Causal chain event graphs for remedial maintenance.

The analysis of system reliability has often benefited from graphical tools such as fault trees and Bayesian networks. In this article, instead of conventional graphical tools, we apply a probabilistic graphical model called the chain event graph (CEG) to represent the failures and processes of deterioration of a system. The CEG is derived from an event tree and can flexibly represent the unfolding of asymmetric processes. For this application, we need to define a new class of formal intervention we call remedial to model the causal effects of remedial maintenance. This fixes the root causes of a failure and returns the status of the system to as good as new. We demonstrate that the semantics of the CEG are rich enough to express this novel type of intervention. Furthermore, through the bespoke causal algebras, the CEG provides a transparent framework with which to guide and express the rationale behind predictive inferences about the effects of various types of remedial intervention. A backdoor theorem is adapted to apply to these interventions to help discover when a system is only partially observed.

Causal Algebras on Chain Event Graphs with Informed Missingness for System Failure.

Graph-based causal inference has recently been successfully applied to explore system reliability and to predict failures in order to improve systems. One popular causal analysis following Pearl and Spirtes et al. to study causal relationships embedded in a system is to use a Bayesian network (BN). However, certain causal constructions that are particularly pertinent to the study of reliability are difficult to express fully through a BN. Our recent work demonstrated the flexibility of using a Chain Event Graph (CEG) instead to capture causal reasoning embedded within engineers' reports. We demonstrated that an event tree rather than a BN could provide an alternative framework that could capture most of the causal concepts needed within this domain. In particular, a causal calculus for a specific type of intervention, called a remedial intervention, was devised on this tree-like graph. In this paper, we extend the use of this framework to show that not only remedial maintenance interventions but also interventions associated with routine maintenance can be well-defined using this alternative class of graphical model. We also show that the complexity in making inference about the potential relationships between causes and failures in a missing data situation in the domain of system reliability can be elegantly addressed using this new methodology. Causal modelling using a CEG is illustrated through examples drawn from the study of reliability of an energy distribution network.

Communicating Geographical Risks in Crisis Management: The Need for Research.

In any crisis, there is a great deal of uncertainty, often geographical uncertainty or, more precisely, spatiotemporal uncertainty. Examples include the spread of contamination from an industrial accident, drifting volcanic ash, and the path of a hurricane. Estimating spatiotemporal probabilities is usually a difficult task, but that is not our primary concern. Rather, we ask how analysts can communicate spatiotemporal uncertainty to those handling the crisis. We comment on the somewhat limited literature on the representation of spatial uncertainty on maps. We note that many cognitive issues arise and that the potential for confusion is high. We note that in the early stages of handling a crisis, the uncertainties involved may be deep, i.e., difficult or impossible to quantify in the time available. In such circumstance, we suggest the idea of presenting multiple scenarios.

Creating a Theoretically Grounded, Gamified Health App: Lessons From Developing the Cigbreak Smoking Cessation Mobile Phone Game.

BACKGROUND: Gaming techniques are increasingly recognized as effective methods for changing behavior and increasing user engagement with mobile phone apps. The rapid uptake of mobile phone games provides an unprecedented opportunity to reach large numbers of people and to influence a wide range of health-related behaviors. However, digital interventions are still nascent in the field of health care, and optimum gamified methods of achieving health behavior change are still being investigated. There is currently a lack of worked methodologies that app developers and health care professionals can follow to facilitate theoretically informed design of gamified health apps. OBJECTIVE: This study aimed to present a series of steps undertaken during the development of Cigbreak, a gamified smoking cessation health app. METHODS: A systematic and iterative approach was adopted by (1) forming an expert multidisciplinary design team, (2) defining the problem and establishing user preferences, (3) incorporating the evidence base, (4) integrating gamification, (5) adding behavior change techniques, (6) forming a logic model, and (7) user testing. A total of 10 focus groups were conducted with 73 smokers. RESULTS: Users found the app an engaging and motivating way to gain smoking cessation advice and a helpful distraction from smoking; 84% (62/73) of smokers said they would play again and recommend it to a friend. CONCLUSIONS: A dedicated gamified app to promote smoking cessation has the potential to modify smoking behavior and to deliver effective smoking cessation advice. Iterative, collaborative development using evidence-based behavior change techniques and gamification may help to make the game engaging and potentially effective. Gamified health apps developed in this way may have the potential to provide effective and low-cost health interventions in a wide range of clinical settings.

Directed functional connectivity using dynamic graphical models.

