Causal Effect Variational Transformer for Public Health Measures and COVID-19 Infection Cluster Analysis

Recent research increasingly integrates causal inference into deep learning models to enhance the explainability and robustness of medical applications. However, data scarcity remains a fundamental challenge due to privacy constraints and the high cost of data collection. This issue, compounded by complex variable dependencies and unobserved latent confounders, hinders the reliable estimation of causal effects. To address these challenges, we collect two real-world COVID-19 infection cluster datasets, including public health measures, from distinct distributions in collaboration with local governments, a medical university, and a hospital. We also propose a cut-off augmentation method that generates diverse feature-label pairs by slicing time-series sequences at different observation windows, effectively simulating partial observations common in real-world settings. We further introduce the Causal Effect Variational Transformer (CEVT), a Transformer-based model that captures temporal structure and addresses the difficulty of causal estimation under scarce data, complex dependencies, and latent confounding by modeling multiple treatments through an iterative conditioning mechanism. We validate the causal modeling capability of CEVT on synthetic datasets and demonstrate that, on two distinct COVID-19 datasets, it consistently outperforms baselines in infection prediction. Notably, the causal effects estimated by CEVT converge with findings from medical studies on infection control, reinforcing its reliability and underscoring its potential to inform public health decision-making.