Using Bayesian Mixture Models That Combine Expert Knowledge and GIS Data to Define Ecoregions

Conservation planning and management programs typically assume relatively homogeneous ecological landscapes. Such “ecoregions” serve multiple purposes: they support assessments of competing environmental values, reveal priorities for allocating scarce resources, and guide effective on-ground actions such as the acquisition of a protected area and habitat restoration. Ecoregions have evolved from a history of organism–environment interactions, and are delineated at the scale or level of detail required to support planning. Depending on the delineation method, scale, or purpose, they have been described as provinces, zones, systems, land units, classes, facets, domains, subregions, and ecological, biological, biogeographical, or environmental regions. In each case, they are essential to the development of conservation strategies and are embedded in government policies at multiple scales.

Bayesian networks for information synthesis in complex systems

This thesis introduces a method of applying Bayesian Networks to combine information from a range of data sources for effective decision support systems. It develops a set of techniques in development, validation, visualisation, and application of Complex Systems models, with a working demonstration in an Australian airport environment. The methods presented here have provided a modelling approach that produces highly flexible, informative and applicable interpretations of a system's behaviour under uncertain conditions. These end-to-end techniques are applied to the development of model based dashboards to support operators and decision makers in the multi-stakeholder airport environment. They provide highly flexible and informative interpretations and confidence in these interpretations of a system's behaviour under uncertain conditions.

Quantifying uncertainty in parameter estimates for stochastic models of collective cell spreading using approximate Bayesian computation

Wound healing and tumour growth involve collective cell spreading, which is driven by individual motility and proliferation events within a population of cells. Mathematical models are often used to interpret experimental data and to estimate the parameters so that predictions can be made. Existing methods for parameter estimation typically assume that these parameters are constants and often ignore any uncertainty in the estimated values. We use approximate Bayesian computation (ABC) to estimate the cell diffusivity, D, and the cell proliferation rate, λ, from a discrete model of collective cell spreading, and we quantify the uncertainty associated with these estimates using Bayesian inference. We use a detailed experimental data set describing the collective cell spreading of 3T3 fibroblast cells. The ABC analysis is conducted for different combinations of initial cell densities and experimental times in two separate scenarios: (i) where collective cell spreading is driven by cell motility alone, and (ii) where collective cell spreading is driven by combined cell motility and cell proliferation. We find that D can be estimated precisely, with a small coefficient of variation (CV) of 2–6%. Our results indicate that D appears to depend on the experimental time, which is a feature that has been previously overlooked. Assuming that the values of D are the same in both experimental scenarios, we use the information about D from the first experimental scenario to obtain reasonably precise estimates of λ, with a CV between 4 and 12%. Our estimates of D and λ are consistent with previously reported values; however, our method is based on a straightforward measurement of the position of the leading edge whereas previous approaches have involved expensive cell counting techniques. Additional insights gained using a fully Bayesian approach justify the computational cost, especially since it allows us to accommodate information from different experiments in a principled way.

Weather variability and influenza A (H7N9) transmission in Shanghai, China: A Bayesian spatial analysis

Abstract Background A novel avian influenza A (H7N9) virus was first found in humans in Shanghai, and infected over 433 patients in China. To date, very little is known about the spatiotemporal variability or environmental drivers of the risk of H7N9 infection. This study explored the spatial and temporal variation of H7N9 infection and assessed the effects of temperature and rainfall on H7N9 incidence. Methods A Bayesian spatial conditional autoregressive (CAR) model was used to assess the spatiotemporal distribution of the risk of H7N9 infection in Shanghai, by district and fortnight for the period 19th February–14th April 2013. Data on daily laboratory-confirmed H7N9 cases, and weather variability including temperature (°C) and rainfall (mm) were obtained from the Chinese Information System for Diseases Control and Prevention and Chinese Meteorological Data Sharing Service System, respectively, and aggregated by fortnight. Results High spatial variations in the H7N9 risk were mainly observed in the east and centre of Shanghai municipality. H7N9 incidence rate was significantly associated with fortnightly mean temperature (Relative Risk (RR): 1.54; 95% credible interval (CI): 1.22–1.94) and fortnightly mean rainfall (RR: 2.86; 95% CI: 1.47–5.56). Conclusion There was a substantial variation in the spatiotemporal distribution of H7N9 infection across different districts in Shanghai. Optimal temperature and rainfall may be one of the driving forces for H7N9.

