Stochastic Neural Networks for Causal Inference with Missing Confounders

Unmeasured confounding is a fundamental obstacle to causal inference from observational data. Latent-variable methods address this challenge by imputing unobserved confounders, yet many lack explicit model-based identification guarantees and are difficult to extend to richer causal structures. We propose Confounder Imputation with Stochastic Neural Networks (CI-StoNet), which parameterizes the conditional structure of a causal directed acyclic graph using a stochastic neural network and imputes latent confounders via adaptive stochastic-gradient Hamiltonian Monte Carlo. Under SUTVA and overlap, and assuming that the structural components of the data-generating process are well approximated by a capacity-controlled sparse deep neural network class, we establish model identification and consistent estimation of the mean potential outcome under a fixed intervention within this class. Although the latent confounder is identifiable only up to reparameterizations that preserve the joint treatment–outcome distribution, the causal estimand is invariant across this observationally equivalent class. We further characterize the effect of overlap on estimation accuracy. Empirical results on simulated and benchmark datasets demonstrate accurate performance, and the framework extends naturally to proxy-variable and multiple-cause settings with overlap diagnostics and bootstrap-based uncertainty quantification.