Hierarchical models for 2D presence/absence data having ambiguous zeroes: With a biogeographical case study on dingo behaviour

This dissertation is primarily an applied statistical modelling investigation, motivated by a case study comprising real data and real questions. Theoretical questions on modelling and computation of normalization constants arose from pursuit of these data analytic questions. The essence of the thesis can be described as follows. Consider binary data observed on a two-dimensional lattice. A common problem with such data is the ambiguity of zeroes recorded. These may represent zero response given some threshold (presence) or that the threshold has not been triggered (absence). Suppose that the researcher wishes to estimate the effects of covariates on the binary responses, whilst taking into account underlying spatial variation, which is itself of some interest. This situation arises in many contexts and the dingo, cypress and toad case studies described in the motivation chapter are examples of this. Two main approaches to modelling and inference are investigated in this thesis. The first is frequentist and based on generalized linear models, with spatial variation modelled by using a block structure or by smoothing the residuals spatially. The EM algorithm can be used to obtain point estimates, coupled with bootstrapping or asymptotic MLE estimates for standard errors. The second approach is Bayesian and based on a three- or four-tier hierarchical model, comprising a logistic regression with covariates for the data layer, a binary Markov Random field (MRF) for the underlying spatial process, and suitable priors for parameters in these main models. The three-parameter autologistic model is a particular MRF of interest. Markov chain Monte Carlo (MCMC) methods comprising hybrid Metropolis/Gibbs samplers is suitable for computation in this situation. Model performance can be gauged by MCMC diagnostics. Model choice can be assessed by incorporating another tier in the modelling hierarchy. This requires evaluation of a normalization constant, a notoriously difficult problem. Difficulty with estimating the normalization constant for the MRF can be overcome by using a path integral approach, although this is a highly computationally intensive method. Different methods of estimating ratios of normalization constants (N Cs) are investigated, including importance sampling Monte Carlo (ISMC), dependent Monte Carlo based on MCMC simulations (MCMC), and reverse logistic regression (RLR). I develop an idea present though not fully developed in the literature, and propose the Integrated mean canonical statistic (IMCS) method for estimating log NC ratios for binary MRFs. The IMCS method falls within the framework of the newly identified path sampling methods of Gelman & Meng (1998) and outperforms ISMC, MCMC and RLR. It also does not rely on simplifying assumptions, such as ignoring spatio-temporal dependence in the process. A thorough investigation is made of the application of IMCS to the three-parameter Autologistic model. This work introduces background computations required for the full implementation of the four-tier model in Chapter 7. Two different extensions of the three-tier model to a four-tier version are investigated. The first extension incorporates temporal dependence in the underlying spatio-temporal process. The second extensions allows the successes and failures in the data layer to depend on time. The MCMC computational method is extended to incorporate the extra layer. A major contribution of the thesis is the development of a fully Bayesian approach to inference for these hierarchical models for the first time. Note: The author of this thesis has agreed to make it open access but invites people downloading the thesis to send her an email via the 'Contact Author' function.

Statistical modeling to determine resonant frequency information present in combustion chamber pressure signals

A statistical modeling method to accurately determine combustion chamber resonance is proposed and demonstrated. This method utilises Markov-chain Monte Carlo (MCMC) through the use of the Metropolis-Hastings (MH) algorithm to yield a probability density function for the combustion chamber frequency and find the best estimate of the resonant frequency, along with uncertainty. The accurate determination of combustion chamber resonance is then used to investigate various engine phenomena, with appropriate uncertainty, for a range of engine cycles. It is shown that, when operating on various ethanol/diesel fuel combinations, a 20% substitution yields the least amount of inter-cycle variability, in relation to combustion chamber resonance.

Correlations between designability and various structural characteristics of protein lattice models

Using six kinds of lattice types (4×4 ,5×5 , and6×6 square lattices;3×3×3 cubic lattice; and2+3+4+3+2 and4+5+6+5+4 triangular lattices), three different size alphabets (HP ,HNUP , and 20 letters), and two energy functions, the designability of proteinstructures is calculated based on random samplings of structures and common biased sampling (CBS) of proteinsequence space. Then three quantities stability (average energy gap),foldability, and partnum of the structure, which are defined to elucidate the designability, are calculated. The authors find that whatever the type of lattice, alphabet size, and energy function used, there will be an emergence of highly designable (preferred) structure. For all cases considered, the local interactions reduce degeneracy and make the designability higher. The designability is sensitive to the lattice type, alphabet size, energy function, and sampling method of the sequence space. Compared with the random sampling method, both the CBS and the Metropolis Monte Carlo sampling methods make the designability higher. The correlation coefficients between the designability, stability, and foldability are mostly larger than 0.5, which demonstrate that they have strong correlation relationship. But the correlation relationship between the designability and the partnum is not so strong because the partnum is independent of the energy. The results are useful in practical use of the designability principle, such as to predict the proteintertiary structure.