Application of a Bayesian Network complex system model to a successful community electricity demand reduction program

Utilities worldwide are focused on supplying peak electricity demand reliably and cost effectively, requiring a thorough understanding of all the factors influencing residential electricity use at peak times. An electricity demand reduction project based on comprehensive residential consumer engagement was established within an Australian community in 2008, and by 2011, peak demand had decreased to below pre-intervention levels. This paper applied field data discovered through qualitative in-depth interviews of 22 residential households at the community to a Bayesian Network complex system model to examine whether the system model could explain successful peak demand reduction in the case study location. The knowledge and understanding acquired through insights into the major influential factors and the potential impact of changes to these factors on peak demand would underpin demand reduction intervention strategies for a wider target group.

Inferring lung cancer risk factor patterns through joint Bayesian spatio-temporal analysis

Background: Preventing risk factor exposure is vital to reduce the high burden from lung cancer. The leading risk factor for developing lung cancer is tobacco smoking. In Australia, despite apparent success in reducing smoking prevalence, there is limited information on small area patterns and small area temporal trends. We sought to estimate spatio-temporal patterns for lung cancer risk factors using routinely collected population-based cancer data. Methods: The analysis used a Bayesian shared component spatio-temporal model, with male and female lung cancer included separately. The shared component reflected exposure to lung cancer risk factors, and was modelled over 477 statistical local areas (SLAs) and 15 years in Queensland, Australia. Analyses were also run adjusting for area-level socioeconomic disadvantage, Indigenous population composition, or remoteness. Results: Strong spatial patterns were observed in the underlying risk factor exposure for both males (median Relative Risk (RR) across SLAs compared to the Queensland average ranged from 0.48-2.00) and females (median RR range across SLAs 0.53-1.80), with high exposure observed in many remote areas. Strong temporal trends were also observed. Males showed a decrease in the underlying risk across time, while females showed an increase followed by a decrease in the final two years. These patterns were largely consistent across each SLA. The high underlying risk estimates observed among disadvantaged, remote and indigenous areas decreased after adjustment, particularly among females. Conclusion: The modelled underlying exposure appeared to reflect previous smoking prevalence, with a lag period of around 30 years, consistent with the time taken to develop lung cancer. The consistent temporal trends in lung cancer risk factors across small areas support the hypothesis that past interventions have been equally effective across the state. However, this also means that spatial inequalities have remained unaddressed, highlighting the potential for future interventions, particularly among remote areas.

Socio-environmental drivers and suicide in Australia: Bayesian spatial analysis

Background The impact of socio-environmental factors on suicide has been examined in many studies. Few of them, however, have explored these associations from a spatial perspective, especially in assessing the association between meteorological factors and suicide. This study examined the association of meteorological and socio-demographic factors with suicide across small areas over different time periods. Methods Suicide, population and socio-demographic data (e.g., population of Aboriginal and Torres Strait Islanders (ATSI), and unemployment rate (UNE) at the Local Government Area (LGA) level were obtained from the Australian Bureau of Statistics for the period of 1986 to 2005. Information on meteorological factors (rainfall, temperature and humidity) was supplied by Australian Bureau of Meteorology. A Bayesian Conditional Autoregressive (CAR) Model was applied to explore the association of socio-demographic and meteorological factors with suicide across LGAs. Results In Model I (socio-demographic factors), proportion of ATSI and UNE were positively associated with suicide from 1996 to 2000 (Relative Risk (RR)ATSI = 1.0107, 95% Credible Interval (CI): 1.0062-1.0151; RRUNE = 1.0187, 95% CI: 1.0060-1.0315), and from 2001 to 2005 (RRATSI = 1.0126, 95% CI: 1.0076-1.0176; RRUNE = 1.0198, 95% CI: 1.0041-1.0354). Socio-Economic Index for Area (SEIFA) and IND, however, had negative associations with suicide between 1986 and 1990 (RRSEIFA = 0.9983, 95% CI: 0.9971-0.9995; RRATSI = 0.9914, 95% CI: 0.9848-0.9980). Model II (meteorological factors): a 1°C higher yearly mean temperature across LGAs increased the suicide rate by an average by 2.27% (95% CI: 0.73%, 3.82%) in 1996–2000, and 3.24% (95% CI: 1.26%, 5.21%) in 2001–2005. The associations between socio-demographic factors and suicide in Model III (socio-demographic and meteorological factors) were similar to those in Model I; but, there is no substantive association between climate and suicide in Model III. Conclusions Proportion of Aboriginal and Torres Strait Islanders, unemployment and temperature appeared to be statistically associated with of suicide incidence across LGAs among all selected variables, especially in recent years. The results indicated that socio-demographic factors played more important roles than meteorological factors in the spatial pattern of suicide incidence.

