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The growing complexity of decision-making in public health and health care has motivated an increasing use of mathematical modeling. An important line of health modeling is based on stock & flow diagrams. Such modeling elevates transparency across the interdisciplinary teams responsible for most impactful models, but existing tools suffer from a number of shortcomings when used at scale. Recent research has sought to address such limitations by establishing a categorical foundation for stock & flow modeling, including the capacity to compose a pair of models through identification of common stocks and sum variables. This work supplements such efforts by contributing two new forms of composition for stock & flow diagrams. We first describe a hierarchical means of diagram composition, in which a single existing stock is replaced by a diagram featuring compatible flow structure. Our composition method offers extra flexibility by allowing a single flow in the stock being replaced to split into several flows totalling to the same overall flow rate. Secondly, to address the common need of docking a stock & flow diagram with another "upstream" diagram depicting antecedent factors, we contribute a composition approach that allows a flow out of an upstream stock in one diagram to be connected to a downstream stock in another diagram. Both of these approaches are enabled by performing colimit decomposition of stock & flow diagrams into single-stock corollas and unit flows.

Agent-based modeling is a computational dynamic modeling technique that may be less familiar to some readers. Agent-based modeling seeks to understand the behaviour of complex systems by situating agents in an environment and studying the emergent outcomes of agent-agent and agent-environment interactions. In comparison with compartmental models, agent-based models offer simpler, more scalable and flexible representation of heterogeneity, the ability to capture dynamic and static network and spatial context, and the ability to consider history of individuals within the model. In contrast, compartmental models offer faster development time with less programming required, lower computational requirements that do not scale with population, and the option for concise mathematical formulation with ordinary, delay or stochastic differential equations supporting derivation of properties of the system behaviour. In this chapter, basic characteristics of agent-based models are introduced, advantages and disadvantages of agent-based models, as compared with compartmental models, are discussed, and two example agent-based infectious disease models are reviewed.

Stock and flow diagrams are already an important tool in epidemiology, but category theory lets us go further and treat these diagrams as mathematical entities in their own right. In this chapter we use communicable disease models created with our software, StockFlow.jl, to explain the benefits of the categorical approach. We first explain the category of stock-flow diagrams and note the clear separation between the syntax of these diagrams and their semantics, demonstrating three examples of semantics already implemented in the software: ODEs, causal loop diagrams, and system structure diagrams. We then turn to two methods for building large stock-flow diagrams from smaller ones in a modular fashion: composition and stratification. Finally, we introduce the open-source ModelCollab software for diagram-based collaborative modeling. The graphical user interface of this web-based software lets modelers take advantage of the ideas discussed here without any knowledge of their categorical foundations.

Stock and flow diagrams are widely used in epidemiology to model the dynamics of populations. Although tools already exist for building these diagrams and simulating the systems they describe, we have created a new package called StockFlow, part of the AlgebraicJulia ecosystem, which uses ideas from category theory to overcome notable limitations of existing software. Compositionality is provided by the theory of decorated cospans: stock and flow diagrams can be composed to form larger ones in an intuitive way formalized by the operad of undirected wiring diagrams. Our approach also cleanly separates the syntax of stock and flow diagrams from the semantics they can be assigned. We consider semantics in ordinary differential equations, although others are possible. As an example, we explain code in StockFlow that implements a simplified version of a COVID-19 model used in Canada., Comment: In Proceedings ACT 2022, arXiv:2307.15519

The objective of this study is to predict suicidal and non-suicidal deaths from DNA methylation data using a modern machine learning algorithm. We used support vector machines to classify existing secondary data consisting of normalized values of methylated DNA probe intensities from tissues of two cortical brain regions to distinguish suicide cases from control cases. Before classification, we employed Principal component analysis (PCA) and t-distributed Stochastic Neighbor Embedding (t-SNE) to reduce the dimension of the data. In comparison to PCA, the modern data visualization method t-SNE performs better in dimensionality reduction. t-SNE accounts for the possible non-linear patterns in low-dimensional data. We applied four-fold cross-validation in which the resulting output from t-SNE was used as training data for the Support Vector Machine (SVM). Despite the use of cross-validation, the nominally perfect prediction of suicidal deaths for BA11 data suggests possible over-fitting of the model. The study also may have suffered from 'spectrum bias' since the individuals were only studied from two extreme scenarios. This research constitutes a baseline study for classifying suicidal and non-suicidal deaths from DNA methylation data. Future studies with larger sample size, while possibly incorporating methylation data from living individuals, may reduce the bias and improve the accuracy of the results.

