Search

The use of in-situ digital sensors for water quality monitoring is becoming increasingly common worldwide. While these sensors provide near real-time data for science, the data are prone to technical anomalies that can undermine the trustworthiness of the data and the accuracy of statistical inferences, particularly in spatial and temporal analyses. Here we propose a framework for detecting anomalies in sensor data recorded in stream networks, which takes advantage of spatial and temporal autocorrelation to improve detection rates. The proposed framework involves the implementation of effective data imputation to handle missing data, alignment of time-series to address temporal disparities, and the identification of water quality events. We explore the effectiveness of a suite of state-of-the-art statistical methods including posterior predictive distributions, finite mixtures, and Hidden Markov Models (HMM). We showcase the practical implementation of automated anomaly detection in near-real time by employing a Bayesian recursive approach. This demonstration is conducted through a comprehensive simulation study and a practical application to a substantive case study situated in the Herbert River, located in Queensland, Australia, which flows into the Great Barrier Reef. We found that methods such as posterior predictive distributions and HMM produce the best performance in detecting multiple types of anomalies. Utilizing data from multiple sensors deployed relatively near one another enhances the ability to distinguish between water quality events and technical anomalies, thereby significantly improving the accuracy of anomaly detection. Thus, uncertainty and biases in water quality reporting, interpretation, and modelling are reduced, and the effectiveness of subsequent management actions improved.

Monitoring of conflict risk in the humanitarian sector is largely based on simple historic averages. To advance our understanding, we propose Hawkes processes, a self-exciting stochastic process used to describe phenomena whereby past events increase the probability of future events occurring. The overarching goal of this work is to assess the potential for using a more statistically rigorous approach to monitor the risk of political violence and conflict events in practice and characterise their temporal and spatial patterns. The region of South Asia was selected as an exemplar of how our model can be applied globally. We individually analyse the various types of conflict events for the countries in this region and compare the results. A Bayesian, spatiotemporal variant of the Hawkes process is fitted to data gathered by the Armed Conflict Location and Event Data (ACLED) project to obtain sub-national estimates of conflict risk over time and space. Our model can effectively estimate the risk level of these events within a statistically sound framework, with a more precise understanding of the uncertainty around these estimates than was previously possible. This work enables a better understanding of conflict events which can inform preventative measures. We demonstrate the advantages of the Bayesian framework by comparing our results to maximum likelihood estimation. While maximum likelihood gives reasonable point estimates, the Bayesian approach is preferred when possible. Practical examples are presented to demonstrate how the proposed model can be used to monitor conflict risk. Comparing to current practices that rely on historical averages, we also show that our model is more stable and robust to outliers. In this work we aim to support actors in the humanitarian sector in making data-informed decisions, such as the allocation of resources in conflict-prone regions.

Coral reefs are increasingly subjected to major disturbances threatening the health of marine ecosystems. Substantial research underway to develop intervention strategies that assist reefs in recovery from, and resistance to, inevitable future climate and weather extremes. To assess potential benefits of interventions, mechanistic understanding of coral reef recovery and resistance patterns is essential. Recent evidence suggests that more than half of the reefs surveyed across the Great Barrier Reef (GBR) exhibit deviations from standard recovery modelling assumptions when the initial coral cover is low ($\leq 10$\%). New modelling is necessary to account for these observed patterns to better inform management strategies. We consider a new model for reef recovery at the coral cover scale that accounts for biphasic recovery patterns. The model is based on a multispecies Richards' growth model that includes a change point in the recovery patterns. Bayesian inference is applied for uncertainty quantification of key parameters for assessing reef health and recovery patterns. This analysis is applied to benthic survey data from the Australian Institute of Marine Sciences (AIMS). We demonstrate agreement between model predictions and data across every recorded recovery trajectory with at least two years of observations following disturbance events occurring between 1992--2020. This new approach will enable new insights into the biological, ecological and environmental factors that contribute to the duration and severity of biphasic coral recovery patterns across the GBR. These new insights will help to inform managements and monitoring practice to mitigate the impacts of climate change on coral reefs.

