When Does Self-Supervised Pretraining Help Tabular Models? A Study of Label Scarcity and Missing Data

Abstract

Self-supervised learning (SSL) has emerged as a promising approach for tabular data, yet its efficacy under extreme label scarcity and test-time missingness remains under-explored. In this paper, we evaluate a mask-and-recover SSL pretraining objective against training from scratch and classical baselines across 14 diverse classification tasks. First, while SSL outperforms training from scratch on average and remains competitive with state-of-the-art tree ensembles (achieving ~0.8954 AUC vs. Random Forest's 0.9015 at 10% labels), the SSL-vs-scratch gains exhibit high inter-task variance and lack significance (p = 0.626 at both 5% and 10% labels). Second, contrary to the hypothesis that missing-value imputation objectives universally benefit datasets with native missingness, SSL yields the most reliable improvements on clean datasets, while frequently degrading performance on datasets with high inherent missingness. Third, despite this training variance, SSL-pretrained models achieve a higher average AUC than scratch-trained models under both test-time missingness completely at random (MCAR) injection (+0.0245 AUC, positive on 11 of 14 tasks) and structured missingness shifts (MNAR, +0.0418 AUC, positive on 8 of 14 tasks), though neither difference remains statistically significant after Holm-Bonferroni correction for multiple comparisons (adjusted p = 0.118 and p = 0.518, respectively). Fourth, comparing our mask-and-recover objective against three established tabular SSL baselines (VIME, SCARF, SubTab) under an identical encoder architecture, we find no significant difference from any of them (adjusted p = 0.459, p = 1.000, p = 1.000), indicating our findings reflect general properties of tabular SSL rather than idiosyncrasies of one particular pretext task.