Accelerating Pseudo-Marginal MCMC using Gaussian Processes

Pseudo-marginal methods such as the grouped independence Metropolis-Hastings (GIMH) and Markov chain within Metropolis (MCWM) algorithms have been introduced in the literature as an approach to perform Bayesian inference in latent variable models. These methods replace intractable likelihood calculations with unbiased estimates within Markov chain Monte Carlo algorithms. The GIMH method has the posterior of interest as its limiting distribution, but suffers from poor mixing if it is too computationally intensive to obtain high-precision likelihood estimates. The MCWM algorithm has better mixing properties, but less theoretical support. In this paper we propose to use Gaussian processes (GP) to accelerate the GIMH method, whilst using a short pilot run of MCWM to train the GP. Our new method, GP-GIMH, is illustrated on simulated data from a stochastic volatility and a gene network model.

Future learning landscapes for architectural education: Linking space, place, pedagogy, technology + context

Diversification and expansion of global higher education in the 21st century, has resulted in Learning Landscapes for architectural education that can no longer be sustained by the traditional model. Changes have resulted because of surging student numbers, extensions to traditional curricula, evolving competency standards and accreditation requirements, and modified geographical and pedagogical boundaries. The influx of available new technology has helped to democratise knowledge, transforming when, where and how learning takes place. Pressures on government funded higher education budgets highlight the need for a critical review of the current approach to the design and use of learning environments. Efficient design of physical space contributes significantly to savings in provision, management and use of facilities, while also potentially improving pedagogical quality. The purpose of this research is to identify emerging trends in the design of future Learning Landscapes for architectural education in Australasia; to understand where and how students of architecture are likely to learn, in the future context. It explores the important linkages between space, place, pedagogy, technology and context, using a multi methodological qualitative research approach. An Australasian context study will explore the Learning Landscapes of 23 Schools of Architecture across Australia, New Zealand and Papua New Guinea. The focus of this paper is on the methodology which is being employed to undertake dynamic data collection for the study. The research will be determined through mapping all forms of architectural learning environments, pedagogical approaches and contextual issues, to bridge the gap between academic theory, and architectural design practice. An initial understanding that pedagogy is an intrinsic component imbedded within the design of learning environments, will play an important role. Active learning environments which are exemplified by the architectural design studio, support dynamic project based and collaborative connected learning models. These have recently become a lot more common in disciplines outside of design and the arts. It is anticipated, therefore, that the implications for this research may well have a positive impact far beyond the confines of the architectural studio learning environment.

On the order of the fractional Laplacian in determining the spatio-temporal evolution of a space-fractional model of cardiac electrophysiology

Space-fractional operators have been used with success in a variety of practical applications to describe transport processes in media characterised by spatial connectivity properties and high structural heterogeneity altering the classical laws of diffusion. This study provides a systematic investigation of the spatio-temporal effects of a space-fractional model in cardiac electrophysiology. We consider a simplified model of electrical pulse propagation through cardiac tissue, namely the monodomain formulation of the Beeler-Reuter cell model on insulated tissue fibres, and obtain a space-fractional modification of the model by using the spectral definition of the one-dimensional continuous fractional Laplacian. The spectral decomposition of the fractional operator allows us to develop an efficient numerical method for the space-fractional problem. Particular attention is paid to the role played by the fractional operator in determining the solution behaviour and to the identification of crucial differences between the non-fractional and the fractional cases. We find a positive linear dependence of the depolarization peak height and a power law decay of notch and dome peak amplitudes for decreasing orders of the fractional operator. Furthermore, we establish a quadratic relationship in conduction velocity, and quantify the increasingly wider action potential foot and more pronounced dispersion of action potential duration, as the fractional order is decreased. A discussion of the physiological interpretation of the presented findings is made.

Connecting the space between design and research: Explorations in participatory research supervision

In this article we offer a single case study using an action research method for gathering and analysing data offering insights valuable to both design and research supervision practice. We do not attempt to generalise from this single case, but offer it as an instance that can improve our understanding of research supervision practice. We question the conventional ‘dyadic’ models of research supervision and outline a more collaborative model, based on the signature pedagogy of architecture: the design studio. A novel approach to the supervision of creatively oriented post-graduate students is proposed, including new approaches to design methods and participatory supervision that draw on established design studio practices. This model collapses the distance between design and research activities. Our case study involving Research Masters student supervision in the discipline of Architecture, shows how ‘connected learning’ emerges from this approach. This type of learning builds strong elements of creativity and fun, which promote and enhance student engagement. The results of our action research suggests that students learn to research more easily in such an environment and supervisory practices are enhanced when we apply the techniques and characteristics of design studio pedagogy to the more conventional research pedagogies imported from the humanities. We believe that other creative disciplines can apply similar tactics to enrich both the creative practice of research and the supervision of HDR students.