Federated learning (FL) allows for collaborative model training across decentralized clients while preserving privacy by avoiding data sharing. However, current FL methods assume conditional independence between client models, limiting the use of priors that capture dependence, such as Gaussian processes (GPs). We introduce the Structured Independence via deep Generative Model Approximation (SIGMA) prior which enables FL for non-factorizable models across clients, expanding the applicability of FL to fields such as spatial statistics, epidemiology, environmental science, and other domains where modeling dependencies is crucial. The SIGMA prior is a pre-trained deep generative model that approximates the desired prior and induces a specified conditional independence structure in the latent variables, creating an approximate model suitable for FL settings. We demonstrate the SIGMA prior's effectiveness on synthetic data and showcase its utility in a real-world example of FL for spatial data, using a conditional autoregressive prior to model spatial dependence across Australia. Our work enables new FL applications in domains where modeling dependent data is essential for accurate predictions and decision-making., Comment: 25 pages, 7 figures, 2 tables

Vertical federated learning (VFL) has emerged as a paradigm for collaborative model estimation across multiple clients, each holding a distinct set of covariates. This paper introduces the first comprehensive framework for fitting Bayesian models in the VFL setting. We propose a novel approach that leverages data augmentation techniques to transform VFL problems into a form compatible with existing Bayesian federated learning algorithms. We present an innovative model formulation for specific VFL scenarios where the joint likelihood factorizes into a product of client-specific likelihoods. To mitigate the dimensionality challenge posed by data augmentation, which scales with the number of observations and clients, we develop a factorized amortized variational approximation that achieves scalability independent of the number of observations. We showcase the efficacy of our framework through extensive numerical experiments on logistic regression, multilevel regression, and a novel hierarchical Bayesian split neural net model. Our work paves the way for privacy-preserving, decentralized Bayesian inference in vertically partitioned data scenarios, opening up new avenues for research and applications in various domains., Comment: 30 pages, 5 figures, 3 tables

Immediate settlement, or single-slot finality (SSF), is a long-term goal for Ethereum. The growing active validator set size is placing an increasing computational burden on the network, making SSF more challenging. EIP-7251 aims to reduce the number of validators by giving stakers the option to merge existing validators. Key to the success of this proposal therefore is whether stakers choose to merge their validators once EIP-7251 is implemented. It is natural to assume stakers participate only if they anticipate greater expected utility (risk-adjusted returns) as a single large validator. In this paper, we focus on one of the duties that a validator performs, viz. being the proposer for the next block. This duty can be quite lucrative, but happens infrequently. Based on previous analysis, we may assume that EIP-7251 implies no change to the security of the protocol. We confirm that the probability of a validator being selected as block proposer is equivalent under each consolidation regime. This result ensures that the decision of one staker to merge has no impact on the opportunity of another to propose the next block, in turn ensuring there is no major systemic change to the economics of the protocol with respect to proposer selection., Comment: 15 pages

Extreme natural hazards are increasing in frequency and intensity. These natural changes in our environment, combined with man-made pollution, have substantial economic, social and health impacts globally. The impact of the environment on human health (environmental health) is becoming well understood in international research literature. However, there are significant barriers to understanding key characteristics of this impact, related to substantial data volumes, data access rights and the time required to compile and compare data over regions and time. This study aims to reduce these barriers in Australia by creating an open data repository of national environmental health data and presenting a methodology for the production of health outcome-weighted population vulnerability indices related to extreme heat, extreme cold and air pollution at various temporal and geographical resolutions. Current state-of-the-art methods for the calculation of vulnerability indices include equal weight percentile ranking and the use of principal component analysis (PCA). The weighted vulnerability index methodology proposed in this study offers an advantage over others in the literature by considering health outcomes in the calculation process. The resulting vulnerability percentiles more clearly align population sensitivity and adaptive capacity with health risks. The temporal and spatial resolutions of the indices enable national monitoring on a scale never before seen across Australia. Additionally, we show that a weekly temporal resolution can be used to identify spikes in vulnerability due to changes in relative national environmental exposure.

Compositional data find broad application across diverse fields due to their efficacy in representing proportions or percentages of various components within a whole. Spatial dependencies often exist in compositional data, particularly when the data represents different land uses or ecological variables. Ignoring the spatial autocorrelations in modelling of compositional data may lead to incorrect estimates of parameters. Hence, it is essential to incorporate spatial information into the statistical analysis of compositional data to obtain accurate and reliable results. However, traditional statistical methods are not directly applicable to compositional data due to the correlation between its observations, which are constrained to lie on a simplex. To address this challenge, the Dirichlet distribution is commonly employed, as its support aligns with the nature of compositional vectors. Specifically, the R package DirichletReg provides a regression model, termed Dirichlet regression, tailored for compositional data. However, this model fails to account for spatial dependencies, thereby restricting its utility in spatial contexts. In this study, we introduce a novel spatial autoregressive Dirichlet regression model for compositional data, adeptly integrating spatial dependencies among observations. We construct a maximum likelihood estimator for a Dirichlet density function augmented with a spatial lag term. We compare this spatial autoregressive model with the same model without spatial lag, where we test both models on synthetic data as well as two real datasets, using different metrics. By considering the spatial relationships among observations, our model provides more accurate and reliable results for the analysis of compositional data. The model is further evaluated against a spatial multinomial regression model for compositional data, and their relative effectiveness is discussed., Comment: 33 pages, 2 figures, submitted to "Computational Statistics & Data Analysis"

