driving style which involves moderate and smooth acceleration. We evaluated both traffic performance (travel time) and environmental performance (fuel consumption and CO2 emission) at traffic intersection level in a simple simulation model. The before-and-after comparisons indicated potentially negative impacts when using eco-driving, which highlighted the necessity to carefully evaluate and improve eco-driving before wide promotion and implementation.

Stochastic models and simulation of ion channel dynamics

The behaviour of ion channels within cardiac and neuronal cells is intrinsically stochastic in nature. When the number of channels is small this stochastic noise is large and can have an impact on the dynamics of the system which is potentially an issue when modelling small neurons and drug block in cardiac cells. While exact methods correctly capture the stochastic dynamics of a system they are computationally expensive, restricting their inclusion into tissue level models and so approximations to exact methods are often used instead. The other issue in modelling ion channel dynamics is that the transition rates are voltage dependent, adding a level of complexity as the channel dynamics are coupled to the membrane potential. By assuming that such transition rates are constant over each time step, it is possible to derive a stochastic differential equation (SDE), in the same manner as for biochemical reaction networks, that describes the stochastic dynamics of ion channels. While such a model is more computationally efficient than exact methods we show that there are analytical problems with the resulting SDE as well as issues in using current numerical schemes to solve such an equation. We therefore make two contributions: develop a different model to describe the stochastic ion channel dynamics that analytically behaves in the correct manner and also discuss numerical methods that preserve the analytical properties of the model.

Some novel techniques of parameter estimation for the dynamical models in biological systems

Inverse problems based on using experimental data to estimate unknown parameters of a system often arise in biological and chaotic systems. In this paper, we consider parameter estimation in systems biology involving linear and non-linear complex dynamical models, including the Michaelis–Menten enzyme kinetic system, a dynamical model of competence induction in Bacillus subtilis bacteria and a model of feedback bypass in B. subtilis bacteria. We propose some novel techniques for inverse problems. Firstly, we establish an approximation of a non-linear differential algebraic equation that corresponds to the given biological systems. Secondly, we use the Picard contraction mapping, collage methods and numerical integration techniques to convert the parameter estimation into a minimization problem of the parameters. We propose two optimization techniques: a grid approximation method and a modified hybrid Nelder–Mead simplex search and particle swarm optimization (MH-NMSS-PSO) for non-linear parameter estimation. The two techniques are used for parameter estimation in a model of competence induction in B. subtilis bacteria with noisy data. The MH-NMSS-PSO scheme is applied to a dynamical model of competence induction in B. subtilis bacteria based on experimental data and the model for feedback bypass. Numerical results demonstrate the effectiveness of our approach.

Stochastic modelling of T cell homeostasis for two competing clonotypes via the master equation

Stochastic models for competing clonotypes of T cells by multivariate, continuous-time, discrete state, Markov processes have been proposed in the literature by Stirk, Molina-París and van den Berg (2008). A stochastic modelling framework is important because of rare events associated with small populations of some critical cell types. Usually, computational methods for these problems employ a trajectory-based approach, based on Monte Carlo simulation. This is partly because the complementary, probability density function (PDF) approaches can be expensive but here we describe some efficient PDF approaches by directly solving the governing equations, known as the Master Equation. These computations are made very efficient through an approximation of the state space by the Finite State Projection and through the use of Krylov subspace methods when evolving the matrix exponential. These computational methods allow us to explore the evolution of the PDFs associated with these stochastic models, and bimodal distributions arise in some parameter regimes. Time-dependent propensities naturally arise in immunological processes due to, for example, age-dependent effects. Incorporating time-dependent propensities into the framework of the Master Equation significantly complicates the corresponding computational methods but here we describe an efficient approach via Magnus formulas. Although this contribution focuses on the example of competing clonotypes, the general principles are relevant to multivariate Markov processes and provide fundamental techniques for computational immunology.

Stochastic chemical kinetics and the quasi-steady-state assumption : application to the stochastic simulation algorithm and chemical master equation

Recently the application of the quasi-steady-state approximation (QSSA) to the stochastic simulation algorithm (SSA) was suggested for the purpose of speeding up stochastic simulations of chemical systems that involve both relatively fast and slow chemical reactions [Rao and Arkin, J. Chem. Phys. 118, 4999 (2003)] and further work has led to the nested and slow-scale SSA. Improved numerical efficiency is obtained by respecting the vastly different time scales characterizing the system and then by advancing only the slow reactions exactly, based on a suitable approximation to the fast reactions. We considerably extend these works by applying the QSSA to numerical methods for the direct solution of the chemical master equation (CME) and, in particular, to the finite state projection algorithm [Munsky and Khammash, J. Chem. Phys. 124, 044104 (2006)], in conjunction with Krylov methods. In addition, we point out some important connections to the literature on the (deterministic) total QSSA (tQSSA) and place the stochastic analogue of the QSSA within the more general framework of aggregation of Markov processes. We demonstrate the new methods on four examples: Michaelis–Menten enzyme kinetics, double phosphorylation, the Goldbeter–Koshland switch, and the mitogen activated protein kinase cascade. Overall, we report dramatic improvements by applying the tQSSA to the CME solver.

