Large Language Models for Missing Data Imputation: Understanding Behavior, Hallucination Effects, and Control Mechanisms
Computer Science Division, Aeronautics Institute of Technology（航空技术研究所计算机科学系）；Technology Institute, Federal University of São Paulo（圣保罗联邦大学技术学院）；University of Coimbra, CISUC/LASI – Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering（科英布拉大学）
Arthur Dantas Mangussi, Ricardo Cardoso Pereira, Ana Carolina Lorena, Pedro Henriques Abreu
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.
Georgia Institute of Technology（佐治亚理工学院）；Anonymous University（匿名大学）
Incomplete instances with various missing attributes in many real-world applications have brought challenges to the classification tasks. Missing values imputation methods are often employed to replace the missing values with substitute values. However, this process often separates the imputation and classification, which may lead to inferior performance since label information are often ignored during imputation. Moreover, traditional methods may rely on improper assumptions to initialize the missing values, whereas the unreliability of such initialization might lead to inferior performance. …
Processed data are insightful, and crude data are obtuse. A serious threat to data reliability is missing values. Such data leads to inaccurate analysis and wrong predictions. We propose an efficient technique to impute the missing value in the dataset based on correlation called FCMI (Feature Correlation based Missing Data Imputation). We have considered the correlation of the attributes of the dataset, and that is our central idea. Our proposed algorithm picks the highly correlated attributes of the dataset and uses these attributes to build a regression model whose parameters are optimized …
Missing data are ubiquitous in the era of big data and, if inadequately handled, are known to lead to biased findings and have deleterious impact on data-driven decision makings. To mitigate its impact, many missing value imputation methods have been developed. However, the fairness of these imputation methods across sensitive groups has not been studied. In this paper, we conduct the first known research on fairness of missing data imputation. By studying the performance of imputation methods in three commonly used datasets, we demonstrate that unfairness of missing value imputation widely ex…
The University of Tokyo（东京大学）；Preferred Networks（首选网络）
Missing value imputation in machine learning is the task of estimating the missing values in the dataset accurately using available information. In this task, several deep generative modeling methods have been proposed and demonstrated their usefulness, e.g., generative adversarial imputation networks. Recently, diffusion models have gained popularity because of their effectiveness in the generative modeling task in images, texts, audio, etc. To our knowledge, less attention has been paid to the investigation of the effectiveness of diffusion models for missing value imputation in tabular data…
ImputeINR: Time Series Imputation via Implicit Neural Representations for Disease Diagnosis with Missing Data
Zhejiang Key Laboratory of Accessible Perception and Intelligent Systems, College of Computer Science, Zhejiang University（浙江可感知与智能系统重点实验室，计算机科学学院，浙江大学）；The Zhejiang University-University of Illinois Urbana-Champaign Institute（浙江大学-伊利诺伊大学厄巴纳-香槟分校联合研究所）
Missing Data Multiple Imputation for Tabular Q-Learning in Online RL
Department of Statistics, Harvard University, Cambridge, United States（哈佛大学统计学系）；Department of Statistics, Stanford University, Stanford, United States（斯坦福大学统计学系）；Department of Computer Science, Harvard University, Cambridge, United States（哈佛大学计算机科学系）
Carnegie Mellon University（卡内基梅隆大学）；AWS AI Labs（AWS人工智能实验室）
In this work, we tackle two widespread challenges in real applications for time-series forecasting that have been largely understudied: distribution shifts and missing data. We propose SpectraNet, a novel multivariate time-series forecasting model that dynamically infers a latent space spectral decomposition to capture current temporal dynamics and correlations on the recent observed history. A Convolution Neural Network maps the learned representation by sequentially mixing its components and refining the output. Our proposed approach can simultaneously produce forecasts and interpolate past …
Missing data is a common problem faced with real-world datasets. Imputation is a widely used technique to estimate the missing data. State-of-the-art imputation approaches, such as Generative Adversarial Imputation Nets (GAIN), model the distribution of observed data to approximate the missing values. Such an approach usually models a single distribution for the entire dataset, which overlooks the class-specific characteristics of the data. Class-specific characteristics are especially useful when there is a class imbalance. We propose a new method for imputing missing data based on its class-…
How to learn a good predictor on data with missing values? Most efforts focus on first imputing as well as possible and second learning on the completed data to predict the outcome. Yet, this widespread practice has no theoretical grounding. Here we show that for almost all imputation functions, an impute-then-regress procedure with a powerful learner is Bayes optimal. This result holds for all missing-values mechanisms, in contrast with the classic statistical results that require missing-at-random settings to use imputation in probabilistic modeling. Moreover, it implies that perfect conditi…
