A hierarchical latent variable model for data visualization

Visualization has proven to be a powerful and widely-applicable tool the analysis and interpretation of data. Most visualization algorithms aim to find a projection from the data space down to a two-dimensional visualization space. However, for complex data sets living in a high-dimensional space it is unlikely that a single two-dimensional projection can reveal all of the interesting structure. We therefore introduce a hierarchical visualization algorithm which allows the complete data set to be visualized at the top level, with clusters and sub-clusters of data points visualized at deeper levels. The algorithm is based on a hierarchical mixture of latent variable models, whose parameters are estimated using the expectation-maximization algorithm. We demonstrate the principle of the approach first on a toy data set, and then apply the algorithm to the visualization of a synthetic data set in 12 dimensions obtained from a simulation of multi-phase flows in oil pipelines and to data in 36 dimensions derived from satellite images.

Flexibility of short-strand RNA in aqueous solution as revealed by molecular dynamics simulation:are A′-RNA and A-RNA distinct conformational structures?

We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A'-RNA forms in the presence of counterions and explicit water. Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA namely major groove width, inclination and the number of base pairs in a helical twist over a 30 ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A'-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors). © CSIRO 2009.

Simulation process templates for e-business modelling

This paper argues the use of reusable simulation templates as a tool that can help to predict the effect of e-business introduction on business processes. First, a set of requirements for e-business modelling is introduced and modelling options described. Traditional business process mapping techniques are examined as a way of identifying potential changes. Whilst paper-based process mapping may not highlight significant differences between traditional and e-business processes, simulation does allow the real effects of e-business to be identified. Simulation has the advantage of capturing the dynamic characteristics of the process, thus reflecting more accurately the changes in behaviour. This paper shows the value of using generic process maps as a starting point for collecting the data that is needed to build the simulation and proposes the use of reusable templates/components for the speedier building of e-business simulation models.

On the use of likert-type scales in multilevel data:Influence on aggregate variables

In multilevel analyses, problems may arise when using Likert-type scales at the lowest level of analysis. Specifically, increases in variance should lead to greater censoring for the groups whose true scores fall at either end of the distribution. The current study used simulation methods to examine the influence of single-item Likert-type scale usage on ICC(1), ICC(2), and group-level correlations. Results revealed substantial underestimation of ICC(1) when using Likert-type scales with common response formats (e.g., 5 points). ICC(2) and group-level correlations were also underestimated, but to a lesser extent. Finally, the magnitude of underestimation was driven in large part to an interaction between Likert-type scale usage and the amounts of within- and between-group variance. © Sage Publications.

Using a simulation model for knowledge elicitation and knowledge management

The work reported in this paper is part of a project simulating maintenance operations in an automotive engine production facility. The decisions made by the people in charge of these operations form a crucial element of this simulation. Eliciting this knowledge is problematic. One approach is to use the simulation model as part of the knowledge elicitation process. This paper reports on the experience so far with using a simulation model to support knowledge management in this way. Issues are discussed regarding the data available, the use of the model, and the elicitation process itself. © 2004 Elsevier B.V. All rights reserved.

Using system dynamics in a discrete-event simulation study of a manufacturing plant

Purpose - To provide an example of the use of system dynamics within the context of a discrete-event simulation study. Design/methodology/approach - A discrete-event simulation study of a production-planning facility in a gas cylinder-manufacturing plant is presented. The case study evidence incorporates questionnaire responses from sales managers involved in the order-scheduling process. Findings - As the project progressed it became clear that, although the discrete-event simulation would meet the objectives of the study in a technical sense, the organizational problem of "delivery performance" would not be solved by the discrete-event simulation study alone. The case shows how the qualitative outcomes of the discrete-event simulation study led to an analysis using the system dynamics technique. The system dynamics technique was able to model the decision-makers in the sales and production process and provide a deeper understanding of the performance of the system. Research limitations/implications - The case study describes a traditional discrete-event simulation study which incorporated an unplanned investigation using system dynamics. Further, case studies using a planned approach to showing consideration of organizational issues in discrete-event simulation studies are required. Then the role of both qualitative data in a discrete-event simulation study and the use of supplementary tools which incorporate organizational aspects may help generate a methodology for discrete-event simulation that incorporates human aspects and so improve its relevance for decision making. Practical implications - It is argued that system dynamics can provide a useful addition to the toolkit of the discrete-event simulation practitioner in helping them incorporate a human aspect in their analysis. Originality/value - Helps decision makers gain a broader perspective on the tools available to them by showing the use of system dynamics to supplement the use of discrete-event simulation. © Emerald Group Publishing Limited.