Data collected from arrays of sensors are essential for informed decision-making in various systems. However, the presence of anomalies can compromise the accuracy and reliability of insights drawn from the collected data or information obtained via statistical analysis. This study aims to develop a robust Bayesian optimal experimental design (BOED) framework with anomaly detection methods for high-quality data collection. We introduce a general framework that involves anomaly generation, detection and error scoring when searching for an optimal design. This method is demonstrated using two comprehensive simulated case studies: the first study uses a spatial dataset, and the second uses a spatio-temporal river network dataset. As a baseline approach, we employed a commonly used prediction-based utility function based on minimising errors. Results illustrate the trade-off between predictive accuracy and anomaly detection performance for our method under various design scenarios. An optimal design robust to anomalies ensures the collection and analysis of more trustworthy data, playing a crucial role in understanding the dynamics of complex systems such as the environment, therefore enabling informed decisions in monitoring, management, and response.

Globally, there is an increased need for guidelines to produce high-quality data outputs for analysis. No framework currently exists that provides guidelines for a comprehensive approach to producing analysis ready data (ARD). Through critically reviewing and summarising current literature, this paper proposes such guidelines for the creation of ARD. The guidelines proposed in this paper inform ten steps in the generation of ARD: ethics, project documentation, data governance, data management, data storage, data discovery and collection, data cleaning, quality assurance, metadata, and data dictionary. These steps are illustrated through a substantive case study that aimed to create ARD for a digital spatial platform: the Australian Child and Youth Wellbeing Atlas (ACYWA)., Comment: 49 pages, 3 figures, 3 tables, and 5 appendices

This study develops a model-based index creation approach called the Generalized Shared Component Model (GSCM) by drawing on the large field of factor models. The proposed fully Bayesian approach accommodates heteroscedastic model error, multiple shared factors and flexible spatial priors. Moreover, our model, unlike previous index approaches, provides indices with uncertainty. Focusing on Australian risk factor data, the proposed GSCM is used to develop the Area Indices of Behaviors Impacting Cancer product - representing the first area level cancer risk factor index in Australia. This advancement aids in identifying communities with elevated cancer risk, facilitating targeted health interventions., Comment: Submitted to Health and Place

In the field of population health research, understanding the similarities between geographical areas and quantifying their shared effects on health outcomes is crucial. In this paper, we synthesise a number of existing methods to create a new approach that specifically addresses this goal. The approach is called a Bayesian spatial Dirichlet process clustered heterogeneous regression model. This non-parametric framework allows for inference on the number of clusters and the clustering configurations, while simultaneously estimating the parameters for each cluster. We demonstrate the efficacy of the proposed algorithm using simulated data and further apply it to analyse influential factors affecting children's health development domains in Queensland. The study provides valuable insights into the contributions of regional similarities in education and demographics to health outcomes, aiding targeted interventions and policy design.

Spatial statistical models are commonly used in geographical scenarios to ensure spatial variation is captured effectively. However, spatial models and cluster algorithms can be complicated and expensive. This paper pursues three main objectives. First, it introduces covariate effect clustering by integrating a Bayesian Geographically Weighted Regression (BGWR) with a Gaussian mixture model and the Dirichlet process mixture model. Second, this paper examines situations in which a particular covariate holds significant importance in one region but not in another in the Bayesian framework. Lastly, it addresses computational challenges present in existing BGWR, leading to notable enhancements in Markov chain Monte Carlo estimation suitable for large spatial datasets. The efficacy of the proposed method is demonstrated using simulated data and is further validated in a case study examining children's development domains in Queensland, Australia, using data provided by Children's Health Queensland and Australia's Early Development Census.

Cancer is a significant health issue globally and it is well known that cancer risk varies geographically. However in many countries there are no small area level data on cancer risk factors with high resolution and complete reach, which hinders the development of targeted prevention strategies. Using Australia as a case study, the 2017-2018 National Health Survey was used to generate prevalence estimates for 2221 small areas across Australia for eight cancer risk factor measures covering smoking, alcohol, physical activity, diet and weight. Utilising a recently developed Bayesian two-stage small area estimation methodology, the model incorporated survey-only covariates, spatial smoothing and hierarchical modelling techniques, along with a vast array of small area level auxiliary data, including census, remoteness, and socioeconomic data. The models borrowed strength from previously published cancer risk estimates provided by the Social Health Atlases of Australia. Estimates were internally and externally validated. We illustrated that in 2017-18 health behaviours across Australia exhibited more spatial disparities than previously realised by improving the reach and resolution of formerly published cancer risk factors. The derived estimates reveal higher prevalence of unhealthy behaviours in more remote areas, and areas of lower socioeconomic status; a trend that aligns well with previous work. Our study addresses the gaps in small area level cancer risk factor estimates in Australia. The new estimates provide improved spatial resolution and reach and will enable more targeted cancer prevention strategies at the small area level, supporting policy makers, researchers, and the general public in understanding the spatial distribution of cancer risk factors in Australia. To help disseminate the results of this work, they will be made available in the Australian Cancer Atlas 2.0., Comment: Submitted to the International Journal of Health Geographics