Exact calculations of survival probability for diffusion on growing lines, disks, and spheres: The role of dimension

Unlike standard applications of transport theory, the transport of molecules and cells during embryonic development often takes place within growing multidimensional tissues. In this work, we consider a model of diffusion on uniformly growing lines, disks, and spheres. An exact solution of the partial differential equation governing the diffusion of a population of individuals on the growing domain is derived. Using this solution, we study the survival probability, S(t). For the standard nongrowing case with an absorbing boundary, we observe that S(t) decays to zero in the long time limit. In contrast, when the domain grows linearly or exponentially with time, we show that S(t) decays to a constant, positive value, indicating that a proportion of the diffusing substance remains on the growing domain indefinitely. Comparing S(t) for diffusion on lines, disks, and spheres indicates that there are minimal differences in S(t) in the limit of zero growth and minimal differences in S(t) in the limit of fast growth. In contrast, for intermediate growth rates, we observe modest differences in S(t) between different geometries. These differences can be quantified by evaluating the exact expressions derived and presented here.

Lost in space: The place of the architectural milieu in the aetiology and treatment of schizophrenia

Purpose – Psychological and epidemiological literature suggests that the built environment plays both causal and therapeutic roles in schizophrenia, but what are the implications for designers? The purpose of this paper is to focus on the role the built environment plays in psycho‐environmental dynamics, in order that negative effects can be avoided and beneficial effects emphasised in architectural design. Design/methodology/approach – The approach taken is a translational exploration of the dynamics between the built environment and psychotic illness, using primary research from disciplines as diverse as epidemiology, neurology and psychology. Findings – The built environment is conceived as being both an agonist and as an antagonist for the underlying processes that present as psychosis. The built environment is implicated through several means, through the opportunities it provides. These may be physical, narrative, emotional, hedonic or personal. Some opportunities may be negative, and others positive. The built environment is also an important source of unexpected aesthetic stimulation, yet in psychotic illnesses, aesthetic sensibilities characteristically suffer from deterioration. Research limitations/implications – The findings presented are based on research that is largely translated from very different fields of enquiry. Whilst findings are cogent and logical, much of the support is correlational rather than empirical. Social implications – The WHO claims that schizophrenia destroys 24 million lives worldwide, with an exponential effect on human and financial capital. Because evidence implicates the built environment, architectural and urban designers may have a role to play in reducing the human costs wrought by the illness. Originality/value – Never before has architecture been so explicitly implicated as a cause of mental illness. This paper was presented to the Symposium of Mental Health Facility Design, and is essential reading for anyone involved in designing for improved mental health.

Reflective perspectives: Negotiations at and within the borders of cultural difference: A post-qualitative inquiry of cultural hybridity within third space enunciations

This research explores the in-between space of intercultural collaboration between Aboriginal and Torres Strait Islander peoples and non-Indigenous peoples in Australia. Using critical and third space theories and a post-qualitative inquiry, I examine negotiations of cultural difference through articulated moments of intercultural collaboration in order to inform intercultural pedagogical practices. This research also explores how ideology, imbued through discourse, has the power to enforce or challenge cultural and social domination. This in turn creates cultural hegemony, a process whereby a particular social and cultural group has the power to influence the thoughts, expectations and behaviours of a particular society.

Calculations of helium separation via uniform pores of stanene-based membranes

The development of low energy cost membranes to separate He from noble gas mixtures is highly desired. In this work, we studied He purification using recently experimentally realized, two-dimensional stanene (2D Sn) and decorated 2D Sn (SnH and SnF) honeycomb lattices by density functional theory calculations. To increase the permeability of noble gases through pristine 2D Sn at room temperature (298 K), two practical strategies (i.e., the application of strain and functionalization) are proposed. With their high concentration of large pores, 2D Sn-based membrane materials demonstrate excellent helium purification and can serve as a superior membrane over traditionally used, porous materials. In addition, the separation performance of these 2D Sn-based membrane materials can be significantly tuned by application of strain to optimize the He purification properties by taking both diffusion and selectivity into account. Our results are the first calculations of He separation in a defect-free honeycomb lattice, highlighting new interesting materials for helium separation for future experimental validation.