A Python package for Bayesian estimation using Markov Chain Monte Carlo

Markov chain Monte Carlo (MCMC) estimation provides a solution to the complex integration problems that are faced in the Bayesian analysis of statistical problems. The implementation of MCMC algorithms is, however, code intensive and time consuming. We have developed a Python package, which is called PyMCMC, that aids in the construction of MCMC samplers and helps to substantially reduce the likelihood of coding error, as well as aid in the minimisation of repetitive code. PyMCMC contains classes for Gibbs, Metropolis Hastings, independent Metropolis Hastings, random walk Metropolis Hastings, orientational bias Monte Carlo and slice samplers as well as specific modules for common models such as a module for Bayesian regression analysis. PyMCMC is straightforward to optimise, taking advantage of the Python libraries Numpy and Scipy, as well as being readily extensible with C or Fortran.

Creative industry clusters and the ‘creative milieu’ in Shanghai.

In 2005 the Shanghai municipal government adopted the notion of ‘creative industries’ as part of their economic development strategy. At the same time, they officially recognized a number of ‘Creative Industry Clusters’ (CIC) in the city; over the next five years these official clusters grew to over ninety in number. The active promotion of CIC by the local state can thus been seen as central to its adoption of the creative industries agenda, in turn part of its aspiration to become a modern, global metropolis. In the first part of this paper we look at the emergence of the creative industry agenda in China, making some general observations about the need to place such policy transfer in its specific context. We suggest how this agenda might be understood in the national context of china’s economic and cultural policy development. In the second we give a critical account of the development of the creative industries agenda in Shanghai and its relationship to that for CIC. We argue that this agenda had more to do with real estate development than the promotion of a ‘creative milieu’ or ‘ecosystem’, and we also give some reasons as to why this was the case. In the third section we provide some new evidence to suggest the increasing disjunction between CIC and such a wider ‘creative milieu’. In the final section we suggest some new ways in which these CIC might be approached by local government in Shanghai

Knowledge based urban development in classrooms : planning Taipei's knowledge based development

Rapid urbanisation of the global population over the last two centuries has inevitably brought with it a number of challenges and opportunities for economic, environmental and social sustainability of regions. This is arguably a result of rapid globalisation and subsequent growth in knowledge and service based economic markets. This paper reviews the introduction of a specialised teaching structure where the concepts of Knowledge Based Urban Development and Knowledge Cities were taught to various students of the discipline of Urban and Regional Planning at the Queensland University of Technology, through their study tour to the city of Taipei, Taiwan. The concepts were conveyed under the name ‘Taipei Metropolis Knowledge Based Regional Planning Studio’ and its methodology reviewed a series of tasks that was considered to provide a stronger level of understanding of how Knowledge Cities and Knowledge Based Urban Development had been formed in some areas of Taiwan. Findings from this international collaborative planning studio indicate that students have gained a greater level of understanding and insight into planning systems and processes in a trans-cultural context. The students have also been exposed to ideas and knowledge that have challenged conventional perspectives and encouraged global awareness.

Creative industry clusters in Shanghai : a success story?

In 2005 the Shanghai municipal government adopted the notion of ‘creative industries’ as part of their economic development strategy. At the same time, they officially recognized a number of ‘Creative Industry Clusters’ (CIC) in the city; over the next five years these official clusters grew to over ninety in number. The active promotion of CIC by the local state can thus been seen as central to its adoption of the creative industries agenda, in turn part of its aspiration to become a modern, global metropolis. In the first part of this paper we look at the emergence of the creative industry agenda in China, making some general observations about the need to place such policy transfer in its specific context. We suggest how this agenda might be understood in the national context of China’s economic and cultural policy development. In the second we give a critical account of the development of the creative industries agenda in Shanghai and its relationship to that for CIC. We argue that this agenda had more to do with real estate development than the promotion of a ‘creative milieu’ or ‘ecosystem’, and we also give some reasons as to why this was the case. In the third section we provide some new evidence to suggest the increasing disjunction between CIC and such a wider ‘creative milieu’. In the final section we suggest some new ways in which these CIC might be approached by local government in Shanghai .