A Directed Acyclic Graph (DAG) can be partitioned or mapped into clusters to support and make inference more computationally efficient in Bayesian Network (BN), Markov process and other models. However, optimal partitioning with an arbitrary cost function is challenging, especially in statistical inference as the local cluster cost is dependent on both nodes within a cluster, and the mapping of clusters connected via parent and/or child nodes, which we call dependent clusters. We propose a novel algorithm called DCMAP for optimal cluster mapping with dependent clusters. Given an arbitrarily defined, positive cost function based on the DAG, we show that DCMAP converges to find all optimal clusters, and returns near-optimal solutions along the way. Empirically, we find that the algorithm is time-efficient for a Dynamic BN (DBN) model of a seagrass complex system using a computation cost function. For a 25 and 50-node DBN, the search space size was $9.91\times 10^9$ and $1.51\times10^{21}$ possible cluster mappings, and the first optimal solution was found at iteration 934 $(\text{95\% CI } 926,971)$, and 2256 $(2150,2271)$ with a cost that was 4\% and 0.2\% of the naive heuristic cost, respectively.

This article provides a comprehensive synthesis of the recent developments in synthetic data generation via deep generative models, focusing on tabular datasets. We specifically outline the importance of synthetic data generation in the context of privacy-sensitive data. Additionally, we highlight the advantages of using deep generative models over other methods and provide a detailed explanation of the underlying concepts, including unsupervised learning, neural networks, and generative models. The paper covers the challenges and considerations involved in using deep generative models for tabular datasets, such as data normalization, privacy concerns, and model evaluation. This review provides a valuable resource for researchers and practitioners interested in synthetic data generation and its applications.

With the rise in popularity of digital Atlases to communicate spatial variation, there is an increasing need for robust small-area estimates. However, current small-area estimation methods suffer from various modeling problems when data are very sparse or when estimates are required for areas with very small populations. These issues are particularly heightened when modeling proportions. Additionally, recent work has shown significant benefits in modeling at both the individual and area levels. We propose a two-stage Bayesian hierarchical small area estimation approach for proportions that can: account for survey design; reduce direct estimate instability; and generate prevalence estimates for small areas with no survey data. Using a simulation study we show that, compared with existing Bayesian small area estimation methods, our approach can provide optimal predictive performance (Bayesian mean relative root mean squared error, mean absolute relative bias and coverage) of proportions under a variety of data conditions, including very sparse and unstable data. To assess the model in practice, we compare modeled estimates of current smoking prevalence for 1,630 small areas in Australia using the 2017-2018 National Health Survey data combined with 2016 census data., Comment: Currently in second round of review at the International Statistical Review

Choosing the Fisher information as the metric tensor for a Riemannian manifold provides a powerful yet fundamental way to understand statistical distribution families. Distances along this manifold become a compelling measure of statistical distance, and paths of shorter distance improve sampling techniques that leverage a sequence of distributions in their operation. Unfortunately, even for a distribution as generally tractable as the multivariate normal distribution, this information geometry proves unwieldy enough that closed-form solutions for shortest-distance paths or their lengths remain unavailable outside of limited special cases. In this review we present for general statisticians the most practical aspects of the Fisher geometry for this fundamental distribution family. Rather than a differential geometric treatment, we use an intuitive understanding of the covariance-induced curvature of this manifold to unify the special cases with known closed-form solution and review approximate solutions for the general case. We also use the multivariate normal information geometry to better understand the paths or distances commonly used in statistics (annealing, Wasserstein). Given the unavailability of a general solution, we also discuss the methods used for numerically obtaining geodesics in the space of multivariate normals, identifying remaining challenges and suggesting methodological improvements., Comment: 22 pages, 8 figures, further figures and algorithms in supplement

