Fast Iterative and Task-Specific Imputation with Online Learning

Missing feature values are a significant hurdle for downstream machine-learning tasks such as classification and regression. However, they are pervasive in multiple real-life use cases, for instance, in drug discovery research. Moreover, imputation methods might be time-consuming and offer few guarantees on the imputation quality, especially for not-missing-at-random mechanisms. We propose an imputation approach named F3I based on the iterative improvement of a K-nearest neighbor imputation that learns the weights for each neighbor of a data point, optimizing for the most likely distribution of points over data points. This algorithm can also be jointly trained with a downstream task on the imputed values. We provide a theoretical analysis of the imputation quality by F3I for several types of missing mechanisms. We also demonstrate the performance of F3I on both synthetic data sets and real-life drug repurposing and handwritten-digit recognition data.