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 imputation


tBayes-MICE: A Bayesian Approach to Multiple Imputation for Time Series Data

Ibenegbu, Amuche, de Micheaux, Pierre Lafaye, Chandra, Rohitash

arXiv.org Machine Learning

Time-series analysis is often affected by missing data, a common problem across several fields, including healthcare and environmental monitoring. Multiple Imputation by Chained Equations (MICE) has been prominent for imputing missing values through "fully conditional specification". We extend MICE using the Bayesian framework (tBayes-MICE), utilising Bayesian inference to impute missing values via Markov Chain Monte Carlo (MCMC) sampling to account for uncertainty in MICE model parameters and imputed values. We also include temporally informed initialisation and time-lagged features in the model to respect the sequential nature of time-series data. We evaluate the tBayes-MICE method using two real-world datasets (AirQuality and PhysioNet), and using both the Random Walk Metropolis (RWM) and the Metropolis-Adjusted Langevin Algorithm (MALA) samplers. Our results demonstrate that tBayes-MICE reduces imputation errors relative to the baseline methods over all variables and accounts for uncertainty in the imputation process, thereby providing a more accurate measure of imputation error. We also found that MALA mixed better than RWM across most variables, achieving comparable accuracy while providing more consistent posterior exploration. Overall, these findings suggest that the tBayes-MICE framework represents a practical and efficient approach to time-series imputation, balancing increased accuracy with meaningful quantification of uncertainty in various environmental and clinical settings.


Generative Modeling under Non-Monotonic MAR Missingness via Approximate Wasserstein Gradient Flows

Kremling, Gitte, Näf, Jeffrey, Lederer, Johannes

arXiv.org Machine Learning

The prevalence of missing values in data science poses a substantial risk to any further analyses. Despite a wealth of research, principled nonparametric methods to deal with general non-monotone missingness are still scarce. Instead, ad-hoc imputation methods are often used, for which it remains unclear whether the correct distribution can be recovered. In this paper, we propose FLOWGEM, a principled iterative method for generating a complete dataset from a dataset with values Missing at Random (MAR). Motivated by convergence results of the ignoring maximum likelihood estimator, our approach minimizes the expected Kullback-Leibler (KL) divergence between the observed data distribution and the distribution of the generated sample over different missingness patterns. To minimize the KL divergence, we employ a discretized particle evolution of the corresponding Wasserstein Gradient Flow, where the velocity field is approximated using a local linear estimator of the density ratio. This construction yields a data generation scheme that iteratively transports an initial particle ensemble toward the target distribution. Simulation studies and real-data benchmarks demonstrate that FLOWGEM achieves state-of-the-art performance across a range of settings, including the challenging case of non-monotonic MAR mechanisms. Together, these results position FLOWGEM as a principled and practical alternative to existing imputation methods, and a decisive step towards closing the gap between theoretical rigor and empirical performance.


Identifiable Deep Latent Variable Models for MNAR Data

Xie, Huiming, Xue, Fei, Wang, Xiao

arXiv.org Machine Learning

Missing data is a ubiquitous challenge in data analysis, often leading to biased and inaccurate results. Traditional imputation methods usually assume that the missingness mechanism is missing-at-random (MAR), where the missingness is independent of the missing values themselves. This assumption is frequently violated in real-world scenarios, prompted by recent advances in imputation methods using deep learning to address this challenge. However, these methods neglect the crucial issue of nonparametric identifiability in missing-not-at-random (MNAR) data, which can lead to biased and unreliable results. This paper seeks to bridge this gap by proposing a novel framework based on deep latent variable models for MNAR data. Building on the assumption of conditional no self-censoring given latent variables, we establish the identifiability of the data distribution. This crucial theoretical result guarantees the feasibility of our approach. To effectively estimate unknown parameters, we develop an efficient algorithm utilizing importance-weighted autoencoders. We demonstrate, both theoretically and empirically, that our estimation process accurately recovers the ground-truth joint distribution under specific regularity conditions. Extensive simulation studies and real-world data experiments showcase the advantages of our proposed method compared to various classical and state-of-the-art approaches to missing data imputation.


