Variational mean-field algorithm for efficient inference in large systems of stochastic differential equations

This work introduces a Gaussian variational mean-field approximation for inference in dynamical systems which can be modeled by ordinary stochastic differential equations. This new approach allows one to express the variational free energy as a functional of the marginal moments of the approximating Gaussian process. A restriction of the moment equations to piecewise polynomial functions, over time, dramatically reduces the complexity of approximate inference for stochastic differential equation models and makes it comparable to that of discrete time hidden Markov models. The algorithm is demonstrated on state and parameter estimation for nonlinear problems with up to 1000 dimensional state vectors and compares the results empirically with various well-known inference methodologies.

Probabilistic DHP adaptive critic for nonlinear stochastic control systems

Following the recently developed algorithms for fully probabilistic control design for general dynamic stochastic systems (Herzallah & Káarnáy, 2011; Kárný, 1996), this paper presents the solution to the probabilistic dual heuristic programming (DHP) adaptive critic method (Herzallah & Káarnáy, 2011) and randomized control algorithm for stochastic nonlinear dynamical systems. The purpose of the randomized control input design is to make the joint probability density function of the closed loop system as close as possible to a predetermined ideal joint probability density function. This paper completes the previous work (Herzallah & Kárnáy, 2011; Kárný, 1996) by formulating and solving the fully probabilistic control design problem on the more general case of nonlinear stochastic discrete time systems. A simulated example is used to demonstrate the use of the algorithm and encouraging results have been obtained.

Using observation ageing to improve Markovian model learning in QoS engineering

Markovian models are widely used to analyse quality-of-service properties of both system designs and deployed systems. Thanks to the emergence of probabilistic model checkers, this analysis can be performed with high accuracy. However, its usefulness is heavily dependent on how well the model captures the actual behaviour of the analysed system. Our work addresses this problem for a class of Markovian models termed discrete-time Markov chains (DTMCs). We propose a new Bayesian technique for learning the state transition probabilities of DTMCs based on observations of the modelled system. Unlike existing approaches, our technique weighs observations based on their age, to account for the fact that older observations are less relevant than more recent ones. A case study from the area of bioinformatics workflows demonstrates the effectiveness of the technique in scenarios where the model parameters change over time.

Transition from time-continuous systems to discrete mappings

Detailed transport studies in plasmas require the solution of the time evolution of many different initial positions of test particles in the phase space of the systems to be investigated. To reduce this amount of numerical work, one would like to replace the integration of the time-continues system with a mapping.

GTM through time

The standard GTM (generative topographic mapping) algorithm assumes that the data on which it is trained consists of independent, identically distributed (iid) vectors. For time series, however, the iid assumption is a poor approximation. In this paper we show how the GTM algorithm can be extended to model time series by incorporating it as the emission density in a hidden Markov model. Since GTM has discrete hidden states we are able to find a tractable EM algorithm, based on the forward-backward algorithm, to train the model. We illustrate the performance of GTM through time using flight recorder data from a helicopter.

Lessons learned from INTAMAP, an interoperable web service for the real-time interpolation of environmental variables

Interpolated data are an important part of the environmental information exchange as many variables can only be measured at situate discrete sampling locations. Spatial interpolation is a complex operation that has traditionally required expert treatment, making automation a serious challenge. This paper presents a few lessons learnt from INTAMAP, a project that is developing an interoperable web processing service (WPS) for the automatic interpolation of environmental data using advanced geostatistics, adopting a Service Oriented Architecture (SOA). The “rainbow box” approach we followed provides access to the functionality at a whole range of different levels. We show here how the integration of open standards, open source and powerful statistical processing capabilities allows us to automate a complex process while offering users a level of access and control that best suits their requirements. This facilitates benchmarking exercises as well as the regular reporting of environmental information without requiring remote users to have specialized skills in geostatistics.

Steps and bumps:precision extraction of discrete states of molecular machines

We report statistical time-series analysis tools providing improvements in the rapid, precision extraction of discrete state dynamics from time traces of experimental observations of molecular machines. By building physical knowledge and statistical innovations into analysis tools, we provide techniques for estimating discrete state transitions buried in highly correlated molecular noise. We demonstrate the effectiveness of our approach on simulated and real examples of steplike rotation of the bacterial flagellar motor and the F1-ATPase enzyme. We show that our method can clearly identify molecular steps, periodicities and cascaded processes that are too weak for existing algorithms to detect, and can do so much faster than existing algorithms. Our techniques represent a step in the direction toward automated analysis of high-sample-rate, molecular-machine dynamics. Modular, open-source software that implements these techniques is provided.

