Bayesian network modelling to identify on-ramps to childhood obesity.

BACKGROUND: When tackling complex public health challenges such as childhood obesity, interventions focused on immediate causes, such as poor diet and physical inactivity, have had limited success, largely because upstream root causes remain unresolved. A priority is to develop new modelling frameworks to infer the causal structure of complex chronic disease networks, allowing disease "on-ramps" to be identified and targeted. METHODS: The system surrounding childhood obesity was modelled as a Bayesian network, using data from The Longitudinal Study of Australian Children. The existence and directions of the dependencies between factors represent possible causal pathways for childhood obesity and were encoded in directed acyclic graphs (DAGs). The posterior distribution of the DAGs was estimated using the Partition Markov chain Monte Carlo. RESULTS: We have implemented structure learning for each dataset at a single time point. For each wave and cohort, socio-economic status was central to the DAGs, implying that socio-economic status drives the system regarding childhood obesity. Furthermore, the causal pathway socio-economic status and/or parental high school levels → parental body mass index (BMI) → child's BMI existed in over 99.99% of posterior DAG samples across all waves and cohorts. For children under the age of 8 years, the most influential proximate causal factors explaining child BMI were birth weight and parents' BMI. After age 8 years, free time activity became an important driver of obesity, while the upstream factors influencing free time activity for boys compared with girls were different. CONCLUSIONS: Childhood obesity is largely a function of socio-economic status, which is manifest through numerous downstream factors. Parental high school levels entangle with socio-economic status, and hence, are on-ramp to childhood obesity. The strong and independent causal relationship between birth weight and childhood BMI suggests a biological link. Our study implies that interventions that improve the socio-economic status, including through increasing high school completion rates, may be effective in reducing childhood obesity prevalence.

A case study in model failure? COVID-19 daily deaths and ICU bed utilisation predictions in New York state.

Forecasting models have been influential in shaping decision-making in the COVID-19 pandemic. However, there is concern that their predictions may have been misleading. Here, we dissect the predictions made by four models for the daily COVID-19 death counts between March 25 and June 5 in New York state, as well as the predictions of ICU bed utilisation made by the influential IHME model. We evaluated the accuracy of the point estimates and the accuracy of the uncertainty estimates of the model predictions. First, we compared the "ground truth" data sources on daily deaths against which these models were trained. Three different data sources were used by these models, and these had substantial differences in recorded daily death counts. Two additional data sources that we examined also provided different death counts per day. For accuracy of prediction, all models fared very poorly. Only 10.2% of the predictions fell within 10% of their training ground truth, irrespective of distance into the future. For accurate assessment of uncertainty, only one model matched relatively well the nominal 95% coverage, but that model did not start predictions until April 16, thus had no impact on early, major decisions. For ICU bed utilisation, the IHME model was highly inaccurate; the point estimates only started to match ground truth after the pandemic wave had started to wane. We conclude that trustworthy models require trustworthy input data to be trained upon. Moreover, models need to be subjected to prespecified real time performance tests, before their results are provided to policy makers and public health officials.

Dynamic learning of individual-level suicidal ideation trajectories to enhance mental health care.

There has recently been an increase in ongoing patient-report routine outcome monitoring for individuals within clinical care, which has corresponded to increased longitudinal information about an individual. However, many models that are aimed at clinical practice have difficulty fully incorporating this information. This is in part due to the difficulty in dealing with the irregularly time-spaced observations that are common in clinical data. Consequently, we built individual-level continuous-time trajectory models of suicidal ideation for a clinical population (N = 585) with data collected via a digital platform. We demonstrate how such models predict an individual's level and variability of future suicide ideation, with implications for the frequency that individuals may need to be observed. These individual-level predictions provide a more personalised understanding than other predictive methods and have implications for enhanced measurement-based care.

The temporal dependencies between social, emotional and physical health factors in young people receiving mental healthcare: a dynamic Bayesian network analysis.

AIMS: The needs of young people attending mental healthcare can be complex and often span multiple domains (e.g., social, emotional and physical health factors). These factors often complicate treatment approaches and contribute to poorer outcomes in youth mental health. We aimed to identify how these factors interact over time by modelling the temporal dependencies between these transdiagnostic social, emotional and physical health factors among young people presenting for youth mental healthcare. METHODS: Dynamic Bayesian networks were used to examine the relationship between mental health factors across multiple domains (social and occupational function, self-harm and suicidality, alcohol and substance use, physical health and psychiatric syndromes) in a longitudinal cohort of 2663 young people accessing youth mental health services. Two networks were developed: (1) 'initial network', that shows the conditional dependencies between factors at first presentation, and a (2) 'transition network', how factors are dependent longitudinally. RESULTS: The 'initial network' identified that childhood disorders tend to precede adolescent depression which itself was associated with three distinct pathways or illness trajectories; (1) anxiety disorder; (2) bipolar disorder, manic-like experiences, circadian disturbances and psychosis-like experiences; (3) self-harm and suicidality to alcohol and substance use or functioning. The 'transition network' identified that over time social and occupational function had the largest effect on self-harm and suicidality, with direct effects on ideation (relative risk [RR], 1.79; CI, 1.59-1.99) and self-harm (RR, 1.32; CI, 1.22-1.41), and an indirect effect on attempts (RR, 2.10; CI, 1.69-2.50). Suicide ideation had a direct effect on future suicide attempts (RR, 4.37; CI, 3.28-5.43) and self-harm (RR, 2.78; CI, 2.55-3.01). Alcohol and substance use, physical health and psychiatric syndromes (e.g., depression and anxiety, at-risk mental states) were independent domains whereby all direct effects remained within each domain over time. CONCLUSIONS: This study identified probable temporal dependencies between domains, which has causal interpretations, and therefore can provide insight into their differential role over the course of illness. This work identified social, emotional and physical health factors that may be important early intervention and prevention targets. Improving social and occupational function may be a critical target due to its impacts longitudinally on self-harm and suicidality. The conditional independence of alcohol and substance use supports the need for specific interventions to target these comorbidities.

Predicting the HMA-LMA Status in Marine Sponges by Machine Learning.

The dichotomy between high microbial abundance (HMA) and low microbial abundance (LMA) sponges has been observed in sponge-microbe symbiosis, although the extent of this pattern remains poorly unknown. We characterized the differences between the microbiomes of HMA (n = 19) and LMA (n = 17) sponges (575 specimens) present in the Sponge Microbiome Project. HMA sponges were associated with richer and more diverse microbiomes than LMA sponges, as indicated by the comparison of alpha diversity metrics. Microbial community structures differed between HMA and LMA sponges considering Operational Taxonomic Units (OTU) abundances and across microbial taxonomic levels, from phylum to species. The largest proportion of microbiome variation was explained by the host identity. Several phyla, classes, and OTUs were found differentially abundant in either group, which were considered "HMA indicators" and "LMA indicators." Machine learning algorithms (classifiers) were trained to predict the HMA-LMA status of sponges. Among nine different classifiers, higher performances were achieved by Random Forest trained with phylum and class abundances. Random Forest with optimized parameters predicted the HMA-LMA status of additional 135 sponge species (1,232 specimens) without a priori knowledge. These sponges were grouped in four clusters, from which the largest two were composed of species consistently predicted as HMA (n = 44) and LMA (n = 74). In summary, our analyses shown distinct features of the microbial communities associated with HMA and LMA sponges. The prediction of the HMA-LMA status based on the microbiome profiles of sponges demonstrates the application of machine learning to explore patterns of host-associated microbial communities.