Starting Off on the Wrong Foot: Pitfalls in Data Preparation

Guo, Jiayi, Dong, Panyi, Quan, Zhiyu

arXiv.org Machine Learning

When working with real-world insurance data, practitioners often encounter challenges during the data preparation stage that can undermine the statistical validity and reliability of downstream modeling. This study illustrates that conventional data preparation procedures such as random train-test partitioning, often yield unreliable and unstable results when confronted with highly imbalanced insurance loss data. To mitigate these limitations, we propose a novel data preparation framework leveraging two recent statistical advancements: support points for representative data splitting to ensure distributional consistency across partitions, and the Chatterjee correlation coefficient for initial, non-parametric feature screening to capture feature relevance and dependence structure. We further integrate these theoretical advances into a unified, efficient framework that also incorporates missing-data handling, and embed this framework within our custom InsurAutoML pipeline. The performance of the proposed approach is evaluated using both simulated datasets and datasets often cited in the academic literature. Our findings definitively demonstrate that incorporating statistically rigorous data preparation methods not only significantly enhances model robustness and interpretability but also substantially reduces computational resource requirements across diverse insurance loss modeling tasks. This work provides a crucial methodological upgrade for achieving reliable results in high stakes insurance applications.


Consistency of the $k$-Nearest Neighbor Regressor under Complex Survey Designs

Hasler, Caren

arXiv.org Machine Learning

We study the consistency of the $k$-nearest neighbor regressor under complex survey designs. While consistency results for this algorithm are well established for independent and identically distributed data, corresponding results for complex survey data are lacking. We show that the $k$-nearest neighbor regressor is consistent under regularity conditions on the sampling design and the distribution of the data. We derive lower bounds for the rate of convergence and show that these bounds exhibit the curse of dimensionality, as in the independent and identically distributed setting. Empirical studies based on simulated and real data illustrate our theoretical findings.


Predictive Uncertainty in Short-Term PV Forecasting under Missing Data: A Multiple Imputation Approach

Pashmchi, Parastoo, Benoit, Jérôme, Kanagawa, Motonobu

arXiv.org Machine Learning

Missing values are common in photovoltaic (PV) power data, yet the uncertainty they induce is not propagated into predictive distributions. We develop a framework that incorporates missing-data uncertainty into short-term PV forecasting by combining stochastic multiple imputation with Rubin's rule. The approach is model-agnostic and can be integrated with standard machine-learning predictors. Empirical results show that ignoring missing-data uncertainty leads to overly narrow prediction intervals. Accounting for this uncertainty improves interval calibration while maintaining comparable point prediction accuracy. These results demonstrate the importance of propagating imputation uncertainty in data-driven PV forecasting.


RFX-Fuse: Breiman and Cutler's Unified ML Engine + Native Explainable Similarity

Kuchar, Chris

arXiv.org Machine Learning

Breiman and Cutler's original Random Forest was designed as a unified ML engine -- not merely an ensemble predictor. Their implementation included classification, regression, unsupervised learning, proximity-based similarity, outlier detection, missing value imputation, and visualization -- capabilities that modern libraries like scikit-learn never implemented. RFX-Fuse (Random Forests X [X=compression] -- Forest Unified Learning and Similarity Engine) delivers Breiman and Cutler's complete vision with native GPU/CPU support. Modern ML pipelines require 5+ separate tools -- XGBoost for prediction, FAISS for similarity, SHAP for explanations, Isolation Forest for outliers, custom code for importance. RFX-Fuse provides a 1 to 2 model object alternative -- a single set of trees grown once. Novel Contributions: (1) Proximity Importance -- native explainable similarity: proximity measures that samples are similar; proximity importance explains why. (2) Dataset-specific imputation validation for general tabular data -- ranking imputation methods by how real the imputed data looks, without ground truth labels.


Multivariate Time Series Imputation with Generative Adversarial Networks

Neural Information Processing Systems

Multivariate time series usually contain a large number of missing values, which hinders the application of advanced analysis methods on multivariate time series data. Conventional approaches to addressing the challenge of missing values, including mean/zero imputation, case deletion, and matrix factorization-based imputation, are all incapable of modeling the temporal dependencies and the nature of complex distribution in multivariate time series. In this paper, we treat the problem of missing value imputation as data generation. Inspired by the success of Generative Adversarial Networks (GAN) in image generation, we propose to learn the overall distribution of a multivariate time series dataset with GAN, which is further used to generate the missing values for each sample. Different from the image data, the time series data are usually incomplete due to the nature of data recording process. A modified Gate Recurrent Unit is employed in GAN to model the temporal irregularity of the incomplete time series. Experiments on two multivariate time series datasets show that the proposed model outperformed the baselines in terms of accuracy of imputation. Experimental results also showed that a simple model on the imputed data can achieve state-of-the-art results on the prediction tasks, demonstrating the benefits of our model in downstream applications.


Unsupervised Anomaly Detection in The Presence of Missing Values

Neural Information Processing Systems

In this work, first, we construct and evaluate a straightforward strategy, "impute-then-detect", via combining state-of-the-art imputation methods with unsupervised anomaly detection methods, where the training data are composed of normal samples only.