Toronto Rehabilitation Institute（多伦多康复研究所）；United Arab Emirates University（阿联酋大学）；University of Toronto（多伦多大学）
Presence of missing values in a dataset can adversely affect the performance of a classifier. Single and Multiple Imputation are normally performed to fill in the missing values. In this paper, we present several variants of combining single and multiple imputation with bootstrapping to create ensembles that can model uncertainty and diversity in the data, and that are robust to high missingness in the data. We present three ensemble strategies: bootstrapping on incomplete data followed by (i) single imputation and (ii) multiple imputation, and (iii) multiple imputation ensemble without bootst…
University of California, Los Angeles（加利福尼亚大学洛杉矶分校）；University of Cambridge（剑桥大学）；University of Oxford（牛津大学）；The Alan Turing Institute（艾伦·图灵研究所）
Missing data is an important problem in machine learning practice. Starting from the premise that imputation methods should preserve the causal structure of the data, we develop a regularization scheme that encourages any baseline imputation method to be causally consistent with the underlying data generating mechanism. Our proposal is a causally-aware imputation algorithm (MIRACLE). MIRACLE iteratively refines the imputation of a baseline by simultaneously modeling the missingness generating mechanism, encouraging imputation to be consistent with the causal structure of the data. We conduct e…
Tennessee State University（田纳西州立大学）；Old Dominion University（老道明大学）
Missing values in tabular data restrict the use and performance of machine learning, requiring the imputation of missing values. The most popular imputation algorithm is arguably multiple imputations using chains of equations (MICE), which estimates missing values from linear conditioning on observed values. This paper proposes methods to improve both the imputation accuracy of MICE and the classification accuracy of imputed data by replacing MICE's linear conditioning with ensemble learning and deep neural networks (DNN). The imputation accuracy is further improved by characterizing individua…
This paper presents algorithm for missing values imputation in categorical data. The algorithm is based on using association rules and is presented in three variants. Experimental shows better accuracy of missing values imputation using the algorithm then using most common attribute value.
University of California Los Angeles (UCLA)（加州大学洛杉矶分校）
In many machine learning applications, we are faced with incomplete datasets. In the literature, missing data imputation techniques have been mostly concerned with filling missing values. However, the existence of missing values is synonymous with uncertainties not only over the distribution of missing values but also over target class assignments that require careful consideration. In this paper, we propose a simple and effective method for imputing missing features and estimating the distribution of target assignments given incomplete data. In order to make imputations, we train a simple and…
We consider the problem of quantitatively evaluating missing value imputation algorithms. Given a dataset with missing values and a choice of several imputation algorithms to fill them in, there is currently no principled way to rank the algorithms using a quantitative metric. We develop a framework based on treating imputation evaluation as a problem of comparing two distributions and show how it can be used to compute quantitative metrics. We present an efficient procedure for applying this framework to practical datasets, demonstrate several metrics derived from the existing literature on c…
Missing data imputation can help improve the performance of prediction models in situations where missing data hide useful information. This paper compares methods for imputing missing categorical data for supervised classification tasks. We experiment on two machine learning benchmark datasets with missing categorical data, comparing classifiers trained on non-imputed (i.e., one-hot encoded) or imputed data with different levels of additional missing-data perturbation. We show imputation methods can increase predictive accuracy in the presence of missing-data perturbation, which can actually …
SimulaMet（西穆拉大都会研究所）；Warsaw University of Technology（华沙理工大学）
Missing data is a commonly occurring problem in practice. Many imputation methods have been developed to fill in the missing entries. However, not all of them can scale to high-dimensional data, especially the multiple imputation techniques. Meanwhile, the data nowadays tends toward high-dimensional. Therefore, in this work, we propose Principal Component Analysis Imputation (PCAI), a simple but versatile framework based on Principal Component Analysis (PCA) to speed up the imputation process and alleviate memory issues of many available imputation techniques, without sacrificing the imputatio…
Missing data are present in most real world problems and need careful handling to preserve the prediction accuracy and statistical consistency in the downstream analysis. As the gold standard of handling missing data, multiple imputation (MI) methods are proposed to account for the imputation uncertainty and provide proper statistical inference. In this work, we propose Multiple Imputation via Generative Adversarial Network (MI-GAN), a deep learning-based (in specific, a GAN-based) multiple imputation method, that can work under missing at random (MAR) mechanism with theoretical support. MI-GA…