The research explores the influence of preschool attendance (one year before full-time school) on the development of children during their first year of school. Using data collected by the Australian Early Development Census, the findings show that areas with high proportions of preschool attendance tended to have lower proportions of children with at least one developmental vulnerability. Developmental vulnerablities include not being able to cope with the school day (tired, hungry, low energy), unable to get along with others or aggressive behaviour, trouble with reading/writing or numbers. These findings, of course, vary by region. Using Data Analysis and Machine Learning, the researchers were able to identify three distinct clusters within Queensland, each characterised by different socio-demographic variables influencing the relationship between preschool attendance and developmental vulnerability. These analyses contribute to understanding regions with high vulnerability and the potential need for tailored policies or investments

Time series often reflect variation associated with other related variables. Controlling for the effect of these variables is useful when modeling or analysing the time series. We introduce a novel approach to normalize time series data conditional on a set of covariates. We do this by modeling the conditional mean and the conditional variance of the time series with generalized additive models using a set of covariates. The conditional mean and variance are then used to normalize the time series. We illustrate the use of conditionally normalized series using two applications involving river network data. First, we show how these normalized time series can be used to impute missing values in the data. Second, we show how the normalized series can be used to estimate the conditional autocorrelation function and conditional cross-correlation functions via additive models. Finally we use the conditional cross-correlations to estimate the time it takes water to flow between two locations in a river network., Comment: 36 pages, 26 Figures, Journal Article

Crowdsourcing methods facilitate the production of scientific information by non-experts. This form of citizen science (CS) is becoming a key source of complementary data in many fields to inform data-driven decisions and study challenging problems. However, concerns about the validity of these data often constrain their utility. In this paper, we focus on the use of citizen science data in addressing complex challenges in environmental conservation. We consider this issue from three perspectives. First, we present a literature scan of papers that have employed Bayesian models with citizen science in ecology. Second, we compare several popular majority vote algorithms and introduce a Bayesian item response model that estimates and accounts for participants' abilities after adjusting for the difficulty of the images they have classified. The model also enables participants to be clustered into groups based on ability. Third, we apply the model in a case study involving the classification of corals from underwater images from the Great Barrier Reef, Australia. We show that the model achieved superior results in general and, for difficult tasks, a weighted consensus method that uses only groups of experts and experienced participants produced better performance measures. Moreover, we found that participants learn as they have more classification opportunities, which substantially increases their abilities over time. Overall, the paper demonstrates the feasibility of CS for answering complex and challenging ecological questions when these data are appropriately analysed. This serves as motivation for future work to increase the efficacy and trustworthiness of this emerging source of data., Comment: 25 pages, 10 figures

Water is the lifeblood of river networks, and its quality plays a crucial role in sustaining both aquatic ecosystems and human societies. Real-time monitoring of water quality is increasingly reliant on in-situ sensor technology. Anomaly detection is crucial for identifying erroneous patterns in sensor data, but can be a challenging task due to the complexity and variability of the data, even under normal conditions. This paper presents a solution to the challenging task of anomaly detection for river network sensor data, which is essential for accurate and continuous monitoring. We use a graph neural network model, the recently proposed Graph Deviation Network (GDN), which employs graph attention-based forecasting to capture the complex spatio-temporal relationships between sensors. We propose an alternate anomaly scoring method, GDN+, based on the learned graph. To evaluate the model's efficacy, we introduce new benchmarking simulation experiments with highly-sophisticated dependency structures and subsequence anomalies of various types. We further examine the strengths and weaknesses of this baseline approach, GDN, in comparison to other benchmarking methods on complex real-world river network data. Findings suggest that GDN+ outperforms the baseline approach in high-dimensional data, while also providing improved interpretability. We also introduce software called gnnad.

Inference on modern Bayesian Neural Networks (BNNs) often relies on a variational inference treatment, imposing violated assumptions of independence and the form of the posterior. Traditional MCMC approaches avoid these assumptions at the cost of increased computation due to its incompatibility to subsampling of the likelihood. New Piecewise Deterministic Markov Process (PDMP) samplers permit subsampling, though introduce a model specific inhomogenous Poisson Process (IPPs) which is difficult to sample from. This work introduces a new generic and adaptive thinning scheme for sampling from these IPPs, and demonstrates how this approach can accelerate the application of PDMPs for inference in BNNs. Experimentation illustrates how inference with these methods is computationally feasible, can improve predictive accuracy, MCMC mixing performance, and provide informative uncertainty measurements when compared against other approximate inference schemes., Comment: Includes correction to software and corrigendum note

Federated learning methods enable model training across distributed data sources without data leaving their original locations and have gained increasing interest in various fields. However, existing approaches are limited, excluding many structured probabilistic models. We present a general and elegant solution based on structured variational inference, widely used in Bayesian machine learning, adapted for the federated setting. Additionally, we provide a communication-efficient variant analogous to the canonical FedAvg algorithm. The proposed algorithms' effectiveness is demonstrated, and their performance is compared with hierarchical Bayesian neural networks and topic models.

