Large Language Models for Missing Data Imputation: Understanding Behavior, Hallucination Effects, and Control Mechanisms

TL;DR

This paper systematically benchmarks large language models for missing data imputation in tabular datasets, revealing their strengths in semantic understanding and highlighting trade-offs with computational costs compared to traditional methods.

Contribution

It provides the first large-scale, comprehensive benchmarking of LLMs for data imputation across diverse datasets and missingness mechanisms, with insights into their behavior and limitations.

Findings

LLMs outperform traditional methods on real-world datasets.

Traditional methods like MICE excel on synthetic datasets.

LLMs incur higher computational costs and monetary expenses.

Abstract

Data imputation is a cornerstone technique for handling missing values in real-world datasets, which are often plagued by missingness. Despite recent progress, prior studies on Large Language Models-based imputation remain limited by scalability challenges, restricted cross-model comparisons, and evaluations conducted on small or domain-specific datasets. Furthermore, heterogeneous experimental protocols and inconsistent treatment of missingness mechanisms (MCAR, MAR, and MNAR) hinder systematic benchmarking across methods. This work investigates the robustness of Large Language Models for missing data imputation in tabular datasets using a zero-shot prompt engineering approach. To this end, we present a comprehensive benchmarking study comparing five widely used LLMs against six state-of-the-art imputation baselines. The experimental design evaluates these methods across 29 datasets (including nine synthetic datasets) under MCAR, MAR, and MNAR mechanisms, with missing rates of up to 20\%. The results demonstrate that leading LLMs, particularly Gemini 3.0 Flash and Claude 4.5 Sonnet, consistently achieve superior performance on real-world open-source datasets compared to traditional methods. However, this advantage appears to be closely tied to the models' prior exposure to domain-specific patterns learned during pre-training on internet-scale corpora. In contrast, on synthetic datasets, traditional methods such as MICE outperform LLMs, suggesting that LLM effectiveness is driven by semantic context rather than purely statistical reconstruction. Furthermore, we identify a clear trade-off: while LLMs excel in imputation quality, they incur significantly higher computational time and monetary costs. Overall, this study provides a large-scale comparative analysis, positioning LLMs as promising semantics-driven imputers for complex tabular data.