Machine learning on large-scale patient medical records can lead to the discovery of novel population-wide patterns enabling advances in genetics, disease mechanisms, drug discovery, healthcare policy, and public health. However, concerns over patient privacy prevent biomedical researchers from running their algorithms on large volumes of patient data, creating a barrier to important new discoveries through machine-learning. The goal of this project is to address this barrier by developing privacy-preserving tools to query, cluster, classify and analyze medical databases.