A hierarchy of phase transitions in optimal neuronal coding:from binary to M-ary discrete optimal codes

We have investigated how optimal coding for neural systems changes with the time available for decoding. Optimization was in terms of maximizing information transmission. We have estimated the parameters for Poisson neurons that optimize Shannon transinformation with the assumption of rate coding. We observed a hierarchy of phase transitions from binary coding, for small decoding times, toward discrete (M-ary) coding with two, three and more quantization levels for larger decoding times. We postulate that the presence of subpopulations with specific neural characteristics could be a signiture of an optimal population coding scheme and we use the mammalian auditory system as an example.

Encouraging the intellectual craft of living research:tattoos, theory and time

This chapter contributes to the anthology on learning to research - researching to learn because it emphases a need to design curricula that enables living research, and on-going researcher development, rather than one that restricts student and staff activities, within a marketised approach towards time. In recent decades higher education (HE) has come to be valued for its contribution to the global economy. Referred to as the neo-liberal university, a strong prioritisation has been placed on meeting the needs of industry by providing a better workforce. This perspective emphasises the role of a degree in HE to secure future material affluence, rather than to study as an on-going investment in the self (Molesworth , Nixon & Scullion, 2009: 280). Students are treated primarily as consumers in this model, where through their tuition fees they purchase a product, rather than benefit from the transformative potential university education offers for the whole of life.Given that HE is now measured by the numbers of students it attracts, and later places into well-paid jobs, there is an intense pressure on time, which has led to a method where the learning experiences of students are broken down into discrete modules. Whilst this provides consistency, students can come to view research processes in a fragmented way within the modular system. Topics are presented chronologically, week-by-week and students simply complete a set of tasks to ‘have a degree’, rather than to ‘be learners’ (Molesworth , Nixon & Scullion, 2009: 277) who are living their research, in relation to their own past, present and future. The idea of living research in this context is my own adaptation of an approach suggested by C. Wright Mills (1959) in The Sociological Imagination. Mills advises that successful scholars do not split their work from the rest of their lives, but treat scholarship as a choice of how to live, as well as a choice of career. The marketised slant in HE thus creates a tension firstly, for students who are learning to research. Mills would encourage them to be creative, not instrumental, in their use of time, yet they are journeying through a system that is structured for a swift progression towards a high paid job, rather than crafted for reflexive inquiry, that transforms their understanding throughout life. Many universities are placing a strong focus on discrete skills for student employability, but I suggest that embedding the transformative skills emphasised by Mills empowers students and builds their confidence to help them make connections that aid their employability. Secondly, the marketised approach creates a problem for staff designing the curriculum, if students do not easily make links across time over their years of study and whole programmes. By researching to learn, staff can discover new methods to apply in their design of the curriculum, to help students make important and creative connections across their programmes of study.

Implementing an agent-based model with a spatial visual display in discrete-event simulation software

There has been an increasing interest in the use of agent-based simulation and some discussion of the relative merits of this approach as compared to discrete-event simulation. There are differing views on whether an agent-based simulation offers capabilities that discrete-event cannot provide or whether all agent-based applications can at least in theory be undertaken using a discrete-event approach. This paper presents a simple agent-based NetLogo model and corresponding discrete-event versions implemented in the widely used ARENA software. The two versions of the discrete-event model presented use a traditional process flow approach normally adopted in discrete-event simulation software and also an agent-based approach to the model build. In addition a real-time spatial visual display facility is provided using a spreadsheet platform controlled by VBA code embedded within the ARENA model. Initial findings from this investigation are that discrete-event simulation can indeed be used to implement agent-based models and with suitable integration elements such as VBA provide the spatial displays associated with agent-based software.

