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The COVID-19 pandemic has highlighted the importance of in-silico epidemiological modelling in predicting the dynamics of infectious diseases to inform health policy and decision makers about suitable prevention and containment strategies. Work in this setting involves solving challenging inference and control problems in individual-based models of ever increasing complexity. Here we discuss recent breakthroughs in machine learning, specifically in simulation-based inference, and explore its potential as a novel venue for model calibration to support the design and evaluation of public health interventions. To further stimulate research, we are developing software interfaces that turn two cornerstone COVID-19 and malaria epidemiology models COVID-sim, (https://github.com/mrc-ide/covid-sim/) and OpenMalaria (https://github.com/SwissTPH/openmalaria) into probabilistic programs, enabling efficient interpretable Bayesian inference within those simulators.
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Scientists and engineers employ stochastic numerical simulators to model empirically observed phenomena. In contrast to purely statistical models, simulators express scientific principles that provide powerful inductive biases, improve generalization to new data or scenarios and allow for fewer, more interpretable and domain-relevant parameters. Despite these advantages, tuning a simulators parameters so that its outputs match data is challenging. Simulation-based inference (SBI) seeks to identify parameter sets that a) are compatible with prior knowledge and b) match empirical observations. Importantly, SBI does not seek to recover a single best data-compatible parameter set, but rather to identify all high probability regions of parameter space that explain observed data, and thereby to quantify parameter uncertainty. In Bayesian terminology, SBI aims to retrieve the posterior distribution over the parameters of interest. In contrast to conventional Bayesian inference, SBI is also applicable when one can run model simulations, but no formula or algorithm exists for evaluating the probability of data given parameters, i.e. the likelihood. We present $texttt{sbi}$, a PyTorch-based package that implements SBI algorithms based on neural networks. $texttt{sbi}$ facilitates inference on black-box simulators for practising scientists and engineers by providing a unified interface to state-of-the-art algorithms together with documentation and tutorials.
Neural processes (NPs) constitute a family of variational approximate models for stochastic processes with promising properties in computational efficiency and uncertainty quantification. These processes use neural networks with latent variable inputs to induce predictive distributions. However, the expressiveness of vanilla NPs is limited as they only use a global latent variable, while target specific local variation may be crucial sometimes. To address this challenge, we investigate NPs systematically and present a new variant of NP model that we call Doubly Stochastic Variational Neural Process (DSVNP). This model combines the global latent variable and local latent variables for prediction. We evaluate this model in several experiments, and our results demonstrate competitive prediction performance in multi-output regression and uncertainty estimation in classification.
Methods for causal inference from observational data are an alternative for scenarios where collecting counterfactual data or realizing a randomized experiment is not possible. Adopting a stacking approach, our proposed method ParKCA combines the results of several causal inference methods to learn new causes in applications with some known causes and many potential causes. We validate ParKCA in two Genome-wide association studies, one real-world and one simulated dataset. Our results show that ParKCA can infer more causes than existing methods.
We present discrete-event simulation models of the operations of primary health centres (PHCs) in the Indian context. Our PHC simulation models incorporate four types of patients seeking medical care: outpatients, inpatients, childbirth cases, and patients seeking antenatal care. A generic modelling approach was adopted to develop simulation models of PHC operations. This involved developing an archetype PHC simulation, which was then adapted to represent two other PHC configurations, differing in numbers of resources and types of services provided, encountered during PHC visits. A model representing a benchmark configuration conforming to government-mandated operational guidelines, with demand estimated from disease burden data and service times closer to international estimates (higher than observed), was also developed. Simulation outcomes for the three observed configurations indicate negligible patient waiting times and low resource utilisation values at observed patient demand estimates. However, simulation outcomes for the benchmark configuration indicated significantly higher resource utilisation. Simulation experiments to evaluate the effect of potential changes in operational patterns on reducing the utilisation of stressed resources for the benchmark case were performed. Our analysis also motivated the development of simple analytical approximations of the average utilisation of a server in a queueing system with characteristics similar to the PHC doctor/patient system. Our study represents the first step in an ongoing effort to establish the computational infrastructure required to analyse public health operations in India, and can provide researchers in other settings with hierarchical health systems a template for the development of simulation models of their primary healthcare facilities.
We consider problems in which a system receives external emph{perturbations} from time to time. For instance, the system can be a train network in which particular lines are repeatedly disrupted without warning, having an effect on passenger behavior. The goal is to predict changes in the behavior of the system at particular points of interest, such as passenger traffic around stations at the affected rails. We assume that the data available provides records of the system functioning at its natural regime (e.g., the train network without disruptions) and data on cases where perturbations took place. The inference problem is how information concerning perturbations, with particular covariates such as location and time, can be generalized to predict the effect of novel perturbations. We approach this problem from the point of view of a mapping from the counterfactual distribution of the system behavior without disruptions to the distribution of the disrupted system. A variant on emph{distribution regression} is developed for this setup.
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