Amortized Variational Inference for Logistic Regression with Missing Covariates

Missing covariates are frequently encountered in supervised learning problems, and classical methods for estimation using such data use carefully chosen imputation schemes for missing data, or likelihood approximations that lead to nonconvex $M$-estimation problems. These methods and their relatives are suitable for scenarios in which the covariate distribution is known, and more broadly, have enjoyed tremendous success in linear models. But even in basic nonlinear problems such as logistic regression in moderate dimensions, such methods can experience drastic failure modes when the covariate distribution is unknown. Motivated by the need for reliable alternatives, we consider the problem of parameter estimation in logistic regression with missing covariates. Crucially, we operate in the assumption-lean setting where the covariate distribution is unknown (but bounded). We design a stochastic approximation method that is based on $Z$-estimation with a novel monotone operator, and establish that our algorithm is computationally efficient and achieves provable signal recovery at parametric rates under the hypothesis that covariates are missing completely at random. Our theory sharply characterizes the $\ell_2^2$ risk of the estimator in terms of the missingness profile, accommodating heterogeneous observation probabilities. Importantly, it shows that our method always outperforms the de facto ``complete-case'' estimator that ignores observations with any missing data. Even in the setting with homogeneous missingness (in which each covariate is observed independently with probability $q$), our bounds exhibit intricate and nonstandard dependence on $q$ that can yield significant improvements over using only complete cases. We complement our upper bounds with new information-theoretic lower bounds that show that this intricate dependence on $q$ is fundamental in a minimax sense.

Missing data, measurement error, and population heterogeneity are pervasive challenges in analyzing data arising from modern observational studies and machine learning applications. Although these problems frequently coexist and interact, they are often treated separately in existing works. We propose a unified probabilistic framework that jointly addresses these issues utilizing deep latent variable representation. The proposed method integrates a novel hierarchical tree-routed variational autoencoder with pattern-aware latent representations and calibration-based denoising. The framework accommodates missing data mechanisms, including MCAR, MAR, and MNAR, while simultaneously learning subgroup-specific and globally shared latent structure. The introduced reconvergent routing mechanism enables selective parameters to be shared across related subpopulations, which offers flexibility as well as improved statistical efficiency. Simulation studies demonstrate substantial improvements over existing deep generative imputation approaches under complex heterogeneous missingness and measurement-error settings. The proposed framework provides a principled approach for learning from noisy and incomplete data in modern healthcare and other high-dimensional applications.

Missing data imputation remains a fundamental challenge in modern data science, especially when uncertainty quantification is essential. In this work, we propose MissBGM, an AI-powered missing data imputation method via Bayesian generative modeling that bridges the expressive flexibility of neural networks with the statistical rigor of Bayesian inference. Unlike existing methods that often focus on point estimates or treat the missingness mechanism implicitly, MissBGM explicitly and jointly models the data-generating and missingness mechanisms, providing principled posterior uncertainty over imputations rather than a single point estimate. We develop a stochastic optimization framework with alternating updates among missing values, model parameters, and latent variables until convergence. Our theoretical analysis shows that estimates of missing values from MissBGM converge consistently under mild assumptions. Empirically, we demonstrate that MissBGM achieves superior performance over traditional imputers and recent neural network-based methods across extensive experimental settings. These results establish MissBGM as a principled and scalable solution for modern missing data imputation. The code for MissBGM is open sourced at https://github.com/liuq-lab/MissBGM.