PRISM: Leveraging Prototype Patient Representations with Feature-Missing-Aware Calibration for EHR Data Sparsity Mitigation

Electronic Health Record (EHR) data, while rich in information, often suffers from sparsity, posing significant challenges in predictive modeling. Traditional imputation methods inadequately distinguish between real and imputed data, leading to potential inaccuracies in models. Addressing this, we introduce PRISM, a framework that indirectly imputes data through prototype representations of similar patients, thus ensuring denser and more accurate embeddings. PRISM also includes a feature confidence learner module, which evaluates the reliability of each feature in light of missing data. Additionally, it incorporates a new patient similarity metric that accounts for feature confidence, avoiding overreliance on imprecise imputed values. Our extensive experiments on the MIMIC-III, MIMIC-IV, PhysioNet Challenge 2012, eICU datasets demonstrate PRISM 's superior performance in predicting in-hospital mortality and 30-day readmission tasks, showcasing its effectiveness in handling EHR data sparsity. For the sake of reproducibility and further research, we have made the code publicly available at https://github.com/yhzhu99/PRISM.