When Pattern-by-Pattern Works: Theoretical and Empirical Insights for Logistic Models with Missing Values

Predicting with missing inputs challenges even parametric models, as parameter estimation alone is insufficient for prediction on incomplete data. While several works study prediction in linear models, we focus on logistic models, where optimal predictors lack closed-form expressions. We prove that a Pattern-by-Pattern strategy (PbP), which learns one logistic model per missingness pattern, accurately approximates Bayes probabilities under a Gaussian Pattern Mixture Model (GPMM). Crucially, this result holds across standard missing data scenarios (MCAR and MAR) and, notably, in Missing Not at Random (MNAR) settings where standard methods often fail. Empirically, we compare PbP against imputation and EM methods across classification, probability estimation, calibration, and inference. Our analysis provides a comprehensive view of logistic regression with missing values. It reveals that mean imputation can be used as baseline for low sample sizes and PbP for large sample sizes, as both methods are fast to train and may have good performances in some settings. The best performances are achieved by non-linear multiple iterative imputation techniques that include the response label (Random Forest MICE with response), which are more computationally expensive.