Engineering education research - the UK perspective at a time of change

Engineering education in the United Kingdom is at the point of embarking upon an interesting journey into uncharted waters. At no point in the past have there been so many drivers for change and so many opportunities for the development of engineering pedagogy. This paper will look at how Engineering Education Research (EER) has developed within the UK and what differentiates it from the many small scale practitioner interventions, perhaps without a clear research question or with little evaluation, which are presented at numerous staff development sessions, workshops and conferences. From this position some examples of current projects will be described, outcomes of funding opportunities will be summarised and the benefits of collaboration with other disciplines illustrated. In this study, I will account for how the design of task structure according to variation theory, as well as the probe-ware technology, make the laws of force and motion visible and learnable and, especially, in the lab studied make Newton's third law visible and learnable. I will also, as a comparison, include data from a mechanics lab that use the same probe-ware technology and deal with the same topics in mechanics, but uses a differently designed task structure. I will argue that the lower achievements on the FMCE-test in this latter case can be attributed to these differences in task structure in the lab instructions. According to my analysis, the necessary pattern of variation is not included in the design. I will also present a microanalysis of 15 hours collected from engineering students' activities in a lab about impulse and collisions based on video recordings of student's activities in a lab about impulse and collisions. The important object of learning in this lab is the development of an understanding of Newton's third law. The approach analysing students interaction using video data is inspired by ethnomethodology and conversation analysis, i.e. I will focus on students practical, contingent and embodied inquiry in the setting of the lab. I argue that my result corroborates variation theory and show this theory can be used as a 'tool' for designing labs as well as for analysing labs and lab instructions. Thus my results have implications outside the domain of this study and have implications for understanding critical features for student learning in labs. Engineering higher education is well used to change. As technology develops the abilities expected by employers of graduates expand, yet our understanding of how to make informed decisions about learning and teaching strategies does not without a conscious effort to do so. With the numerous demands of academic life, we often fail to acknowledge our incomplete understanding of how our students learn within our discipline. The journey facing engineering education in the UK is being driven by two classes of driver. Firstly there are those which we have been working to expand our understanding of, such as retention and employability, and secondly the new challenges such as substantial changes to funding systems allied with an increase in student expectations. Only through continued research can priorities be identified, addressed and a coherent and strong voice for informed change be heard within the wider engineering education community. This new position makes it even more important that through EER we acquire the knowledge and understanding needed to make informed decisions regarding approaches to teaching, curriculum design and measures to promote effective student learning. This then raises the question 'how does EER function within a diverse academic community?' Within an existing community of academics interested in taking meaningful steps towards understanding the ongoing challenges of engineering education a Special Interest Group (SIG) has formed in the UK. The formation of this group has itself been part of the rapidly changing environment through its facilitation by the Higher Education Academy's Engineering Subject Centre, an entity which through the Academy's current restructuring will no longer exist as a discrete Centre dedicated to supporting engineering academics. The aims of this group, the activities it is currently undertaking and how it expects to network and collaborate with the global EER community will be reported in this paper. This will include explanation of how the group has identified barriers to the progress of EER and how it is seeking, through a series of activities, to facilitate recognition and growth of EER both within the UK and with our valued international colleagues.

Strongly localized moving discrete dissipative breather-solitons in Kerr nonlinear media supported by intrinsic gain

We investigate the mobility of nonlinear localized modes in a generalized discrete Ginzburg-Landau-type model, describing a one-dimensional waveguide array in an active Kerr medium with intrinsic, saturable gain and damping. It is shown that exponentially localized, traveling discrete dissipative breather-solitons may exist as stable attractors supported only by intrinsic properties of the medium, i.e., in the absence of any external field or symmetry-breaking perturbations. Through an interplay by the gain and damping effects, the moving soliton may overcome the Peierls-Nabarro barrier, present in the corresponding conservative system, by self-induced time-periodic oscillations of its power (norm) and energy (Hamiltonian), yielding exponential decays to zero with different rates in the forward and backward directions. In certain parameter windows, bistability appears between fast modes with small oscillations and slower, large-oscillation modes. The velocities and the oscillation periods are typically related by lattice commensurability and exhibit period-doubling bifurcations to chaotically "walking" modes under parameter variations. If the model is augmented by intersite Kerr nonlinearity, thereby reducing the Peierls-Nabarro barrier of the conservative system, the existence regime for moving solitons increases considerably, and a richer scenario appears including Hopf bifurcations to incommensurately moving solutions and phase-locking intervals. Stable moving breathers also survive in the presence of weak disorder. © 2014 American Physical Society.