Neural Information Processing Systems http://nips.cc/

Neural Information Processing Systems http://nips.cc/

--This paper presents a multitask learning approach based on long-short-term memory (LSTM) networks for the joint prediction of arboviral outbreaks and case counts of dengue, chikungunya, and Zika in Recife, Brazil. Leveraging historical public health data from DataSUS (2017-2023), the proposed model concurrently performs binary classification (outbreak detection) and regression (case forecasting) tasks. A sliding window strategy was adopted to construct temporal features using varying input lengths (60, 90, and 120 days), with hyperparameter optimization carried out using Keras T uner . Model evaluation used time series cross-validation for robustness and a held-out test from 2023 for generalization assessment. The results show that longer windows improve dengue regression accuracy, while classification performance peaked at intermediate windows, suggesting an optimal trade-off between sequence length and generalization. The multitask architecture delivers competitive performance across diseases and tasks, demonstrating the feasibility and advantages of unified modeling strategies for scalable epidemic forecasting in data-limited public health scenarios.

In this work, we integrate the predictive capabilities of compartmental disease dynamics models with machine learning ability to analyze complex, high-dimensional data and uncover patterns that conventional models may overlook. Specifically, we present a proof of concept demonstrating the application of data-driven methods and deep neural networks to a recently introduced SIR-type model with social features, including a saturated incidence rate, to improve epidemic prediction and forecasting. Our results show that a robust data augmentation strategy trough suitable data-driven models can improve the reliability of Feed-Forward Neural Networks (FNNs) and Nonlinear Autoregressive Networks (NARs), making them viable alternatives to Physics-Informed Neural Networks (PINNs). This approach enhances the ability to handle nonlinear dynamics and offers scalable, data-driven solutions for epidemic forecasting, prioritizing predictive accuracy over the constraints of physics-based models. Numerical simulations of the post-lockdown phase of the COVID-19 epidemic in Italy and Spain validate our methodology.

Tuberculosis (TB) remains a formidable global health challenge, driven by complex spatiotemporal transmission dynamics and influenced by factors such as population mobility and behavioral changes. We propose an Epidemic-Guided Deep Learning (EGDL) approach that fuses mechanistic epidemiological principles with advanced deep learning techniques to enhance early warning systems and intervention strategies for TB outbreaks. Our framework is built upon a networked Susceptible-Infectious-Recovered (SIR) model augmented with a saturated incidence rate and graph Laplacian diffusion, capturing both long-term transmission dynamics and region-specific population mobility patterns. Compartmental model parameters are rigorously estimated using Bayesian inference via the Markov Chain Monte Carlo (MCMC) approach. Theoretical analysis leveraging the comparison principle and Green's formula establishes global stability properties of the disease-free and endemic equilibria. Building on these epidemiological insights, we design two forecasting architectures, EGDL-Parallel and EGDL-Series, that integrate the mechanistic outputs of the networked SIR model within deep neural networks. This integration mitigates the overfitting risks commonly encountered in data-driven methods and filters out noise inherent in surveillance data, resulting in reliable forecasts of real-world epidemic trends. Experiments conducted on TB incidence data from 47 prefectures in Japan demonstrate that our approach delivers robust and accurate predictions across multiple time horizons (short to medium-term forecasts). Additionally, incorporating uncertainty quantification through conformal prediction enhances the model's practical utility for guiding targeted public health interventions.

When an individual reports a negative interaction with some system, how can their personal experience be contextualized within broader patterns of system behavior? We study the incident database problem, where individual reports of adverse events arrive sequentially, and are aggregated over time. In this work, our goal is to identify whether there are subgroups--defined by any combination of relevant features--that are disproportionately likely to experience harmful interactions with the system. We formalize this problem as a sequential hypothesis test, and identify conditions on reporting behavior that are sufficient for making inferences about disparities in true rates of harm across subgroups. We show that algorithms for sequential hypothesis tests can be applied to this problem with a standard multiple testing correction. We then demonstrate our method on real-world datasets, including mortgage decisions and vaccine side effects; on each, our method (re-)identifies subgroups known to experience disproportionate harm using only a fraction of the data that was initially used to discover them.

