Order-Agnostic Autoregressive Modelling with Missing Data

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.

Missing data frequently arises across diverse domains, including time-series and image domains. In the real world, missing occurrences often depend on the unobservable values themselves, which are referred to as Missing Not at Random (MNAR). In this work, we introduce the Missing Pattern Recognized Diffusion Imputation Model (PRDIM), a novel framework that explicitly captures the missing pattern and precisely imputes unobserved values. PRDIM iteratively maximizes the likelihood of the joint distribution for observed values and missing mask under an Expectation-Maximization (EM) algorithm. In this sense, we first employ a pattern recognizer, which approximates the underlying missing pattern and provides guidance during every inference toward more plausible imputations with respect to the missing information. Through extensive experiments, we demonstrate that PRDIM consistently achieves strong imputation performance under MNAR settings across multiple data modalities.

Diffusion models have emerged as powerful generative approaches for missing-data imputation, yet most existing methods operate directly in data space and degrade when training data are heavily incomplete. We investigate whether shifting diffusion to a learned latent representation improves robustness under missing-completely-at-random (MCAR) corruption. To this end, we propose a two-stage framework: a robust VAE-based imputer first learns compact semantic features from incomplete observations, and a diffusion model is then trained in the resulting latent space. Across training missing rates, we perform a controlled comparison against pixel-space diffusion models under the same incomplete-data setting. The latent diffusion model maintains high sample quality and remains stable up to 50% missingness, while pixel-space diffusion degrades progressively as missingness increases. For downstream imputation, latent diffusion also achieves consistently better performance than pixel-space diffusion. These findings indicate that latent-space modeling mitigates artifact amplification from zero-imputed inputs and provides a more robust generative prior for incomplete-data learning. Overall, our results support latent diffusion as a strong and practically useful alternative to pixel-space diffusion for missing-data problems.