Ashna Desai | Searcharxiv

arXiv2026

From Ecological Connectivity to Outbreak Risk: A Heterogeneous Graph Network for Epidemiological Reasoning under Sparse Spatiotemporal Data

Estimating population-level prevalence and transmission dynamics of wildlife pathogens can be challenging, partly because surveillance data is sparse, detection-driven, and unevenly sequenced. Using highly pathogenic avian influenza A/H5 clade 2.3.4.4b as a case study, we develop zooNet, a graph-based epidemiological framework that integrates mechanistic transmission simulation, metadata-driven genetic distance imputation, and spatiotemporal graph learning to reconstruct outbreak dynamics from incomplete observations. Applied to wild bird surveillance data from the United States during 2022, zooNet recovered coherent spatiotemporal structure despite intermittent detections, revealing sustained regional circulation across multiple migratory flyways. The framework consistently identified counties with ongoing transmission weeks to months before confirmed detections, including persistent activity in northeastern regions prior to documented re-emergence. These signals were detectable even in areas with sparse sequencing and irregular reporting. These results show that explicitly representing ecological processes and inferred genomic connectivity within a unified graph structure allows persistence and spatial risk structure to be inferred from detection-driven wildlife surveillance data.

q-bio.PE↗

arXiv2025

Genomic-Informed Heterogeneous Graph Learning for Spatiotemporal Avian Influenza Outbreak Forecasting

Accurate forecasting of Avian Influenza Virus (AIV) outbreaks within wild bird populations necessitates models that account for complex, multi-scale transmission patterns driven by diverse factors. While conventional spatiotemporal epidemic models are robust for human-centric diseases, they rely on spatial homophily and diffusive transmission between geographic regions. This simplification is incomplete for AIV as it neglects valuable genomic information critical for capturing dynamics like high-frequency reassortment and lineage turnover at the case level (e.g., genetic descent across regions), which are essential for understanding AIV spread. To address these limitations, we systematically formulate the AIV forecasting problem and propose a Bi-Layer genomic-aware heterogeneous graph fusion pipeline. This pipeline integrates genetic, spatial, and ecological data to achieve highly accurate outbreak forecasting. It 1) defines a multi-layered graph structure incorporating information from diverse sources and multiple layers (case and location), 2) applies cross-relation smoothing to smooth information flow across edge types, 3) performs graph fusion that preserves critical structural patterns backed by theoretical spectral guarantees, and 4) forecasts future outbreaks using an autoregressive graph sequence model to capture transmission dynamics. To support research, we release the Avian-US dataset, which provides comprehensive genetic, spatial, and ecological data on US avian influenza outbreaks. BLUE demonstrates superior performance over existing baselines, highlighting the efficacy of integrating multi-layer information for infectious disease forecasting. The code is available at: https://github.com/cruiseresearchgroup/BLUE.

cs.SI↗