Missing value imputation is a challenging and well-researched topic in data mining. In this paper, we propose IFGAN, a missing value imputation algorithm based on Feature-specific Generative Adversarial Networks (GAN). Our idea is intuitive yet effective: a feature-specific generator is trained to impute missing values, while a discriminator is expected to distinguish the imputed values from observed ones. The proposed architecture is capable of handling different data types, data distributions, missing mechanisms, and missing rates. It also improves post-imputation analysis by preserving inte…
Missing value imputation is an important practical problem. There is a large body of work on it, but there does not exist any work that formulates the problem in a structured output setting. Also, most applications have constraints on the imputed data, for example on the distribution associated with each variable. None of the existing imputation methods use these constraints. In this paper we propose a structured output approach for missing value imputation that also incorporates domain constraints. We focus on large margin models, but it is easy to extend the ideas to probabilistic models. We…
Cardiovascular disease (CVD) is a class of diseases that involve the heart or blood vessels and according to World Health Organization is the leading cause of death worldwide. EHR data regarding this case, as well as medical cases in general, contain missing values very frequently. The percentage of missingness may vary and is linked with instrument errors, manual data entry procedures, etc. Even though the missing rate is usually significant, in many cases the missing value imputation part is handled poorly either with case-deletion or with simple statistical approaches such as mode and media…
Due to the cost or interference of measurement, we need to control measurement system. Assuming that each variable can be measured sequentially, there exists optimal policy choosing next measurement for the former observations. Though optimal measurement policy is actually dependent on the goal of measurement, we mainly focus on retrieving complete data, so called as imputation. Also, we adapt the imputation method to missingness varying with measurement policy. However, learning measurement policy and imputation requires complete data which is impossible to be observed, unfortunately. To tack…
We propose Conditional Imputation GAN, an extended missing data imputation method based on Generative Adversarial Networks (GANs). The motivating use case is learning-to-rank, the cornerstone of modern search, recommendation system, and information retrieval applications. Empirical ranking datasets do not always follow standard Gaussian distributions or Missing Completely At Random (MCAR) mechanism, which are standard assumptions of classic missing data imputation methods. Our methodology provides a simple solution that offers compatible imputation guarantees while relaxing assumptions for mis…
When sensors collect spatio-temporal data in a large geographical area, the existence of missing data cannot be escaped. Missing data negatively impacts the performance of data analysis and machine learning algorithms. In this paper, we study deep autoencoders for missing data imputation in spatio-temporal problems. We propose a convolution bidirectional-LSTM for capturing spatial and temporal patterns. Moreover, we analyze an autoencoder's latent feature representation in spatio-temporal data and illustrate its performance for missing data imputation. Traffic flow data are used for evaluation…
Imputation of missing data is a common application in various classification problems where the feature training matrix has missingness. A widely used solution to this imputation problem is based on the lazy learning technique, $k$-nearest neighbor (kNN) approach. However, most of the previous work on missing data does not take into account the presence of the class label in the classification problem. Also, existing kNN imputation methods use variants of Minkowski distance as a measure of distance, which does not work well with heterogeneous data. In this paper, we propose a novel iterative k…
Institute for Infocomm Research（资讯通信研究院）；Agency for Science, Technology and Research (A*STAR)（新加坡科技研究局（A*STAR））
Real-world clinical time series data sets exhibit a high prevalence of missing values. Hence, there is an increasing interest in missing data imputation. Traditional statistical approaches impose constraints on the data-generating process and decouple imputation from prediction. Recent works propose recurrent neural network based approaches for missing data imputation and prediction with time series data. However, they generate deterministic outputs and neglect the inherent uncertainty. In this work, we introduce a unified Bayesian recurrent framework for simultaneous imputation and prediction…
Intelligent Systems Group（智能系统研究组）；Univ. of the Basque Country（巴斯克大学）；UPV/EHU（巴斯克大学）