Despite a general reduction in smoking in many areas of the developed world, it remains one of the biggest public health threats. As an alternative to tobacco, the use of electronic cigarettes (ECig) has been increased dramatically over the last decade. ECig use is hypothesized to impact smoking behavior through several pathways, not only as a means of quitting cigarettes and lowering risk of relapse, but also as both an alternative nicotine delivery device to cigarettes, as a visible use of nicotine that can lead to imitative behavior in the form of smoking, and as a gateway nicotine delivery technology that can build high levels of nicotine tolerance and pave the way for initiation of smoking. Evidence regarding the effect of ECig use on smoking behavior change remains inconclusive. To address these challenges, we built an agent-based model (ABM) of smoking and ECig use to examine the effects of ECig use on smoking behavior change. The impact of social network (SN) on the initiation of smoking and ECig use were also explored. Findings from the simulation suggest that the use of ECig generates substantially lower prevalence of current smoker (PCS), which demonstrates the potential for reducing smoking and lowering the risk of relapse. The effects of proximity-based influences within SN increases the prevalence of current ECig user (PCEU). The model also suggests the importance of improved understanding of drivers in cessation and relapse in ECig use, in light of findings that such aspects of behavior change may notably influence smoking behavior change and burden., Comment: 10 pages, SBP-BRiMS 2019

Diabetes in pregnancy (DIP) is an increasing public health priority in the Australian Capital Territory, particularly due to its impact on risk for developing Type 2 diabetes. While earlier diagnostic screening results in greater capacity for early detection and treatment, such benefits must be balanced with the greater demands this imposes on public health services. To address such planning challenges, a multi-scale hybrid simulation model of DIP was built to explore the interaction of risk factors and capture the dynamics underlying the development of DIP. The impact of interventions on health outcomes at the physiological, health service and population level is measured. Of particular central significance in the model is a compartmental model representing the underlying physiological regulation of glycemic status based on beta-cell dynamics and insulin resistance. The model also simulated the dynamics of continuous BMI evolution, glycemic status change during pregnancy and diabetes classification driven by the individual-level physiological model. We further modeled public health service pathways providing diagnosis and care for DIP to explore the optimization of resource use during service delivery. The model was extensively calibrated against empirical data., Comment: 10 pages, SBP-BRiMS 2019

Respiratory infections and chronic respiratory diseases impose a heavy health burden worldwide. Coughing is one of the most common symptoms of many such infections, and can be indicative of flare-ups of chronic respiratory diseases. Whether at a clinical or public health level, the capacity to identify bouts of coughing can aid understanding of population and individual health status. Developing health monitoring models in the context of respiratory diseases and also seasonal diseases with symptoms such as cough has the potential to improve quality of life, help clinicians and public health authorities with their decisions and decrease the cost of health services. In this paper, we investigated the ability to which a simple machine learning approach in the form of Hidden Markov Models (HMMs) could be used to classify different states of coughing using univariate (with a single energy band as the input feature) and multivariate (with a multiple energy band as the input features) binned time series using both of cough data. We further used the model to distinguish cough events from other events and environmental noise. Our Hidden Markov algorithm achieved 92% AUR (Area Under Receiver Operating Characteristic Curve) in classifying coughing events in noisy environments. Moreover, comparison of univariate with multivariate HMMs suggest a high accuracy of multivariate HMMs for cough event classifications., Comment: SBP-BRiMS 2019