Geospatial health disproportionality remains a critical public health concern, as communities face heterogeneous illness risks due to varying exposures to adverse socioeconomic and environmental conditions. While statistical models have been adopted to identify risk factors, studies that account for the complex, non-linear dependencies and spatial regularities inherent in comorbid disease patterns are underdeveloped. In this work, we propose a novel spatially regularized variational autoencoder (VAE) to characterize and map the geospatial disproportion of childhood comorbidity in West Africa, focusing on diarrhea, fever, and acute respiratory infection (ARI). To model dependence between these conditions, this study integrates a bivariate Gumbel copula into the VAE framework, enabling flexible modeling of asymmetric dependence and quantification of joint and conditional morbidity risks. Additionally, covariate effects within the framework were quantified to facilitate epidemiological interpretation of risk factors. The proposed method was benchmarked against commonly used methods and applied to characterize comorbidity in West Africa using the Demographic and Health Survey data. Findings reveal pronounced spatial heterogeneity in the likelihood of comorbidity among West African children, with the strongest co-occurrence observed between fever and ARI. Household wealth, maternal education, and access to improved water sources were associated with the likelihood of comorbidity. These patterns highlight high-risk areas and underscore the need for targeted, location-specific public health interventions.

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