Self-Supervised Bipartite Graph Neural Networks with Missing Value Imputation for Small Tabular Data Predictions

This article introduces the Missingness-aware Self-Supervised Graph Neural Network (MissGNN), a novel model for tabular data predictions in scenarios with missing values. Addressing a significant challenge in fields like finance, healthcare, and environmental studies, MissGNN innovatively integrates feature imputation and label prediction within a unified framework. Utilizing a Tabular Bipartite Graph, it distinctively represents data points and features, enabling intricate modeling of their relationships. This approach is pivotal in contexts where missing data can significantly skew model training and predictions. MissGNN employs a Graph Neural Network to generate embeddings, capturing interactions between data points and features for accurate missing value imputation and label prediction. It features a dual-focus mechanism, comprising edge-wise feature imputation and node-wise label prediction. A pre-training phase for feature imputation enhances the model’s predictive ability for both features and labels. Additionally, MissGNN incorporates a multi-view learning strategy through feature subsetting, further enriching its representation learning. Experiments on 14 tabular datasets demonstrate MissGNN’s superiority over existing models in managing missing values across both regression and classification tasks. The results underscore its robustness and practical applicability, establishing it as a versatile tool for tackling tabular data prediction challenges with missing values. MissGNN’s contributions significantly redefine the approach to missing value imputation, aligning feature imputation and label prediction in a cohesive manner and underscoring the potential of Graph Neural Networks in processing tabular data.