Deep learning with missing data

Missing data is ubiquitous in real-world datasets. Traditional methods either discard incomplete samples or apply imputation techniques that ignore potentially informative missingness patterns, implicitly assuming that missingness occurs randomly. However, missingness patterns might provide additional information. We propose pattern-aware graph neural networks that explicitly encode which features are missing alongside observed values. We used four encoding strategies -- learned embeddings, frozen random embeddings, statistical features, and hierarchical representations -- across seven UCI datasets with naturally occurring missingness. Our Pattern-aware methods achieve substantial improvements over baselines, with an average improvement of 17% in balanced accuracy and 22% in F1-macro across all datasets. The benefits vary significantly by dataset: annealing shows dramatic improvement (+80% balanced accuracy), while hepatitis and soybean show minimal gains (+4--5%). Notably, even simple random pattern embeddings perform comparably to learned embeddings (0.650 vs 0.663 balanced accuracy), suggesting that distinguishing between patterns may be more important than task-specific optimization. Our ablation study reveals that attention mechanisms, while helpful, are not critical when pattern information is available -- simple mean aggregation with pattern awareness achieves 0.640 balanced accuracy compared to 0.645 for attention-based variants.

Missing data frequently arises across diverse domains, including time-series and image domains. In the real world, missing occurrences often depend on the unobservable values themselves, which are referred to as Missing Not at Random (MNAR). In this work, we introduce the Missing Pattern Recognized Diffusion Imputation Model (PRDIM), a novel framework that explicitly captures the missing pattern and precisely imputes unobserved values. PRDIM iteratively maximizes the likelihood of the joint distribution for observed values and missing mask under an Expectation-Maximization (EM) algorithm. In this sense, we first employ a pattern recognizer, which approximates the underlying missing pattern and provides guidance during every inference toward more plausible imputations with respect to the missing information. Through extensive experiments, we demonstrate that PRDIM consistently achieves strong imputation performance under MNAR settings across multiple data modalities.

Covariate shift often occurs because, in many real applications, the source and the target observations may be generated from different distributions. In this case, the standard metric under the source distribution is not appropriate. This paper considers deep neural network estimators for nonparametric quantile and Huber regression under covariate shift and from dependent observations. We deal with a generalized Bernstein-type inequality that is satisfied by many classical models, including i.i.d. observations, $φ$-mixing, strong mixing, and $\mathcal{C}$-mixing processes. To perform the covariate shift phenomenon, we propose a sparse-penalized deep neural network (SPDNN) estimator that takes into account the discrepancy between the source and target distributions of the data. When the density ratio (between the source and target distributions of the covariate) is unknown, a two steps pre-training procedure is carried out: the first step is devoted to the construction of a least squares SPDNN estimator of the density ratio; which is used in the second step to perform a pre-training reweighted SPDNN estimator of the regression function. For both the quantile and the Huber regression, non-asymptotic error bounds of the proposed SPDNN estimators are established in the class of Hölder smooth functions. These estimators can adaptively attain (up to a logarithmic factor) the minimax optimal convergence rate from i.i.d. data as well as from several classical time series models.