Physics-Informed Neural Network (PINN) is a deep learning framework that integrates the governing equations underlying data into a loss function. In this study, we consider the problem of estimating state variables and parameters in epidemiological models governed by ordinary differential equations using PINNs. In practice, not all trajectory data corresponding to the population described by models can be measured. Learning PINNs to estimate the unmeasured state variables and epidemiological parameters using partial measurements is challenging. Accordingly, we introduce the concept of algebraic observability of the state variables. Specifically, we propose augmenting the unmeasured data based on algebraic observability analysis. The validity of the proposed method is demonstrated through numerical experiments under three scenarios in the context of epidemiological modelling. Specifically, given noisy and partial measurements, the accuracy of unmeasured states and parameter estimation of the proposed method is shown to be higher than that of the conventional methods. The proposed method is also shown to be effective in practical scenarios, such as when the data corresponding to certain variables cannot be reconstructed from the measurements.

Many of society's most pressing challenges, from pandemic response to supply chain disruptions to climate adaptation, emerge from the collective behavior of millions of autonomous agents making decisions over time. Large Population Models (LPMs) offer an approach to understand these complex systems by simulating entire populations with realistic behaviors and interactions at unprecedented scale. LPMs extend traditional modeling approaches through three key innovations: computational methods that efficiently simulate millions of agents simultaneously, mathematical frameworks that learn from diverse real-world data streams, and privacy-preserving communication protocols that bridge virtual and physical environments. This allows researchers to observe how agent behavior aggregates into system-level outcomes and test interventions before real-world implementation. While current AI advances primarily focus on creating "digital humans" with sophisticated individual capabilities, LPMs develop "digital societies" where the richness of interactions reveals emergent phenomena. By bridging individual agent behavior and population-scale dynamics, LPMs offer a complementary path in AI research illuminating collective intelligence and providing testing grounds for policies and social innovations before real-world deployment. We discuss the technical foundations and some open problems here. LPMs are implemented by the AgentTorch framework (github.com/AgentTorch/AgentTorch)

In this study, we focus on developing efficient calibration methods via Bayesian decision-making for the family of compartmental epidemiological models. The existing calibration methods usually assume that the compartmental model is cheap in terms of its output and gradient evaluation, which may not hold in practice when extending them to more general settings. Therefore, we introduce model calibration methods based on a "graybox" Bayesian optimization (BO) scheme, more efficient calibration for general epidemiological models. This approach uses Gaussian processes as a surrogate to the expensive model, and leverages the functional structure of the compartmental model to enhance calibration performance. Additionally, we develop model calibration methods via a decoupled decision-making strategy for BO, which further exploits the decomposable nature of the functional structure. The calibration efficiencies of the multiple proposed schemes are evaluated based on various data generated by a compartmental model mimicking real-world epidemic processes, and real-world COVID-19 datasets. Experimental results demonstrate that our proposed graybox variants of BO schemes can efficiently calibrate computationally expensive models and further improve the calibration performance measured by the logarithm of mean square errors and achieve faster performance convergence in terms of BO iterations. We anticipate that the proposed calibration methods can be extended to enable fast calibration of more complex epidemiological models, such as the agent-based models.

Recent pandemics have highlighted vulnerabilities in our global economic systems, especially supply chains. Possible future pandemic raises a dilemma for businesses owners between short-term profitability and long-term supply chain resilience planning. In this study, we propose a novel agent-based simulation model integrating extended Susceptible-Infected-Recovered (SIR) epidemiological model and supply and demand economic model to evaluate supply chain resilience strategies during pandemics. Using this model, we explore a range of supply chain resilience strategies under pandemic scenarios using in silico experiments. We find that a balanced approach to supply chain resilience performs better in both pandemic and non-pandemic times compared to extreme strategies, highlighting the importance of preparedness in the form of a better supply chain resilience. However, our analysis shows that the exact supply chain resilience strategy is hard to obtain for each firm and is relatively sensitive to the exact profile of the pandemic and economic state at the beginning of the pandemic. As such, we used a machine learning model that uses the agent-based simulation to estimate a near-optimal supply chain resilience strategy for a firm. The proposed model offers insights for policymakers and businesses to enhance supply chain resilience in the face of future pandemics, contributing to understanding the trade-offs between short-term gains and long-term sustainability in supply chain management before and during pandemics.

