Prior Knowledge-enhanced Spatio-temporal Epidemic Forecasting

Epidemic forecasting models typically rely on surveillance data reported over administrative regions, treating them as atomic units, thereby obscuring sub-regional spatial structure that shapes disease dynamics. We introduce a spatially structured multimodal epidemic forecasting setting that integrates region-level temporal surveillance data with spatially localized auxiliary signals that are misaligned in resolution and structure, reflecting realistic public health reporting constraints. Building on this formulation, we propose M-SPICE (Multimodal SPatIal Context for Epidemic Forecasting), a structure-aware spatiotemporal forecasting framework that performs joint reasoning over temporal disease dynamics and spatial context via attention-based multimodal fusion, allowing spatial signals to selectively condition temporal representations across forecast horizons. We evaluate our approach on real-world COVID-19, influenza, and influenza-like illness (ILI) forecasting tasks under realistic real-time evaluation protocols. Across all forecasting settings, our method consistently outperforms state-of-the-art multivariate time-series, multimodal, and epidemiological forecasting baselines while maintaining strong probabilistic forecasting performance. Finally, interpretability analyses reveal when, where, and how spatial signals are leveraged, highlighting settings in which purely temporal, region-aggregated models are most likely to fail.

Accurate epidemic forecasting is crucial for public health response, resource allocation, and outbreak intervention, but remains difficult with sparse, noisy, and highly non-stationary data. Because epidemics unfold across interacting regions, spatiotemporal methods are natural candidates for improving forecasts. Despite growing interest in spatial information, no standardized benchmark exists, and current evaluations often use simple chronological train-test splits that do not reflect real-time forecasting practice. We address this gap with SpatialEpiBench, a challenging benchmark for spatiotemporal epidemic forecasting in realistic public-health settings. SpatialEpiBench includes 11 epidemic datasets with standardized rolling evaluations and outbreak-specific metrics. We evaluate adjacency-informed forecasting models with widely used epidemic priors that adapt general models to epidemiology, but find that most methods underperform a simple last-value baseline from 1 day to 1 month ahead, even during outbreaks and with these priors. We identify three major failure modes: (1) poor outbreak anticipation, (2) difficulty handling sparsity and noise, and (3) limited utility of common geographic adjacency for epidemiological spatial information. We release benchmark data, code, and instructions at https://github.com/Rachel-Lyu/SpatialEpiBench to support development of operationally useful epidemic forecasting models.

Accurate and reliable forecasting of epidemic incidences is critical for public health preparedness, yet it remains a challenging task due to complex nonlinear temporal dependencies and heterogeneous spatial interactions. Often, point forecasts generated by spatiotemporal models are unreliable in assigning uncertainty to future epidemic events. Probabilistic forecasting of epidemics is therefore crucial for providing the best or worst-case scenarios rather than a simple, often inaccurate, point estimate. We present deep spatiotemporal engression methods to generate accurate and reliable probabilistic forecasts on low-frequency epidemic datasets. The proposed methods act as distributional lenses, and out-of-sample probabilistic forecasts are generated by sampling from the trained models. Our frameworks encapsulate lightweight deep generative architectures, wherein uncertainty is quantified endogenously, driven by a pre-additive noise component during model construction. We establish geometric ergodicity and asymptotic stationarity of the spatiotemporal engression processes under mild assumptions on the network weights and pre-additive noise process. Comprehensive evaluations across six epidemiological datasets over three forecast horizons demonstrate that the proposal consistently outperforms several temporal and spatiotemporal benchmarks in both point and probabilistic forecasting. Additionally, we explore the explainability of the proposal to enhance the models' practical application for informed, timely public health interventions.