Using DEA and simulation in guiding operating units to improved performance

The potential for the use of DEA and simulation in a mutually supporting role in guiding operating units to improved performance is presented. An analysis following a three-stage process is suggested. Stage one involves obtaining the data for the DEA analysis. This can be sourced from historical data, simulated data or a combination of the two. Stage two involves the DEA analysis that identifies benchmark operating units. In the third stage simulation can now be used in order to offer practical guidance to operating units towards improved performance. This can be achieved by the use of sensitivity analysis of the benchmark unit using a simulation model to offer direct support as to the feasibility and efficiency of any variations in operating practices to be tested. Alternatively, the simulation can be used as a mechanism to transmit the practices of the benchmark unit to weaker performing units by building a simulation model of the weaker unit to the process design of the benchmark unit. The model can then compare performance of the current and benchmark process designs. Quantifying improvement in this way provides a useful driver to any process change initiative that is required to bring the performance of weaker units up to the best in class. © 2005 Operational Research Society Ltd. All rights reserved.

Simulation modelling for business

Simulation modelling has been used for many years in the manufacturing sector but has now become a mainstream tool in business situations. This is partly because of the popularity of business process re-engineering (BPR) and other process based improvement methods that use simulation to help analyse changes in process design. This textbook includes case studies in both manufacturing and service situations to demonstrate the usefulness of the approach. A further reason for the increasing popularity of the technique is the development of business orientated and user-friendly Windows-based software. This text provides a guide to the use of ARENA, SIMUL8 and WITNESS simulation software systems that are widely used in industry and available to students. Overall this text provides a practical guide to building and implementing the results from a simulation model. All the steps in a typical simulation study are covered including data collection, input data modelling and experimentation.

The case for the organisational use of simulation

This paper describes the use of simulation in a large manufacturing organisation and analyses how it could have been used more fully. Although the benefits from using simulation were clear, it was seen that the technique could have been deployed more effectively by considering the organisational context of the use. From the analysis of the case study, certain recommendations are made on how to maximise the benefits from simulation within the organisation, thereby extending the benefits from what is often a considerable investment in developing a simulation model. Recent developments in simulation software in terms of improvements in usability and integration with organisational data are seen to increase the feasibility of a wider role for simulation if the organisational barriers discussed can be overcome.

Analysis and simulation of computer controlled cellular mobile radio systems

Cellular mobile radio systems will be of increasing importance in the future. This thesis describes research work concerned with the teletraffic capacity and the canputer control requirements of such systems. The work involves theoretical analysis and experimental investigations using digital computer simulation. New formulas are derived for the congestion in single-cell systems in which there are both land-to-mobile and mobile-to-mobile calls and in which mobile-to-mobile calls go via the base station. Two approaches are used, the first yields modified forms of the familiar Erlang and Engset formulas, while the second gives more complicated but more accurate formulas. The results of computer simulations to establish the accuracy of the formulas are described. New teletraffic formulas are also derived for the congestion in multi -cell systems. Fixed, dynamic and hybrid channel assignments are considered. The formulas agree with previously published simulation results. Simulation programs are described for the evaluation of the speech traffic of mobiles and for the investigation of a possible computer network for the control of the speech traffic. The programs were developed according to the structured progranming approach leading to programs of modular construction. Two simulation methods are used for the speech traffic: the roulette method and the time-true method. The first is economical but has some restriction, while the second is expensive but gives comprehensive answers. The proposed control network operates at three hierarchical levels performing various control functions which include: the setting-up and clearing-down of calls, the hand-over of calls between cells and the address-changing of mobiles travelling between cities. The results demonstrate the feasibility of the control netwvork and indicate that small mini -computers inter-connected via voice grade data channels would be capable of providing satisfactory control

