Three-factor models versus time series models:quantifying time-dependencies of interactions between stimuli in cell biology and psychobiology for short longitudinal data

Signal integration determines cell fate on the cellular level, affects cognitive processes and affective responses on the behavioural level, and is likely to be involved in psychoneurobiological processes underlying mood disorders. Interactions between stimuli may subjected to time effects. Time-dependencies of interactions between stimuli typically lead to complex cell responses and complex responses on the behavioural level. We show that both three-factor models and time series models can be used to uncover such time-dependencies. However, we argue that for short longitudinal data the three factor modelling approach is more suitable. In order to illustrate both approaches, we re-analysed previously published short longitudinal data sets. We found that in human embryonic kidney 293 cells cells the interaction effect in the regulation of extracellular signal-regulated kinase (ERK) 1 signalling activation by insulin and epidermal growth factor is subjected to a time effect and dramatically decays at peak values of ERK activation. In contrast, we found that the interaction effect induced by hypoxia and tumour necrosis factor-alpha for the transcriptional activity of the human cyclo-oxygenase-2 promoter in HEK293 cells is time invariant at least in the first 12-h time window after stimulation. Furthermore, we applied the three-factor model to previously reported animal studies. In these studies, memory storage was found to be subjected to an interaction effect of the beta-adrenoceptor agonist clenbuterol and certain antagonists acting on the alpha-1-adrenoceptor / glucocorticoid-receptor system. Our model-based analysis suggests that only if the antagonist drug is administer in a critical time window, then the interaction effect is relevant.

Modelling data and voice traffic over IP networks using continuous-time Markov models

Common approaches to IP-traffic modelling have featured the use of stochastic models, based on the Markov property, which can be classified into black box and white box models based on the approach used for modelling traffic. White box models, are simple to understand, transparent and have a physical meaning attributed to each of the associated parameters. To exploit this key advantage, this thesis explores the use of simple classic continuous-time Markov models based on a white box approach, to model, not only the network traffic statistics but also the source behaviour with respect to the network and application. The thesis is divided into two parts: The first part focuses on the use of simple Markov and Semi-Markov traffic models, starting from the simplest two-state model moving upwards to n-state models with Poisson and non-Poisson statistics. The thesis then introduces the convenient to use, mathematically derived, Gaussian Markov models which are used to model the measured network IP traffic statistics. As one of the most significant contributions, the thesis establishes the significance of the second-order density statistics as it reveals that, in contrast to first-order density, they carry much more unique information on traffic sources and behaviour. The thesis then exploits the use of Gaussian Markov models to model these unique features and finally shows how the use of simple classic Markov models coupled with use of second-order density statistics provides an excellent tool for capturing maximum traffic detail, which in itself is the essence of good traffic modelling. The second part of the thesis, studies the ON-OFF characteristics of VoIP traffic with reference to accurate measurements of the ON and OFF periods, made from a large multi-lingual database of over 100 hours worth of VoIP call recordings. The impact of the language, prosodic structure and speech rate of the speaker on the statistics of the ON-OFF periods is analysed and relevant conclusions are presented. Finally, an ON-OFF VoIP source model with log-normal transitions is contributed as an ideal candidate to model VoIP traffic and the results of this model are compared with those of previously published work.

Summary of the 6th international workshop on models@run.time

The 6th edition of the workshop Models@run.time was held at the 14th International Conference MODELS. The workshop took place in the city of Wellington, New Zealand, on the 17th of October 2011. The workshop was organised by Nelly Bencomo, Gordon Blair, Robert France, Betty H.C. Cheng, and Cédric Jeanneret. We present a summary of the workshop and a synopsis of the papers presented during the workshop. © 2012 Springer-Verlag Berlin Heidelberg.

Second international workshop on models@run.time

The second edition of the workshop Models@run.time was co-located with the ACM/IEEE 10th International Conference on Model Driven Engineering Languages and Systems. The workshop took place in the lively city of Nashville, USA, on the 2nd of October, 2007. The workshop was organised by Nelly Bencomo, Robert France, and Gordon Blair and was attended by at least 25 people from 7 countries. This summary gives an overview of the presentations and lively discussions that took place during the workshop. © 2008 Springer-Verlag Berlin Heidelberg.

Summary of the 5th international workshop on models@run.time

The 5th edition of the workshop Models@run.time was held at the 13th International Conference MODELS. The workshop took place in the exciting city of Oslo, Norway, on the 5th of October 2010. The workshop was organised by Nelly Bencomo, Gordon Blair, Franck Fleurey, and Cédric Jeanneret. It was attended by at least 33 people from more than 11 countries. In this summary we present a synopsis of the presentations and discussions that took place during the workshop. © 2011 Springer-Verlag Berlin Heidelberg.

4th international workshop on Models@run.time

The 4th edition of the workshop Models@run.time was held at the 12th International Conference on Model Driven Engineering Languages and Systems (MODELS). The workshop took place in the city of Denver, Colorado, USA, on the 5th of October 2009. The workshop was organised by Nelly Bencomo, Robert France, Gordon Blair, Freddy Muñoz, and Cédric Jeanneret. It was attended by at least 45 people from more than 10 countries. In this summary we present a synopsis of the presentations and discussions that took place during the 4th International Workshop on Models@run.time. © Springer-Verlag Berlin Heidelberg 2010.