Train service timetabling in railway open markets by particle swarm optimisation

Railway timetabling is an important process in train service provision as it matches the transportation demand with the infrastructure capacity while customer satisfaction is also considered. It is a multi-objective optimisation problem, in which a feasible solution, rather than the optimal one, is usually taken in practice because of the time constraint. The quality of services may suffer as a result. In a railway open market, timetabling usually involves rounds of negotiations among a number of self-interested and independent stakeholders and hence additional objectives and constraints are imposed on the timetabling problem. While the requirements of all stakeholders are taken into consideration simultaneously, the computation demand is inevitably immense. Intelligent solution-searching techniques provide a possible solution. This paper attempts to employ a particle swarm optimisation (PSO) approach to devise a railway timetable in an open market. The suitability and performance of PSO are studied on a multi-agent-based railway open-market negotiation simulation platform.

Accelerated leap methods for simulating discrete stochastic chemical kinetics

Biologists are increasingly conscious of the critical role that noise plays in cellular functions such as genetic regulation, often in connection with fluctuations in small numbers of key regulatory molecules. This has inspired the development of models that capture this fundamentally discrete and stochastic nature of cellular biology - most notably the Gillespie stochastic simulation algorithm (SSA). The SSA simulates a temporally homogeneous, discrete-state, continuous-time Markov process, and of course the corresponding probabilities and numbers of each molecular species must all remain positive. While accurately serving this purpose, the SSA can be computationally inefficient due to very small time stepping so faster approximations such as the Poisson and Binomial τ-leap methods have been suggested. This work places these leap methods in the context of numerical methods for the solution of stochastic differential equations (SDEs) driven by Poisson noise. This allows analogues of Euler-Maruyuma, Milstein and even higher order methods to be developed through the Itô-Taylor expansions as well as similar derivative-free Runge-Kutta approaches. Numerical results demonstrate that these novel methods compare favourably with existing techniques for simulating biochemical reactions by more accurately capturing crucial properties such as the mean and variance than existing methods.

Parallel implementation of stochastic simulation for large scale cellular processes

Experimental and theoretical studies have shown the importance of stochastic processes in genetic regulatory networks and cellular processes. Cellular networks and genetic circuits often involve small numbers of key proteins such as transcriptional factors and signaling proteins. In recent years stochastic models have been used successfully for studying noise in biological pathways, and stochastic modelling of biological systems has become a very important research field in computational biology. One of the challenge problems in this field is the reduction of the huge computing time in stochastic simulations. Based on the system of the mitogen-activated protein kinase cascade that is activated by epidermal growth factor, this work give a parallel implementation by using OpenMP and parallelism across the simulation. Special attention is paid to the independence of the generated random numbers in parallel computing, that is a key criterion for the success of stochastic simulations. Numerical results indicate that parallel computers can be used as an efficient tool for simulating the dynamics of large-scale genetic regulatory networks and cellular processes

Issues and concerns of microscopic calibration process at different network levels : case study of Pacific Motorway

Calibration process in micro-simulation is an extremely complicated phenomenon. The difficulties are more prevalent if the process encompasses fitting aggregate and disaggregate parameters e.g. travel time and headway. The current practice in calibration is more at aggregate level, for example travel time comparison. Such practices are popular to assess network performance. Though these applications are significant there is another stream of micro-simulated calibration, at disaggregate level. This study will focus on such microcalibration exercise-key to better comprehend motorway traffic risk level, management of variable speed limit (VSL) and ramp metering (RM) techniques. Selected section of Pacific Motorway in Brisbane will be used as a case study. The discussion will primarily incorporate the critical issues encountered during parameter adjustment exercise (e.g. vehicular, driving behaviour) with reference to key traffic performance indicators like speed, lane distribution and headway; at specific motorway points. The endeavour is to highlight the utility and implications of such disaggregate level simulation for improved traffic prediction studies. The aspects of calibrating for points in comparison to that for whole of the network will also be briefly addressed to examine the critical issues such as the suitability of local calibration at global scale. The paper will be of interest to transport professionals in Australia/New Zealand where micro-simulation in particular at point level, is still comparatively a less explored territory in motorway management.

Issues and concerns of microscopic calibration process at different network levels : case study of pacific motorway

Calibration process in micro-simulation is an extremely complicated phenomenon. The difficulties are more prevalent if the process encompasses fitting aggregate and disaggregate parameters e.g. travel time and headway. The current practice in calibration is more at aggregate level, for example travel time comparison. Such practices are popular to assess network performance. Though these applications are significant there is another stream of micro-simulated calibration, at disaggregate level. This study will focus on such micro-calibration exercise-key to better comprehend motorway traffic risk level, management of variable speed limit (VSL) and ramp metering (RM) techniques. Selected section of Pacific Motorway in Brisbane will be used as a case study. The discussion will primarily incorporate the critical issues encountered during parameter adjustment exercise (e.g. vehicular, driving behaviour) with reference to key traffic performance indicators like speed, land distribution and headway; at specific motorway points. The endeavour is to highlight the utility and implications of such disaggregate level simulation for improved traffic prediction studies. The aspects of calibrating for points in comparison to that for whole of the network will also be briefly addressed to examine the critical issues such as the suitability of local calibration at global scale. The paper will be of interest to transport professionals in Australia/New Zealand where micro-simulation in particular at point level, is still comparatively a less explored territory in motorway management.

A traffic simulation standard based on data marts

Traffic Simulation models tend to have their own data input and output formats. In an effort to standardise the input for traffic simulations, we introduce in this paper a set of data marts that aim to serve as a common interface between the necessaary data, stored in dedicated databases, and the swoftware packages, that require the input in a certain format. The data marts are developed based on real world objects (e.g. roads, traffic lights, controllers) rather than abstract models and hence contain all necessary information that can be transformed by the importing software package to their needs. The paper contains a full description of the data marts for network coding, simulation results, and scenario management, which have been discussed with industry partners to ensure sustainability.