Hermes: High-Performance Homomorphically Encrypted Vector Databases

Abstract: Fully Homomorphic Encryption (FHE) has long promised the ability to compute over encrypted data without revealing sensitive contents -- a foundational goal for secure cloud analytics. Yet despite decades of cryptographic advances, practical integration of FHE into real-world relational databases remains elusive. This paper presents \textbf{Hermes}, the first system to enable FHE-native vector query processing inside a standard SQL engine. By leveraging the multi-slot capabilities of modern schemes, Hermes introduces a novel data model that packs multiple records per ciphertext and embeds encrypted auxiliary statistics (e.g., local sums) to support in-place updates and aggregation. To reconcile ciphertext immutability with record-level mutability, we develop new homomorphic algorithms based on slot masking, shifting, and rewriting. Hermes is implemented as native C++ loadable functions in MySQL using OpenFHE v1.2.4, comprising over 3,500 lines of code. Experiments on real-world datasets show up to 1{,}600$\times$ throughput gain in encryption and over 30$\times$ speedup in insertion compared to per-tuple baselines. Hermes brings FHE from cryptographic promise to practical reality -- realizing a long-standing vision at the intersection of databases and secure computation.