Third international workshop on models@run.time

The third edition of the workshop Models@run.time was held at the ACM/IEEE 11th International Conference on Model Driven Engineering Languages and Systems (MODELS). The workshop took place in the beautiful city of Toulouse, France, on the 30th of October, 2008. The workshop was organised by Nelly Bencomo, Robert France, Gordon Blair, Freddy Muñoz, and Cèdric Jeanneret.It was attended by at least 44 people from more than 10 countries. In this summary we present an overview of the presentations and fruitful discussions that took place during the 3rd edition of the workshop Models@run.time.

Forecasting exchange rates with linear and nonlinear models

In this paper, the exchange rate forecasting performance of neural network models are evaluated against the random walk, autoregressive moving average and generalised autoregressive conditional heteroskedasticity models. There are no guidelines available that can be used to choose the parameters of neural network models and therefore, the parameters are chosen according to what the researcher considers to be the best. Such an approach, however,implies that the risk of making bad decisions is extremely high, which could explain why in many studies, neural network models do not consistently perform better than their time series counterparts. In this paper, through extensive experimentation, the level of subjectivity in building neural network models is considerably reduced and therefore giving them a better chance of Forecasting exchange rates with linear and nonlinear models 415 performing well. The results show that in general, neural network models perform better than the traditionally used time series models in forecasting exchange rates.

Forecasting exchange rates with linear and nonlinear models

In this paper the exchange rate forecasting performance of neural network models are evaluated against random walk and a range of time series models. There are no guidelines available that can be used to choose the parameters of neural network models and therefore the parameters are chosen according to what the researcher considers to be the best. Such an approach, however, implies that the risk of making bad decisions is extremely high which could explain why in many studies neural network models do not consistently perform better than their time series counterparts. In this paper through extensive experimentation the level of subjectivity in building neural network models is considerably reduced and therefore giving them a better chance of performing well. Our results show that in general neural network models perform better than traditionally used time series models in forecasting exchange rates.

Short-term electricity demand and gas price forecasts using wavelet transforms and adaptive models

This paper presents some forecasting techniques for energy demand and price prediction, one day ahead. These techniques combine wavelet transform (WT) with fixed and adaptive machine learning/time series models (multi-layer perceptron (MLP), radial basis functions, linear regression, or GARCH). To create an adaptive model, we use an extended Kalman filter or particle filter to update the parameters continuously on the test set. The adaptive GARCH model is a new contribution, broadening the applicability of GARCH methods. We empirically compared two approaches of combining the WT with prediction models: multicomponent forecasts and direct forecasts. These techniques are applied to large sets of real data (both stationary and non-stationary) from the UK energy markets, so as to provide comparative results that are statistically stronger than those previously reported. The results showed that the forecasting accuracy is significantly improved by using the WT and adaptive models. The best models on the electricity demand/gas price forecast are the adaptive MLP/GARCH with the multicomponent forecast; their MSEs are 0.02314 and 0.15384 respectively.

Self-explanation in adaptive systems based on runtime goal-based models

The behaviour of self adaptive systems can be emergent, which means that the system’s behaviour may be seen as unexpected by its customers and its developers. Therefore, a self-adaptive system needs to garner confidence in its customers and it also needs to resolve any surprise on the part of the developer during testing and maintenance. We believe that these two functions can only be achieved if a self-adaptive system is also capable of self-explanation. We argue a self-adaptive system’s behaviour needs to be explained in terms of satisfaction of its requirements. Since self-adaptive system requirements may themselves be emergent, we propose the use of goal-based requirements models at runtime to offer self-explanation of how a system is meeting its requirements. We demonstrate the analysis of run-time requirements models to yield a self-explanation codified in a domain specific language, and discuss possible future work.

Integrated manufacturing, empowerment, and company performance

There is controversy over whether integrated manufacturing (IM), comprising advanced manufacturing technology, just-in-time inventory control and total quality management, empowers or deskills shop floor work. Moreover, both IM and empowerment are promoted on the assumption that they enhance competitiveness. We examine these issues in a study of 80 manufacturing companies. The extent of use of IM was positively associated with empowerment (i.e., job enrichment and employee skill enhancement), but, with the minor exception of AMT, bore little relationship with subsequent company performance. In contrast, the extent of empowerment within companies predicted the subsequent level of company performance controlling for prior performance, with the effect on productivity mediating that on profit. Copyright © 2004 John Wiley & Sons, Ltd.

The time dimension of neural network models

This review attempts to provide an insightful perspective on the role of time within neural network models and the use of neural networks for problems involving time. The most commonly used neural network models are defined and explained giving mention to important technical issues but avoiding great detail. The relationship between recurrent and feedforward networks is emphasised, along with the distinctions in their practical and theoretical abilities. Some practical examples are discussed to illustrate the major issues concerning the application of neural networks to data with various types of temporal structure, and finally some highlights of current research on the more difficult types of problems are presented.

Analysing time series structure with hidden Markov models

This paper consides the problem of extracting the relationships between two time series in a non-linear non-stationary environment with Hidden Markov Models (HMMs). We describe an algorithm which is capable of identifying associations between variables. The method is applied both to synthetic data and real data. We show that HMMs are capable of modelling the oil drilling process and that they outperform existing methods.

Modelling financial time series with switching state space models

The deficiencies of stationary models applied to financial time series are well documented. A special form of non-stationarity, where the underlying generator switches between (approximately) stationary regimes, seems particularly appropriate for financial markets. We use a dynamic switching (modelled by a hidden Markov model) combined with a linear dynamical system in a hybrid switching state space model (SSSM) and discuss the practical details of training such models with a variational EM algorithm due to [Ghahramani and Hilton,1998]. The performance of the SSSM is evaluated on several financial data sets and it is shown to improve on a number of existing benchmark methods.