Meaning of public space and sense of community: The case of new neighbourhoods in the Kathmandu Valley

This paper examines the meaning of public space and sense of community among neighbourhood residents in the changing urban context of the Kathmandu Valley in Nepal. Two new neighbourhoods were selected for the purpose of this study with data collected from interviews with the residents. The study has found that most residents of the new neighbourhoods have an understanding of the significance of public space in community life. However, such understandings are based less on the actual use of public space. The existing public spaces in these neighbourhoods are less successful in offering a meaning to the residents, due to their poor development and the lack of active use. Despite these changes, some residents believe they have developed a sense of community, which is an outcome of other individual factors than the use of public space. It is argued that the role of contemporary neighbourhood public space in fostering a sense of community appears to be less significant in the valley’s present context.

Samoa’s education policy: Negotiating a hybrid space for values

This paper analyses the education policy of Samoa to examine the values that are presented within as relevant to the education system. Drawing on the theory of postcolonialism and globalization, we illustrate how the global and local interact within the education policy to create a hybrid, heterogeneous mix of values and, while the policy acknowledges the significance of Samoan values, it is principally directed towards universal values being incorporated into the education system. We undertake a critical policy analysis to illustrate how the hybrid set of values are indicative of a neo-colonial discourse and argue that universal values are required, however, these need to be equally matched with local Samoan values for the education policy to be highly relevant, authentic and applicable to the Samoan education context.

Effective earth and space science analogies

There are several good reasons why Earth and Space Science should be a part of any science curriculum. Nearly everything we do each day is connected in some way to the Earth: to its land, oceans, atmosphere, plants and animals. By 2025, eight billion people will live on Earth. If we are to continue extracting resources to maintain a high quality of life, then it is important that our children are scientifically literate in a way that allows them to exploit the Earth’s resources in a sustainable way. People who understand how earth systems work can make informed decisions and may be able to help resolve issues surrounding clean water, urban planning and development, global climate change and the use and management of natural resources.

Find my office: Navigating real space from semantic descriptions

This paper shows that by using only symbolic language phrases, a mobile robot can purposefully navigate to specified rooms in previously unexplored environments. The robot intelligently organises a symbolic language description of the unseen environment and “imagines” a representative map, called the abstract map. The abstract map is an internal representation of the topological structure and spatial layout of symbolically defined locations. To perform goal-directed exploration, the abstract map creates a high-level semantic plan to reason about spaces beyond the robot’s known world. While completing the plan, the robot uses the metric guidance provided by a spatial layout, and grounded observations of door labels, to efficiently guide its navigation. The system is shown to complete exploration in unexplored spaces by travelling only 13.3% further than the optimal path.

Free energy calculations of glycosaminoglycan - Protein interactions

Glycosaminoglycans (GAGs) are complex highly charged linear polysaccharides that have a variety of roles in biological processes. We report the first use of molecular dynamics (MD) free energy calculations using the MM/PBSA method to investigate the binding of GAGs to protein molecules, namely the platelet endothelial cell adhesion molecule 1 (PECAM-1) and annexin A2. Calculations of the free energy of the binding of heparin fragments of different sizes reveal the existence of a region of low GAG-binding affinity in domains 5-6 of PECAM-1 and a region of high affinity in domains 2-3, consistent with experimental data and ligand-protein docking studies. A conformational hinge movement between domains 2 and 3 was observed, which allows the binding of heparin fragments of increasing size (pentasaccharides to octasaccharides) with an increasingly higher binding affinity. Similar simulations of the binding of a heparin fragment to annexin A2 reveal the optimization of electrostatic and hydrogen bonding interactions with the protein and protein-bound calcium ions. In general, these free energy calculations reveal that the binding of heparin to protein surfaces is dominated by strong electrostatic interactions for longer fragments, with equally important contributions from van der Waals interactions and vibrational entropy changes, against a large unfavorable desolvation penalty due to the high charge density of these molecules.

Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein

The c-Fos–c-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c-Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions.