# Diffusion Transformers for Imputation: Statistical Efficiency and Uncertainty Quantification

arXiv: https://arxiv.org/abs/2510.02216 · HTML: https://mlsanity.com/paper/2510.02216/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Flow matching, time series and science, one of 14 directions in Diffusion models.
- Builds on 38 of its 71 references that are in the map.
- First posted on arXiv 2 Oct 2025.

## Placed in

- Diffusion models / [Flow matching, time series and science](https://mlsanity.com/diffusion/flow-matching-time-series-and-science/)

## Builds on (most cited first, 30 of 38)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [TimesNet: Temporal 2D-Variation Modeling for General Time Series Analysis](https://mlsanity.com/paper/2210.02186/) (2022)
- [CSDI: Conditional Score-based Diffusion Models for Probabilistic Time Series Imputation](https://mlsanity.com/paper/2107.03502/) (2021)
- [Convex Optimization: Algorithms and Complexity](https://mlsanity.com/paper/1405.4980/) (2014)
- [Recurrent Neural Networks for Multivariate Time Series with Missing Values](https://mlsanity.com/paper/1606.01865/) (2016)
- [Sampling is as easy as learning the score: theory for diffusion models with minimal data assumptions](https://mlsanity.com/paper/2209.11215/) (2022)
- [GAIN: Missing Data Imputation using Generative Adversarial Nets](https://mlsanity.com/paper/1806.02920/) (2018)
- [BRITS: Bidirectional Recurrent Imputation for Time Series](https://mlsanity.com/paper/1805.10572/) (2018)
- [Nearly d-Linear Convergence Bounds for Diffusion Models via Stochastic Localization](https://mlsanity.com/paper/2308.03686/) (2023)
- [Unsupervised Representation Learning for Time Series with Temporal Neighborhood Coding](https://mlsanity.com/paper/2106.00750/) (2021)
- [Diffusion-based Time Series Imputation and Forecasting with Structured State Space Models](https://mlsanity.com/paper/2208.09399/) (2022)
- [Score Approximation, Estimation and Distribution Recovery of Diffusion Models on Low-Dimensional Data](https://mlsanity.com/paper/2302.07194/) (2023)
- [GP-VAE: Deep Probabilistic Time Series Imputation](https://mlsanity.com/paper/1907.04155/) (2019)
- [SAITS: Self-Attention-based Imputation for Time Series](https://mlsanity.com/paper/2202.08516/) (2022)
- [Diffusion Models are Minimax Optimal Distribution Estimators](https://mlsanity.com/paper/2303.01861/) (2023)
- [Filling the G_ap_s: Multivariate Time Series Imputation by Graph Neural Networks](https://mlsanity.com/paper/2108.00298/) (2021)
- [Estimating Missing Data in Temporal Data Streams Using Multi-directional Recurrent Neural Networks](https://mlsanity.com/paper/1711.08742/) (2017)
- [Diffusion models for missing value imputation in tabular data](https://mlsanity.com/paper/2210.17128/) (2022)
- [Accelerating Convergence of Score-Based Diffusion Models, Provably](https://mlsanity.com/paper/2403.03852/) (2024)
- [Mat'ern Gaussian Processes on Graphs](https://mlsanity.com/paper/2010.15538/) (2020)
- [PriSTI: A Conditional Diffusion Framework for Spatiotemporal Imputation](https://mlsanity.com/paper/2302.09746/) (2023)
- [Unveil Conditional Diffusion Models with Classifier-free Guidance: A Sharp Statistical Theory](https://mlsanity.com/paper/2403.11968/) (2024)
- [Score-based Diffusion Models via Stochastic Differential Equations -- a Technical Tutorial](https://mlsanity.com/paper/2402.07487/) (2024)
- [Deep Learning for Multivariate Time Series Imputation: A Survey](https://mlsanity.com/paper/2402.04059/) (2024)
- [MissDiff: Training Diffusion Models on Tabular Data with Missing Values](https://mlsanity.com/paper/2307.00467/) (2023)
- [Deep Networks as Denoising Algorithms: Sample-Efficient Learning of Diffusion Models in High-Dimensional Graphical Models](https://mlsanity.com/paper/2309.11420/) (2023)
- [Time Series Data Imputation: A Survey on Deep Learning Approaches](https://mlsanity.com/paper/2011.11347/) (2020)
- [Uncertainty-Aware Variational-Recurrent Imputation Network for Clinical Time Series](https://mlsanity.com/paper/2003.00662/) (2020)

## Abstract (arXiv)

Imputation methods play a critical role in enhancing the quality of practical time-series data, which often suffer from pervasive missing values. Recently, diffusion-based generative imputation methods have demonstrated remarkable success compared to autoregressive and conventional statistical approaches. Despite their empirical success, the theoretical understanding of how well diffusion-based models capture complex spatial and temporal dependencies between the missing values and observed ones remains limited. Our work addresses this gap by investigating the statistical efficiency of conditional diffusion transformers for imputation and quantifying the uncertainty in missing values. Specifically, we derive statistical sample complexity bounds based on a novel approximation theory for conditional score functions using transformers, and, through this, construct tight confidence regions for missing values. Our findings also reveal that the efficiency and accuracy of imputation are significantly influenced by the missing patterns. Furthermore, we validate these theoretical insights through simulation and propose a mixed-masking training strategy to enhance the imputation performance.