Construction of dictionaries using nonnegative matrix factorisation (NMF) has extensive applications in signal processing and machine learning. With the advances in deep learning, training compact and robust dictionaries using deep neural networks, i.e., dictionaries of deep features, has been proposed. In this study, we propose a probabilistic generative model which employs a variational autoencoder (VAE) to perform nonnegative dictionary learning. In contrast to the existing VAE models, we cast the model under a statistical framework with latent variables obeying a Gamma distribution and design a new loss function to guarantee the nonnegative dictionaries. We adopt an acceptance-rejection sampling reparameterization trick to update the latent variables iteratively. We apply the dictionaries learned from VAE-NMF to two signal processing tasks, i.e., enhancement of speech and extraction of muscle synergies. Experimental results demonstrate that VAE-NMF performs better in learning the latent nonnegative dictionaries in comparison with state-of-the-art methods., Comment: 7 pages, 2 figures

This study aimed to better understand the vulnerability of 5 to 6 year old children in their first year of school, based on five health and development domains. Identification of subgroups of children within these domains can lead to more targeted research and policies to reduce these vulnerabilities. The study focused on finding clusters of geographical regions with high and low proportions of vulnerable children in Queensland, Australia. K-means analysis was conducted on data from the Australian Early Development Census and the Australian Bureau of Statistics. The clusters were then compared with respect to their geographic locations and risk factor profiles. The results are made publicly available via an interactive dashboard application in R Shiny

Building on a strong foundation of philosophy, theory, methods and computation over the past three decades, Bayesian approaches are now an integral part of the toolkit for most statisticians and data scientists. Whether they are dedicated Bayesians or opportunistic users, applied professionals can now reap many of the benefits afforded by the Bayesian paradigm. In this paper, we touch on six modern opportunities and challenges in applied Bayesian statistics: intelligent data collection, new data sources, federated analysis, inference for implicit models, model transfer and purposeful software products., Comment: 27 pages, 8 figures

Various methods have been developed to combine inference across multiple sets of results for unsupervised clustering, within the ensemble clustering literature. The approach of reporting results from one `best' model out of several candidate clustering models generally ignores the uncertainty that arises from model selection, and results in inferences that are sensitive to the particular model and parameters chosen. Bayesian model averaging (BMA) is a popular approach for combining results across multiple models that offers some attractive benefits in this setting, including probabilistic interpretation of the combined cluster structure and quantification of model-based uncertainty. In this work we introduce clusterBMA, a method that enables weighted model averaging across results from multiple unsupervised clustering algorithms. We use clustering internal validation criteria to develop an approximation of the posterior model probability, used for weighting the results from each model. From a consensus matrix representing a weighted average of the clustering solutions across models, we apply symmetric simplex matrix factorisation to calculate final probabilistic cluster allocations. In addition to outperforming other ensemble clustering methods on simulated data, clusterBMA offers unique features including probabilistic allocation to averaged clusters, combining allocation probabilities from 'hard' and 'soft' clustering algorithms, and measuring model-based uncertainty in averaged cluster allocation. This method is implemented in an accompanying R package of the same name.

Hawkes processes are a self-exciting stochastic process used to describe phenomena whereby past events increase the probability of the occurrence of future events. This work presents a flexible approach for modelling a variant of these, namely discrete-time Hawkes processes. Most standard models of Hawkes processes rely on a parametric form for the function describing the influence of past events, referred to as the triggering kernel. This is likely to be insufficient to capture the true excitation pattern, particularly for complex data. By utilising trans-dimensional Markov chain Monte Carlo inference techniques, our proposed model for the triggering kernel can take the form of any step function, affording significantly more flexibility than a parametric form. We first demonstrate the utility of the proposed model through a comprehensive simulation study. This includes univariate scenarios, and multivariate scenarios whereby there are multiple interacting Hawkes processes. We then apply the proposed model to several case studies: the interaction between two countries during the early to middle stages of the COVID-19 pandemic, taking Italy and France as an example, and the interaction of terrorist activity between two countries in close spatial proximity, Indonesia and the Philippines, and then within three regions of the Philippines.

Optimal design facilitates intelligent data collection. In this paper, we introduce a fully Bayesian design approach for spatial processes with complex covariance structures, like those typically exhibited in natural ecosystems. Coordinate Exchange algorithms are commonly used to find optimal design points. However, collecting data at specific points is often infeasible in practice. Currently, there is no provision to allow for flexibility in the choice of design. We also propose an approach to find Bayesian sampling windows, rather than points, via Gaussian process emulation to identify regions of high design efficiency across a multi-dimensional space. These developments are motivated by two ecological case studies: monitoring water temperature in a river network system in the northwestern United States and monitoring submerged coral reefs off the north-west coast of Australia.