There are a growing number of neuroimaging methods that model spatio-temporal patterns of brain activity to allow more meaningful characterizations of brain networks. This paper proposes dynamic graphical models (DGMs) for dynamic, directed functional connectivity. DGMs are a multivariate graphical model with time-varying coefficients that describe instantaneous directed relationships between nodes. A further benefit of DGMs is that networks may contain loops and that large networks can be estimated. We use network simulations and human resting-state fMRI (N = 500) to investigate the validity and reliability of the estimated networks. We simulate systematic lags of the hemodynamic response at different brain regions to investigate how these lags potentially bias directionality estimates. In the presence of such lag confounds (0.4-0.8 s offset between connected nodes), our method has a sensitivity of 72%-77% to detect the true direction. Stronger lag confounds have reduced sensitivity, but do not increase false positives (i.e., directionality estimates of the opposite direction). In human resting-state fMRI, the default mode network has consistent influence on the cerebellar, the limbic and the auditory/temporal networks. We also show a consistent reciprocal relationship between the visual medial and visual lateral network. Finally, we apply the method in a small mouse fMRI sample and discover a highly plausible relationship between areas in the hippocampus feeding into the cingulate cortex. We provide a computationally efficient implementation of DGM as a free software package for R.

Principles of Bayesian Inference Using General Divergence Criteria.

When it is acknowledged that all candidate parameterised statistical models are misspecified relative to the data generating process, the decision maker (DM) must currently concern themselves with inference for the parameter value minimising the Kullback-Leibler (KL)-divergence between the model and this process (Walker, 2013). However, it has long been known that minimising the KL-divergence places a large weight on correctly capturing the tails of the sample distribution. As a result, the DM is required to worry about the robustness of their model to tail misspecifications if they want to conduct principled inference. In this paper we alleviate these concerns for the DM. We advance recent methodological developments in general Bayesian updating (Bissiri, Holmes & Walker, 2016) to propose a statistically well principled Bayesian updating of beliefs targeting the minimisation of more general divergence criteria. We improve both the motivation and the statistical foundations of existing Bayesian minimum divergence estimation (Hooker & Vidyashankar, 2014; Ghosh & Basu, 2016), allowing the well principled Bayesian to target predictions from the model that are close to the genuine model in terms of some alternative divergence measure to the KL-divergence. Our principled formulation allows us to consider a broader range of divergences than have previously been considered. In fact, we argue defining the divergence measure forms an important, subjective part of any statistical analysis, and aim to provide some decision theoretic rational for this selection. We illustrate how targeting alternative divergence measures can impact the conclusions of simple inference tasks, and discuss then how our methods might apply to more complicated, high dimensional models.

Orchestrated transcription of biological processes in the marine picoeukaryote Ostreococcus exposed to light/dark cycles.

BACKGROUND: Picoeukaryotes represent an important, yet poorly characterized component of marine phytoplankton. The recent genome availability for two species of Ostreococcus and Micromonas has led to the emergence of picophytoplankton comparative genomics. Sequencing has revealed many unexpected features about genome structure and led to several hypotheses on Ostreococcus biology and physiology. Despite the accumulation of genomic data, little is known about gene expression in eukaryotic picophytoplankton. RESULTS: We have conducted a genome-wide analysis of gene expression in Ostreococcus tauri cells exposed to light/dark cycles (L/D). A Bayesian Fourier Clustering method was implemented to cluster rhythmic genes according to their expression waveform. In a single L/D condition nearly all expressed genes displayed rhythmic patterns of expression. Clusters of genes were associated with the main biological processes such as transcription in the nucleus and the organelles, photosynthesis, DNA replication and mitosis. CONCLUSIONS: Light/Dark time-dependent transcription of the genes involved in the main steps leading to protein synthesis (transcription basic machinery, ribosome biogenesis, translation and aminoacid synthesis) was observed, to an unprecedented extent in eukaryotes, suggesting a major input of transcriptional regulations in Ostreococcus. We propose that the diurnal co-regulation of genes involved in photoprotection, defence against oxidative stress and DNA repair might be an efficient mechanism, which protects cells against photo-damage thereby, contributing to the ability of O. tauri to grow under a wide range of light intensities.

Kalman filtration of radiation monitoring data from atmospheric dispersion of radioactive materials.

A Kalman filter method using off-site radiation monitoring data is proposed as a tool for on-line estimation of the source term for short-range atmospheric dispersion of radioactive materials. The method is based on the Gaussian plume model, in which the plume parameters including the source term exhibit a 'random walk' process. The embedded parameters of the Kalman filter are determined through maximum-likelihood estimation making the filter essentially free of external parameters. The method is tested using both real and simulated radiation monitoring data. For simulated data, the method is shown to retrieve the embedded parameters employed in generating the data and to reconstruct the plume model parameters, including the source term. When tested against experimental radiation monitoring data the method is found accurately to uncover the known source term.