Packet voice/data in local broadcast networks

A local area network that can support both voice and data packets offers economic advantages due to the use of only a single network for both types of traffic, greater flexibility to changing user demands, and it also enables efficient use to be made of the transmission capacity. The latter aspect is very important in local broadcast networks where the capacity is a scarce resource, for example mobile radio. This research has examined two types of local broadcast network, these being the Ethernet-type bus local area network and a mobile radio network with a central base station. With such contention networks, medium access control (MAC) protocols are required to gain access to the channel. MAC protocols must provide efficient scheduling on the channel between the distributed population of stations who want to transmit. No access scheme can exceed the performance of a single server queue, due to the spatial distribution of the stations. Stations cannot in general form a queue without using part of the channel capacity to exchange protocol information. In this research, several medium access protocols have been examined and developed in order to increase the channel throughput compared to existing protocols. However, the established performance measures of average packet time delay and throughput cannot adequately characterise protocol performance for packet voice. Rather, the percentage of bits delivered within a given time bound becomes the relevant performance measure. Performance evaluation of the protocols has been examined using discrete event simulation and in some cases also by mathematical modelling. All the protocols use either implicit or explicit reservation schemes, with their efficiency dependent on the fact that many voice packets are generated periodically within a talkspurt. Two of the protocols are based on the existing 'Reservation Virtual Time CSMA/CD' protocol, which forms a distributed queue through implicit reservations. This protocol has been improved firstly by utilising two channels, a packet transmission channel and a packet contention channel. Packet contention is then performed in parallel with a packet transmission to increase throughput. The second protocol uses variable length packets to reduce the contention time between transmissions on a single channel. A third protocol developed, is based on contention for explicit reservations. Once a station has achieved a reservation, it maintains this effective queue position for the remainder of the talkspurt and transmits after it has sensed the transmission from the preceeding station within the queue. In the mobile radio environment, adaptions to the protocols were necessary in order that their operation was robust to signal fading. This was achieved through centralised control at a base station, unlike the local area network versions where the control was distributed at the stations. The results show an improvement in throughput compared to some previous protocols. Further work includes subjective testing to validate the protocols' effectiveness.

Digital communication networks incorporating mobile data terminals

The use of digital communication systems is increasing very rapidly. This is due to lower system implementation cost compared to analogue transmission and at the same time, the ease with which several types of data sources (data, digitised speech and video, etc.) can be mixed. The emergence of packet broadcast techniques as an efficient type of multiplexing, especially with the use of contention random multiple access protocols, has led to a wide-spread application of these distributed access protocols in local area networks (LANs) and a further extension of them to radio and mobile radio communication applications. In this research, a proposal for a modified version of the distributed access contention protocol which uses the packet broadcast switching technique has been achieved. The carrier sense multiple access with collision avoidance (CSMA/CA) is found to be the most appropriate protocol which has the ability to satisfy equally the operational requirements for local area networks as well as for radio and mobile radio applications. The suggested version of the protocol is designed in a way in which all desirable features of its precedents is maintained. However, all the shortcomings are eliminated and additional features have been added to strengthen its ability to work with radio and mobile radio channels. Operational performance evaluation of the protocol has been carried out for the two types of non-persistent and slotted non-persistent, through mathematical and simulation modelling of the protocol. The results obtained from the two modelling procedures validate the accuracy of both methods, which compares favourably with its precedent protocol CSMA/CD (with collision detection). A further extension of the protocol operation has been suggested to operate with multichannel systems. Two multichannel systems based on the CSMA/CA protocol for medium access are therefore proposed. These are; the dynamic multichannel system, which is based on two types of channel selection, the random choice (RC) and the idle choice (IC), and the sequential multichannel system. The latter has been proposed in order to supress the effect of the hidden terminal, which always represents a major problem with the usage of the contention random multiple access protocols with radio and mobile radio channels. Verification of their operation performance evaluation has been carried out using mathematical modelling for the dynamic system. However, simulation modelling has been chosen for the sequential system. Both systems are found to improve system operation and fault tolerance when compared to single channel operation.