This work introduces a comprehensive approach to assess the sensitivity of model outputs to changes in parameter values, constrained by the combination of prior beliefs and data. This novel approach identifies stiff parameter combinations strongly affecting the quality of the model-data fit while simultaneously revealing which of these key parameter combinations are informed primarily by the data or are also substantively influenced by the priors. We focus on the very common context in complex systems where the amount and quality of data are low compared to the number of model parameters to be collectively estimated, and showcase the benefits of this technique for applications in biochemistry, ecology, and cardiac electrophysiology. We also show how stiff parameter combinations, once identified, uncover controlling mechanisms underlying the system being modeled and inform which of the model parameters need to be prioritized in future experiments for improved parameter inference from collective model-data fitting.

The concept of 'Stateless Ethereum' was conceived with the primary aim of mitigating Ethereum's unbounded state growth. The key facilitator of Stateless Ethereum is through the introduction of 'witnesses' into the ecosystem. The changes and potential consequences that these additional data packets pose on the network need to be identified and analysed to ensure that the Ethereum ecosystem can continue operating securely and efficiently. In this paper we propose a Bayesian Network model, a probabilistic graphical modelling approach, to capture the key factors and their interactions in Ethereum mainnet, the public Ethereum blockchain, focussing on the changes being introduced by Stateless Ethereum to estimate the health of the resulting Ethereum ecosystem. We use a mixture of empirical data and expert knowledge, where data are unavailable, to quantify the model. Based on the data and expert knowledge available to use at the time of modelling, the Ethereum ecosystem is expected to remain healthy following the introduction of Stateless Ethereum., Comment: In Proceedings MARS 2022, arXiv:2203.09299

This paper aims to develop a global perspective of the complexity of the relationship between the standardised per-capita growth rate of Covid-19 cases, deaths, and the OxCGRT Covid-19 Stringency Index, a measure describing a country's stringency of lockdown policies. To achieve our goal, we use a heterogeneous intrinsic dimension estimator implemented as a Bayesian mixture model, called Hidalgo. We identify that the Covid-19 dataset may project onto two low-dimensional manifolds without significant information loss. The low dimensionality suggests strong dependency among the standardised growth rates of cases and deaths per capita and the OxCGRT Covid-19 Stringency Index for a country over 2020-2021. Given the low dimensional structure, it may be feasible to model observable Covid-19 dynamics with few parameters. Importantly, we identify spatial autocorrelation in the intrinsic dimension distribution worldwide. Moreover, we highlight that high-income countries are more likely to lie on low-dimensional manifolds, likely arising from aging populations, comorbidities, and increased per capita mortality burden from Covid-19. Finally, we temporally stratify the dataset to examine the intrinsic dimension at a more granular level throughout the Covid-19 pandemic.

Spatio-temporal models are widely used in many research areas from ecology to epidemiology. However, most covariance functions describe spatial relationships based on Euclidean distance only. In this paper, we introduce the R package SSNbayes for fitting Bayesian spatio-temporal models and making predictions on branching stream networks. SSNbayes provides a linear regression framework with multiple options for incorporating spatial and temporal autocorrelation. Spatial dependence is captured using stream distance and flow connectivity while temporal autocorrelation is modelled using vector autoregression approaches. SSNbayes provides the functionality to make predictions across the whole network, compute exceedance probabilities and other probabilistic estimates such as the proportion of suitable habitat. We illustrate the functionality of the package using a stream temperature dataset collected in Idaho, USA.

The communication of uncertainty estimates, predictions and insights based on spatio-temporal models is important for decision-making as it impacts the utilisation and interpretation of information. Bivariate mapping is commonly used for communication of estimates and associated uncertainty; however, it is known that different visual qualities resulting from choics of symbols and consequent interaction between the display dimensions can lead to different interpretations and consequently affect resultant decisions. Characteristics of the data to be presented, such as spatial format, statistical level and continuousness, shape the range of available bivairate symbols. The subsequent utility of these bivariate symbols depends on their ability to achieve end-user's goals. In this paper we present a novel design framework, which, through consideration of both input data characteristics and potential operational tasks (as proxy to end-user goals), assists map designers in appropriate selection of bivariate symbols for the coincident presentation of spatio-temporal modelled data and associated uncertainty. The framework is showcased through application to a case study pertaining to sediment pollution in the Great Barrier Reef.