Observational studies of recurrent event rates are common in biomedical statistics. Broadly, the goal is to estimate differences in event rates under two treatments within a defined target population over a specified followup window. Estimation with observational claims data is challenging because while membership in the target population is defined in terms of eligibility criteria, treatment is rarely assigned exactly at the time of eligibility. Ad-hoc solutions to this timing misalignment, such as assigning treatment at eligibility based on subsequent assignment, incorrectly attribute prior event rates to treatment - resulting in immortal risk bias. Even if eligibility and treatment are aligned, a terminal event process (e.g. death) often stops the recurrent event process of interest. Both processes are also censored so that events are not observed over the entire followup window. Our approach addresses misalignment by casting it as a treatment switching problem: some patients are on treatment at eligibility while others are off treatment but may switch to treatment at a specified time - if they survive long enough. We define and identify an average causal effect of switching under specified causal assumptions. Estimation is done using a g-computation framework with a joint semiparametric Bayesian model for the death and recurrent event processes. Computing the estimand for various switching times allows us to assess the impact of treatment timing. We apply the method to contrast hospitalization rates under different opioid treatment strategies among patients with chronic back pain using Medicare claims data.

Within epidemiological modeling, the majority of analyses assume a single epidemic process for generating ground-truth data. However, this assumed data generation process can be unrealistic, since data sources for epidemics are often aggregated across geographic regions and communities. As a result, state-of-the-art models for estimating epidemiological parameters, e.g.~transmission rates, can be inappropriate when faced with complex systems. Our work empirically demonstrates some limitations of applying epidemiological models to aggregated datasets. We generate three complex outbreak scenarios by combining incidence curves from multiple epidemics that are independently simulated via SEIR models with different sets of parameters. Using these scenarios, we assess the robustness of a state-of-the-art Bayesian inference method that estimates the epidemic trajectory from viral load surveillance data. We evaluate two data-generating models within this Bayesian inference framework: a simple exponential growth model and a highly flexible Gaussian process prior model. Our results show that both models generate accurate transmission rate estimates for the combined incidence curve at the cost of generating biased estimates for each underlying epidemic, reflecting highly heterogeneous underlying population dynamics. The exponential growth model, while interpretable, is unable to capture the complexity of the underlying epidemics. With sufficient surveillance data, the Gaussian process prior model captures the shape of complex trajectories, but is imprecise for periods of low data coverage. Thus, our results highlight the potential pitfalls of neglecting complexity and heterogeneity in the data generation process, which can mask underlying location- and population-specific epidemic dynamics.

While a typical supervised learning framework assumes that the inputs and the outputs are measured at the same levels of granularity, many applications, including global mapping of disease, only have access to outputs at a much coarser level than that of the inputs. Aggregation of outputs makes generalization to new inputs much more difficult. We consider an approach to this problem based on variational learning with a model of output aggregation and Gaussian processes, where aggregation leads to intractability of the standard evidence lower bounds. We propose new bounds and tractable approximations, leading to improved prediction accuracy and scalability to large datasets, while explicitly taking uncertainty into account. We develop a framework which extends to several types of likelihoods, including the Poisson model for aggregated count data. We apply our framework to a challenging and important problem, the fine-scale spatial modelling of malaria incidence, with over 1 million observations.

While a typical supervised learning framework assumes that the inputs and the outputs are measured at the same levels of granularity, many applications, including global mapping of disease, only have access to outputs at a much coarser level than that of the inputs. Aggregation of outputs makes generalization to new inputs much more difficult. We consider an approach to this problem based on variational learning with a model of output aggregation and Gaussian processes, where aggregation leads to intractability of the standard evidence lower bounds. We propose new bounds and tractable approximations, leading to improved prediction accuracy and scalability to large datasets, while explicitly taking uncertainty into account. We develop a framework which extends to several types of likelihoods, including the Poisson model for aggregated count data. We apply our framework to a challenging and important problem, the fine-scale spatial modelling of malaria incidence, with over 1 million observations.