Brisbane : urban construction, suburban dreaming

Brisbane, the capital city of Queensland, has catapulted from a small, provincial town to a larger metropolis within two decades from the inception of urban renewal in 1992. Once a low-density suburban city, its inner-city and some suburban areas are now medium to high density, with the rise in apartment buildings creating new and denser modes of living. This article suggests that urbanism demands different habits of living from suburbanism and examines the relationship between the material and representational city to explore the ways in which promotions of the “new” Brisbane during its early urban renewal period reproduces the ethos of suburban living.

Land use planning for privatized airports

Problem, research strategy, and findings: The privatization of airports in Australia included airport property development rights, regulated only by federal, not local, land use control. Airports then developed commercial and retail centers outside local community plans, resulting in a history of poor coordination of planning and reflecting strong differences between public and private values in the role of the airport. Private owners embraced the concept of an Airport City, envisioning the airport as a portal of global infrastructure, whereas public planning agencies are struggling with infrastructure coordination and the development of real estate outside of the local planning regulations. Stakeholder workshops were conducted in each of the cases where key stakeholders from airports, regulating agencies, state and local governments participated in identifying key issues impacting the planning in and around airports. This research demonstrates that if modes of infrastructure provision change significantly (such as through privatization of public services), that transformation would best be accompanied by comprehensive changes in planning regimes to accommodate metropolitan and airport interdependencies. Privatization has exacerbated the poor coordination of planning in the past, and a focus on coordination between public and private infrastructure planning is needed to overcome differences in values and interests. Takeaway for practice: Governance styles differ considerably between public agencies and private corporations. Planners should understand the drivers and value differences to better coordinate infrastructure delivery and effective planning. Research support: The Airport Metropolis Research Project under the Australian Research Council's Linkage Projects funding scheme (LP0775225).

The use of CCTV to police public spaces : a case of big brother or big friend?

This paper considers the role of CCTV (closed circuit television) in the surveillance, policing and control of public space in urban and rural locations, specifically in relation to the use of public space by young people. The use of CCTV technology in public spaces is now an established and largely uncontested feature of everyday life in a number of countries and the assertion that they are essentially there for the protection of law abiding and consuming citizens has broadly gone unchallenged. With little or no debate in the U.K. to critique the claims made by the burgeoning security industry that CCTV protects people in the form of a ‘Big Friend’, the state at both central and local levels has endorsed the installation of CCTV apparatus across the nation. Some areas assert in their promotional material that the centre of the shopping and leisure zone is fully surveilled by cameras in order to reassure visitors that their personal safety is a matter of civic concern, with even small towns and villages expending monies on sophisticated and expensive to maintain camera systems. It is within a context of monitoring, recording and control procedures that young people’s use of public space is constructed as a threat to social order, in need of surveillance and exclusion which forms a major and contemporary feature in shaping thinking about urban and rural working class young people in the U.K. As Loader (1996) notes, young people’s claims on public space rarely gain legitimacy if ‘colliding’ with those of local residents, and Davis (1990) describes the increasing ‘militarization and destruction of public space’, while Jacobs (1965) asserts that full participation in the ‘daily life of urban streets’ is essential to the development of young people and beneficial for all who live in an area. This paper challenges the uncritical acceptance of widespread use of CCTV and identifies its oppressive and malevolent potential in forming a ‘surveillance gaze’ over young people (adapting Foucault’s ‘clinical gaze’c. 1973) which can jeopardise mental health and well being in coping with the ‘metropolis’, after Simmel, (1964).

Brisbane : creative city, cinema city?

Brisbane stands at the cross roads of many major economic, social and cultural opportunities as it positions itself as a cosmopolitan, globally networked metropolis of the twenty-first century. In order to link and leverage the existing screen industries infrastructure into Brisbane’s creative city’s plans, the paper argues for a re-think of the existing policy frameworks that support Australian screen culture and the national screen industries. Instead of remaining premised on a separation of these two activities the paper argues for a greater recognition of the overlaps occurring in both production and consumption of screen content. By acknowledging the impact new media technologies and social behaviours and the way they are re-shaping media consumption and media production practices, film and media policy could be better positioned to complement the emerging creative city policy frameworks that are being fostered in a city like Brisbane. The paper argues that reconsideration of the culture/industry separation that characterizes contemporary policy settings underpinning Australian media and screen production assistance would not only assist in identifying crucial synergies within a creative city policy it would also invigorate policy settings for the screen industries and enable them to connect more efficiently to a shifting film and media production and consumption landscape.