Organizations such as government departments and financial institutions provide online service facilities accessible via an increasing number of internet connected devices which make their operational environment vulnerable to cyber attacks. Consequently, there is a need to have mechanisms in place to detect cyber security attacks in a timely manner. A variety of Network Intrusion Detection Systems (NIDS) have been proposed and can be categorized into signature-based NIDS and anomaly-based NIDS. The signature-based NIDS, which identify the misuse through scanning the activity signature against the list of known attack activities, are criticized for their inability to identify new attacks (never-before-seen attacks). Among anomaly-based NIDS, which declare a connection anomalous if it expresses deviation from a trained model, the unsupervised learning algorithms circumvent this issue since they have the ability to identify new attacks. In this study, we use an unsupervised learning algorithm based on principal component analysis to detect cyber attacks. In the training phase, our approach has the advantage of also identifying outliers in the training dataset. In the monitoring phase, our approach first identifies the affected dimensions and then calculates an anomaly score by aggregating across only those components that are affected by the anomalies. We explore the performance of the algorithm via simulations and through two applications, namely to the UNSW-NB15 dataset recently released by the Australian Centre for Cyber Security and to the well-known KDD'99 dataset. The algorithm is scalable to large datasets in both training and monitoring phases, and the results from both the simulated and real datasets show that the method has promise in detecting suspicious network activities.

Real time monitoring using in situ sensors is becoming a common approach for measuring water quality within watersheds. High frequency measurements produce big data sets that present opportunities to conduct new analyses for improved understanding of water quality dynamics and more effective management of rivers and streams. Of primary importance is enhancing knowledge of the relationships between nitrate, one of the most reactive forms of inorganic nitrogen in the aquatic environment, and other water quality variables. We analysed high frequency water quality data from in situ sensors deployed in three sites from different watersheds and climate zones within the National Ecological Observatory Network, USA. We used generalised additive mixed models to explain the nonlinear relationships at each site between nitrate concentration and conductivity, turbidity, dissolved oxygen, water temperature, and elevation. Temporal auto correlation was modelled with an auto regressive moving average model and we examined the relative importance of the explanatory variables. Total deviance explained by the models was high for all sites. Although variable importance and the smooth regression parameters differed among sites, the models explaining the most variation in nitrate contained the same explanatory variables. This study demonstrates that building a model for nitrate using the same set of explanatory water quality variables is achievable, even for sites with vastly different environmental and climatic characteristics. Applying such models will assist managers to select cost effective water quality variables to monitor when the goals are to gain a spatially and temporally in depth understanding of nitrate dynamics and adapt management plans accordingly., Comment: 4 figures, 17 pages

Relative abundance is a common metric to estimate the composition of species in ecological surveys reflecting patterns of commonness and rarity of biological assemblages. Measurements of coral reef compositions formed by four communities along Australia's Great Barrier Reef (GBR) gathered between 2012 and 2017 are the focus of this paper. We undertake the task of finding clusters of transect locations with similar community composition and investigate changes in clustering dynamics over time. During these years, an unprecedented sequence of extreme weather events (cyclones and coral bleaching) impacted the 58 surveyed locations. The dependence between constituent parts of a composition presents a challenge for existing multivariate clustering approaches. In this paper, we introduce a finite mixture of Dirichlet distributions with group-specific parameters, where cluster memberships are dictated by unobserved latent variables. The inference is carried in a Bayesian framework, where MCMC strategies are outlined to sample from the posterior model. Simulation studies are presented to illustrate the performance of the model in a controlled setting. The application of the model to the 2012 coral reef data reveals that clusters were spatially distributed in similar ways across reefs which indicates a potential influence of wave exposure at the origin of coral reef community composition. The number of clusters estimated by the model decreased from four in 2012 to two from 2014 until 2017. Posterior probabilities of transect allocations to the same cluster substantially increase through time showing a potential homogenization of community composition across the whole GBR. The Bayesian model highlights the diversity of coral reef community composition within a coral reef and rapid changes across large spatial scales that may contribute to undermining the future of the GBR's biodiversity., Comment: Paper submitted for publication

Climate change is commonly associated with an overall increase in mean temperature in a defined past time period. Many studies consider temperature trends at the global scale, but the literature is lacking in in-depth analysis of the temperature trends across Australia in recent decades. In addition to heterogeneity in mean and median values, daily Australia temperature data suffers from quasi-periodic heterogeneity in variance. However, this issue has barely been overlooked in climate research. A contribution of this article is that we propose a joint model of quantile regression and variability. By accounting appropriately for the heterogeneity in these types of data, our analysis reveals that daily maximum temperature is warming by 0.21 Celsius per decade and daily minimum temperature by 0.13 Celsius per decade. However, our modeling also shows nuanced patterns of climate change depends on location, season, and the percentiles of the temperature series over Australia., Comment: 30 pages, 10 figures, and 3 tables