Multiple Imputation with Neural Network Gaussian Process for High-dimensional Incomplete Data

Zongyu Dai, Zhiqi Bu, Qi Long
Proceedings of The 14th Asian Conference on Machine Learning, PMLR 189:265-279, 2023.

Abstract

Missing data are ubiquitous in real world applications and, if not adequately handled, may lead to the loss of information and biased findings in downstream analysis. Particularly, high-dimensional incomplete data with a moderate sample size, such as analysis of multi-omics data, present daunting challenges. Imputation is arguably the most popular method for handling missing data, though existing imputation methods have a number of limitations. Single imputation methods such as matrix completion methods do not adequately account for imputation uncertainty and hence would yield improper statistical inference. In contrast, multiple imputation (MI) methods allow for proper inference but existing methods do not perform well in high-dimensional settings. Our work aims to address these significant methodological gaps, leveraging recent advances in neural network Gaussian process (NNGP) from a Bayesian viewpoint. We propose two NNGP-based MI methods, namely MI-NNGP, that can apply multiple imputations for missing values from a joint (posterior predictive) distribution. The MI-NNGP methods are shown to significantly outperform existing state-of-the-art methods on synthetic and real datasets, in terms of imputation error, statistical inference, robustness to missing rates, and computation costs, under three missing data mechanisms, MCAR, MAR, and MNAR.

Cite this Paper

BibTeX
@InProceedings{pmlr-v189-dai23a, title = {Multiple Imputation with Neural Network Gaussian Process for High-dimensional Incomplete Data}, author = {Dai, Zongyu and Bu, Zhiqi and Long, Qi}, booktitle = {Proceedings of The 14th Asian Conference on Machine Learning}, pages = {265--279}, year = {2023}, editor = {Khan, Emtiyaz and Gonen, Mehmet}, volume = {189}, series = {Proceedings of Machine Learning Research}, month = {12--14 Dec}, publisher = {PMLR}, pdf = {https://proceedings.mlr.press/v189/dai23a/dai23a.pdf}, url = {https://proceedings.mlr.press/v189/dai23a.html}, abstract = {Missing data are ubiquitous in real world applications and, if not adequately handled, may lead to the loss of information and biased findings in downstream analysis. Particularly, high-dimensional incomplete data with a moderate sample size, such as analysis of multi-omics data, present daunting challenges. Imputation is arguably the most popular method for handling missing data, though existing imputation methods have a number of limitations. Single imputation methods such as matrix completion methods do not adequately account for imputation uncertainty and hence would yield improper statistical inference. In contrast, multiple imputation (MI) methods allow for proper inference but existing methods do not perform well in high-dimensional settings. Our work aims to address these significant methodological gaps, leveraging recent advances in neural network Gaussian process (NNGP) from a Bayesian viewpoint. We propose two NNGP-based MI methods, namely MI-NNGP, that can apply multiple imputations for missing values from a joint (posterior predictive) distribution. The MI-NNGP methods are shown to significantly outperform existing state-of-the-art methods on synthetic and real datasets, in terms of imputation error, statistical inference, robustness to missing rates, and computation costs, under three missing data mechanisms, MCAR, MAR, and MNAR.} }
Endnote
%0 Conference Paper %T Multiple Imputation with Neural Network Gaussian Process for High-dimensional Incomplete Data %A Zongyu Dai %A Zhiqi Bu %A Qi Long %B Proceedings of The 14th Asian Conference on Machine Learning %C Proceedings of Machine Learning Research %D 2023 %E Emtiyaz Khan %E Mehmet Gonen %F pmlr-v189-dai23a %I PMLR %P 265--279 %U https://proceedings.mlr.press/v189/dai23a.html %V 189 %X Missing data are ubiquitous in real world applications and, if not adequately handled, may lead to the loss of information and biased findings in downstream analysis. Particularly, high-dimensional incomplete data with a moderate sample size, such as analysis of multi-omics data, present daunting challenges. Imputation is arguably the most popular method for handling missing data, though existing imputation methods have a number of limitations. Single imputation methods such as matrix completion methods do not adequately account for imputation uncertainty and hence would yield improper statistical inference. In contrast, multiple imputation (MI) methods allow for proper inference but existing methods do not perform well in high-dimensional settings. Our work aims to address these significant methodological gaps, leveraging recent advances in neural network Gaussian process (NNGP) from a Bayesian viewpoint. We propose two NNGP-based MI methods, namely MI-NNGP, that can apply multiple imputations for missing values from a joint (posterior predictive) distribution. The MI-NNGP methods are shown to significantly outperform existing state-of-the-art methods on synthetic and real datasets, in terms of imputation error, statistical inference, robustness to missing rates, and computation costs, under three missing data mechanisms, MCAR, MAR, and MNAR.
APA
Dai, Z., Bu, Z. & Long, Q.. (2023). Multiple Imputation with Neural Network Gaussian Process for High-dimensional Incomplete Data. Proceedings of The 14th Asian Conference on Machine Learning, in Proceedings of Machine Learning Research 189:265-279 Available from https://proceedings.mlr.press/v189/dai23a.html.

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