Abstract Predictive phenotyping is about accurately predicting what phenotypes will occur in the next clinical visit based on longitudinal Electronic Health Record (EHR) data. While deep learning (DL) models have recently demonstrated strong performance in predictive phenotyping, they require access to a large amount of labeled data, which are expensive to acquire. To address this label-insufficient challenge, we propose a deep dictionary learning framework (DDL) for phenotyping, which utilizes unlabeled data as a complementary source of information to generate a better, more succinct data representation. Our empirical evaluations on multiple EHR datasets demonstrated that DDL outperforms the existing predictive phenotyping methods on a wide variety of clinical tasks that require patient phenotyping. The results also show that unlabeled data can be used to generate better data representation that helps improve DDL’s phenotyping performance over existing methods that only uses labeled data