Secure federated Boolean count queries using fully-homomorphic cryptography

Abstract

Electronic health records (EHR) are often siloed across a network of hospitals, but researchers may wish to perform aggregate count queries on said records in entirety—e.g. How many patients have diabetes? Prior work has established a strong approach to answering these queries in the form of probabilistic sketching algorithms like LogLog and HyperLogLog; however, it has remained somewhat of an open question how these algorithms should be made truly private. While many works in the computational biology community—as well as the computer science community at large—have attempted to solve this problem using differential privacy, these methods involve adding noise and still reveal some amount of non-trivial information. Here, we prototype a new protocol using fully homomorphic encryption that is trivially secured even in the setting of quantum-capable adversaries, as it reveals no information other than that which can be trivially gained from final numerical estimation. Simulating up to 16 parties on a single CPU thread takes no longer than 20 minutes to return an estimate with expected 6% approximation error; furthermore, the protocol is parallelizable across both parties and cores, so, in practice, with optimized code, we might expect sub-minute processing time for each party.AvailibilityOur software is available at https://github.com/atleighton/rlwe-hll