Epidemiological compartmental models are useful for understanding infectious disease propagation and directing public health policy decisions. Calibration of these models is an important step in offering accurate forecasts of disease dynamics and the effectiveness of interventions. In this study, we present an overview of calibrating strategies that can be employed, including several optimization methods and reinforcement learning (RL). We discuss the benefits and drawbacks of these methods and highlight relevant practical conclusions from our experiments. Optimization methods iteratively adjust the parameters of the model until the model output matches the available data, whereas RL uses trial and error to learn the optimal set of parameters by maximizing a reward signal. Finally, we discuss how the calibration of parameters of epidemiological compartmental models is an emerging field that has the potential to improve the accuracy of disease modeling and public health decision-making. Further research is needed to validate the effectiveness and scalability of these approaches in different epidemiological contexts. All codes and resources are available on https://github.com/Nikunj-Gupta/

Epidemiological models must be calibrated to ground truth for downstream tasks such as producing forward projections or running what-if scenarios. The meaning of calibration changes in case of a stochastic model since output from such a model is generally described via an ensemble or a distribution. Each member of the ensemble is usually mapped to a random number seed (explicitly or implicitly). With the goal of finding not only the input parameter settings but also the random seeds that are consistent with the ground truth, we propose a class of Gaussian process (GP) surrogates along with an optimization strategy based on Thompson sampling. This Trajectory Oriented Optimization (TOO) approach produces actual trajectories close to the empirical observations instead of a set of parameter settings where only the mean simulation behavior matches with the ground truth.

Infectious diseases, either emerging or long-lasting, place numerous people at risk and bring heavy public health burdens worldwide. In the process against infectious diseases, predicting the epidemic risk by modeling the disease transmission plays an essential role in assisting with preventing and controlling disease transmission in a more effective way. In this paper, we systematically describe how machine learning can play an essential role in quantitatively characterizing disease transmission patterns and accurately predicting infectious disease risks. First, we introduce the background and motivation of using machine learning for infectious disease risk prediction. Next, we describe the development and components of various machine learning models for infectious disease risk prediction. Specifically, existing models fall into three categories: Statistical prediction, data-driven machine learning, and epidemiology-inspired machine learning. Subsequently, we discuss challenges encountered when dealing with model inputs, designing task-oriented objectives, and conducting performance evaluation. Finally, we conclude with a discussion of open questions and future directions.

The human race is facing one of the most meaningful public health emergencies in the modern era caused by the COVID-19 pandemic. This pandemic introduced various challenges, from lock-downs with significant economic costs to fundamentally altering the way of life for many people around the world. The battle to understand and control the virus is still at its early stages yet meaningful insights have already been made. The uncertainty of why some patients are infected and experience severe symptoms, while others are infected but asymptomatic, and others are not infected at all, makes managing this pandemic very challenging. Furthermore, the development of treatments and vaccines relies on knowledge generated from an ever evolving and expanding information space. Given the availability of digital data in the modern era, artificial intelligence (AI) is a meaningful tool for addressing the various challenges introduced by this unexpected pandemic. Some of the challenges include: outbreak prediction, risk modeling including infection and symptom development, testing strategy optimization, drug development, treatment repurposing, vaccine development, and others.

Machine learning (ML) formalizes the problem of getting computers to learn from experience as optimization of performance according to some metric(s) on a set of data examples. This is in contrast to requiring behaviour specified in advance (e.g. by hard-coded rules). Formalization of this problem has enabled great progress in many applications with large real-world impact, including translation, speech recognition, self-driving cars, and drug discovery. But practical instantiations of this formalism make many assumptions - for example, that data are i.i.d.: independent and identically distributed - whose soundness is seldom investigated. And in making great progress in such a short time, the field has developed many norms and ad-hoc standards, focused on a relatively small range of problem settings. As applications of ML, particularly in artificial intelligence (AI) systems, become more pervasive in the real world, we need to critically examine these assumptions, norms, and problem settings, as well as the methods that have become de-facto standards. There is much we still do not understand about how and why deep networks trained with stochastic gradient descent are able to generalize as well as they do, why they fail when they do, and how they will perform on out-of-distribution data. In this thesis I cover some of my work towards better understanding deep net generalization, identify several ways assumptions and problem settings fail to generalize to the real world, and propose ways to address those failures in practice.

In this work we present a framework which may transform research and praxis in epidemic planning. Introduced in the context of the ongoing COVID-19 pandemic, we provide a concrete demonstration of the way algorithms may learn from epidemiological models to scale their value for epidemic preparedness. Our contributions in this work are two fold: 1) a novel platform which makes it easy for decision making stakeholders to interact with epidemiological models and algorithms developed within the Machine learning community, and 2) the release of this work under the Apache-2.0 The objective of this paper is not to look closely at any particular models or algorithms, but instead to highlight how they can be coupled and shared to empower evidence-based decision making. This work provides a concrete example of a new paradigm to inform decision support processes in a public health context.