Missing data has a ubiquitous presence in real-life applications of machine learning techniques. Imputation methods are algorithms conceived for restoring missing values in the data, based on other entries in the database. The choice of the imputation method has an influence on the performance of the machine learning technique, e.g., it influences the accuracy of the classification algorithm applied to the data. Therefore, selecting and applying the right imputation method is important and usually requires a substantial amount of human intervention. In this paper we propose the use of genetic …
Missing value imputation is crucial for real-world data science workflows. Imputation is harder in the online setting, as it requires the imputation method itself to be able to evolve over time. For practical applications, imputation algorithms should produce imputations that match the true data distribution, handle data of mixed types, including ordinal, boolean, and continuous variables, and scale to large datasets. In this work we develop a new online imputation algorithm for mixed data using the Gaussian copula. The online Gaussian copula model meets all the desiderata: its imputations mat…
Hainan University（海南大学）；Beijing University of Technology（北京工业大学）
Missing value is a very common and unavoidable problem in sensors, and researchers have made numerous attempts for missing value imputation, particularly in deep learning models. However, for real sensor data, the specific data distribution and data periods are rarely considered, making it difficult to choose the appropriate evaluation indexes and models for different sensors. To address this issue, this study proposes a multistage imputation framework based on deep learning with adaptability for missing value imputation. The model presents a mixture measurement index of low- and higher-order …
Missing data imputation for noisy time-series data and applications in healthcare
Faculty of Mathematics and Computer Science, University of Science（胡志明市科学大学数学与计算机科学学院）；Vietnam National University（越南国家大学）；University of Medicine and Pharmacy at Ho Chi Minh City（胡志明市医药大学）；Simula Metropolitan（西穆拉都会研究院）；AISIA Research Laboratory（AISIA研究院）
Clinical decision support using data mining techniques offers more intelligent way to reduce the decision error in the last few years. However, clinical datasets often suffer from high missingness, which adversely impacts the quality of modelling if handled improperly. Imputing missing values provides an opportunity to resolve the issue. Conventional imputation methods adopt simple statistical analysis, such as mean imputation or discarding missing cases, which have many limitations and thus degrade the performance of learning. This study examines a series of machine learning based imputation …
Korea Advanced Institute of Science and Technology (KAIST)（韩国科学技术院（KAIST））；Konkuk University Medical Center（建国大学医学中心）
In many applications requiring multiple inputs to obtain a desired output, if any of the input data is missing, it often introduces large amounts of bias. Although many techniques have been developed for imputing missing data, the image imputation is still difficult due to complicated nature of natural images. To address this problem, here we proposed a novel framework for missing image data imputation, called Collaborative Generative Adversarial Network (CollaGAN). CollaGAN converts an image imputation problem to a multi-domain images-to-image translation task so that a single generator and d…
DiffPuter: Empowering Diffusion Models for Missing Data Imputation
Computer Science Department, University of Illinois at Chicago（伊利诺伊大学芝加哥分校计算机科学系）；Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard（MIT和哈佛大学Broad研究所埃里克和文迪·施密特中心）
National Remote Sensing Centre (ISRO), India（印度国家遥感中心（ISRO））
Decision making from data involves identifying a set of attributes that contribute to effective decision making through computational intelligence. The presence of missing values greatly influences the selection of right set of attributes and this renders degradation in classification accuracies of the classifiers. As missing values are quite common in data collection phase during field experiments or clinical trails appropriate handling would improve the classifier performance. In this paper we present a review of recently developed missing value imputation algorithms and compare their perfor…
In the last couple of decades, there has been major advancements in the domain of missing data imputation. The techniques in the domain include amongst others: Expectation Maximization, Neural Networks with Evolutionary Algorithms or optimization techniques and K-Nearest Neighbor approaches to solve the problem. The presence of missing data entries in databases render the tasks of decision-making and data analysis nontrivial. As a result this area has attracted a lot of research interest with the aim being to yield accurate and time efficient and sensitive missing data imputation techniques es…
The most common strategy of imputing missing values in a table is to study either the column-column relationship or the row-row relationship of the data table, then use the relationship to impute the missing values based on the non-missing values from other columns of the same row, or from the other rows of the same column. This paper introduces a double autoencoder for imputation ($Ae^2I$) that simultaneously and collaboratively uses both row-row relationship and column-column relationship to impute the missing values. Empirical tests on Movielens 1M dataset demonstrated that $Ae^2I$ outperfo…