Spatial aspects of MRSA epidemiology:A case study using stochastic simulation, kernel estimation and SaTScan

The identification of disease clusters in space or space-time is of vital importance for public health policy and action. In the case of methicillin-resistant Staphylococcus aureus (MRSA), it is particularly important to distinguish between community and health care-associated infections, and to identify reservoirs of infection. 832 cases of MRSA in the West Midlands (UK) were tested for clustering and evidence of community transmission, after being geo-located to the centroids of UK unit postcodes (postal areas roughly equivalent to Zip+4 zip code areas). An age-stratified analysis was also carried out at the coarser spatial resolution of UK Census Output Areas. Stochastic simulation and kernel density estimation were combined to identify significant local clusters of MRSA (p<0.025), which were supported by SaTScan spatial and spatio-temporal scan. In order to investigate local sampling effort, a spatial 'random labelling' approach was used, with MRSA as cases and MSSA (methicillin-sensitive S. aureus) as controls. Heavy sampling in general was a response to MRSA outbreaks, which in turn appeared to be associated with medical care environments. The significance of clusters identified by kernel estimation was independently supported by information on the locations and client groups of nursing homes, and by preliminary molecular typing of isolates. In the absence of occupational/ lifestyle data on patients, the assumption was made that an individual's location and consequent risk is adequately represented by their residential postcode. The problems of this assumption are discussed, with recommendations for future data collection.

Computer simulation of liquid flow patterns on distillation trays

This thesis describes work carried out to improve the fundamental modelling of liquid flows on distillation trays. A mathematical model is presented based on the principles of computerised fluid dynamics. It models the liquid flow in the horizontal directions allowing for the effects of the vapour through the use of an increased liquid turbulence, modelled by an eddy viscosity, and a resistance to liquid flow caused by the vapour being accelerated horizontally by the liquid. The resultant equations are similar to the Navier-Stokes equations with the addition of a resistance term.A mass-transfer model is used to calculate liquid concentration profiles and tray efficiencies. A heat and mass transfer analogy is used to compare theoretical concentration profiles to experimental water-cooling data obtained from a 2.44 metre diameter air-water distillation simulation rig. The ratios of air to water flow rates are varied in order to simulate three pressures: vacuum, atmospheric pressure and moderate pressure.For simulated atmospheric and moderate pressure distillation, the fluid mechanical model constantly over-predicts tray efficiencies with an accuracy of between +1.7% and +11.3%. This compares to -1.8% to -10.9% for the stagnant regions model (Porter et al. 1972) and +12.8% to +34.7% for the plug flow plus back-mixing model (Gerster et al. 1958). The model fails to predict the flow patterns and tray efficiencies for vacuum simulation due to the change in the mechanism of liquid transport, from a liquid continuous layer to a spray as the liquid flow-rate is reduced. This spray is not taken into account in the development of the fluid mechanical model. A sensitivity analysis carried out has shown that the fluid mechanical model is relatively insensitive to the prediction of the average height of clear liquid, and a reduction in the resistance term results in a slight loss of tray efficiency. But these effects are not great. The model is quite sensitive to the prediction of the eddy viscosity term. Variations can produce up to a 15% decrease in tray efficiency. The fluid mechanical model has been incorporated into a column model so that statistical optimisation techniques can be employed to fit a theoretical column concentration profile to experimental data. Through the use of this work mass-transfer data can be obtained.