Cell migration and proliferation on homogeneous and non-homogeneous domains : modelling on the scale of individuals and populations

Cell migration is a behaviour critical to many key biological effects, including wound healing, cancerous cell invasion and morphogenesis, the development of an organism from an embryo. However, given that each of these situations is distinctly different and cells are extremely complicated biological objects, interest lies in more basic experiments which seek to remove conflating factors and present a less complex environment within which cell migration can be experimentally examined. These include in vitro studies like the scratch assay or circle migration assay, and ex vivo studies like the colonisation of the hindgut by neural crest cells. The reduced complexity of these experiments also makes them much more enticing as problems to mathematically model, like done here. The primary goal of the mathematical models used in this thesis is to shed light on which cellular behaviours work to generate the travelling waves of invasion observed in these experiments, and to explore how variations in these behaviours can potentially predict differences in this invasive pattern which are experimentally observed when cell types or chemical environment are changed. Relevant literature has already identified the difficulty of distinguishing between these behaviours when using traditional mathematical biology techniques operating on a macroscopic scale, and so here a sophisticated individual-cell-level model, an extension of the Cellular Potts Model (CPM), is been constructed and used to model a scratch assay experiment. This model includes a novel mechanism for dealing with cell proliferations that allowed for the differing properties of quiescent and proliferative cells to be implemented into their behaviour. This model is considered both for its predictive power and used to make comparisons with the travelling waves which result in more traditional macroscopic simulations. These comparisons demonstrate a surprising amount of agreement between the two modelling frameworks, and suggest further novel modifications to the CPM that would allow it to better model cell migration. Considerations of the model’s behaviour are used to argue that the dominant effect governing cell migration (random motility or signal-driven taxis) likely depends on the sort of invasion demonstrated by cells, as easily seen by microscopic photography. Additionally, a scratch assay simulated on a non-homogeneous domain consisting of a ’fast’ and ’slow’ region is also used to further differentiate between these different potential cell motility behaviours. A heterogeneous domain is a novel situation which has not been considered mathematically in this context, nor has it been constructed experimentally to the best of the candidate’s knowledge. Thus this problem serves as a thought experiment used to test the conclusions arising from the simulations on homogeneous domains, and to suggest what might be observed should this non-homogeneous assay situation be experimentally realised. Non-intuitive cell invasion patterns are predicted for diffusely-invading cells which respond to a cell-consumed signal or nutrient, contrasted with rather expected behaviour in the case of random-motility-driven invasion. The potential experimental observation of these behaviours is demonstrated by the individual-cell-level model used in this thesis, which does agree with the PDE model in predicting these unexpected invasion patterns. In the interest of examining such a case of a non-homogeneous domain experimentally, some brief suggestion is made as to how this could be achieved.

Recursive pathways to marginal likelihood estimation with prior-sensitivity analysis

We investigate the utility to computational Bayesian analyses of a particular family of recursive marginal likelihood estimators characterized by the (equivalent) algorithms known as "biased sampling" or "reverse logistic regression" in the statistics literature and "the density of states" in physics. Through a pair of numerical examples (including mixture modeling of the well-known galaxy dataset) we highlight the remarkable diversity of sampling schemes amenable to such recursive normalization, as well as the notable efficiency of the resulting pseudo-mixture distributions for gauging prior-sensitivity in the Bayesian model selection context. Our key theoretical contributions are to introduce a novel heuristic ("thermodynamic integration via importance sampling") for qualifying the role of the bridging sequence in this procedure, and to reveal various connections between these recursive estimators and the nested sampling technique.

‘Pop Melayu vs. Pop Indonesia: Marketeers, producers and new interpretations of a genre into the 2000s’ in Sonic Modernities in Southeast Asia Leiden: Brill pp. 187- 215

Kangen Band, as an example of reclaiming of the derisive term kampungan. In it, I argue that this reclaiming represents an interesting case of genre manipulation, and consider what this can reveal about how Indonesian pop genres are constituted, what they ‘are’ and what they ‘do’. In so doing, I seek to rework existing scholarship relating to Indonesian pop genres and modernity, as well as interrogate some broader theories of genre. In this essay, I extend the argument that Indonesian pop genres are not purely technical categories, they touch on myths of class and nation (Wallach 2008; Weintraub 2010; Yampolsky 1989. As we shall see, in the New Order period, pop music genres reached out to these myths by positioning themselves variously vis-à-vis the capital city, Jakarta. Such positioning, achieved through use of the terms gedongan (a term that strives to infer refinement by stressing the non-masses’ central position in the urban environment) and kampungan (a term that strives to enforce subalterns’ marginal position in relation to the metropolis, see also the previous contribution by Weintraub), continues to haunt the constitution of genre in the post-New Order period, but in novel ways. These novel ways, I argue, may be seen to result from industrial transformation and new systems of knowledge production.