Alive SMC^2: Bayesian model selection for low-count time series models with intractable likelihoods

In this paper we present a new method for performing Bayesian parameter inference and model choice for low count time series models with intractable likelihoods. The method involves incorporating an alive particle filter within a sequential Monte Carlo (SMC) algorithm to create a novel pseudo-marginal algorithm, which we refer to as alive SMC^2. The advantages of this approach over competing approaches is that it is naturally adaptive, it does not involve between-model proposals required in reversible jump Markov chain Monte Carlo and does not rely on potentially rough approximations. The algorithm is demonstrated on Markov process and integer autoregressive moving average models applied to real biological datasets of hospital-acquired pathogen incidence, animal health time series and the cumulative number of poison disease cases in mule deer.

Melanoma cell colony expansion parameters revealed by approximate Bayesian computation

In vitro studies and mathematical models are now being widely used to study the underlying mechanisms driving the expansion of cell colonies. This can improve our understanding of cancer formation and progression. Although much progress has been made in terms of developing and analysing mathematical models, far less progress has been made in terms of understanding how to estimate model parameters using experimental in vitro image-based data. To address this issue, a new approximate Bayesian computation (ABC) algorithm is proposed to estimate key parameters governing the expansion of melanoma cell (MM127) colonies, including cell diffusivity, D, cell proliferation rate, λ, and cell-to-cell adhesion, q, in two experimental scenarios, namely with and without a chemical treatment to suppress cell proliferation. Even when little prior biological knowledge about the parameters is assumed, all parameters are precisely inferred with a small posterior coefficient of variation, approximately 2–12%. The ABC analyses reveal that the posterior distributions of D and q depend on the experimental elapsed time, whereas the posterior distribution of λ does not. The posterior mean values of D and q are in the ranges 226–268 µm2h−1, 311–351 µm2h−1 and 0.23–0.39, 0.32–0.61 for the experimental periods of 0–24 h and 24–48 h, respectively. Furthermore, we found that the posterior distribution of q also depends on the initial cell density, whereas the posterior distributions of D and λ do not. The ABC approach also enables information from the two experiments to be combined, resulting in greater precision for all estimates of D and λ.

Prior and posterior linear pooling for combining expert opinions: Uses and impact on Bayesian Networks

The use of expert knowledge to quantify a Bayesian Network (BN) is necessary when data is not available. This however raises questions regarding how opinions from multiple experts can be used in a BN. Linear pooling is a popular method for combining probability assessments from multiple experts. In particular, Prior Linear Pooling (PrLP), which pools opinions then places them into the BN is a common method. This paper firstly proposes an alternative pooling method, Posterior Linear Pooling (PoLP). This method constructs a BN for each expert, then pools the resulting probabilities at the nodes of interest. Secondly, it investigates the advantages and disadvantages of using these pooling methods to combine the opinions of multiple experts. Finally, the methods are applied to an existing BN, the Wayfinding Bayesian Network Model, to investigate the behaviour of different groups of people and how these different methods may be able to capture such differences. The paper focusses on 6 nodes Human Factors, Environmental Factors, Wayfinding, Communication, Visual Elements of Communication and Navigation Pathway, and three subgroups Gender (female, male),Travel Experience (experienced, inexperienced), and Travel Purpose (business, personal) and finds that different behaviors can indeed be captured by the different methods.