Secure Genomic String Search with Parallel Homomorphic Encryption

Fully homomorphic encryption (FHE) cryptographic systems enable limitless computations over encrypted data, providing solutions to many of today’s data security problems. While effective FHE platforms can address modern data security concerns in unsecure environments, the extended execution time for these platforms hinders their broader application. This project aims to enhance FHE systems through an efficient parallel framework, specifically building upon the existing torus FHE (TFHE) system chillotti2016faster. The TFHE system was chosen for its superior bootstrapping computations and precise results for countless Boolean gate evaluations, such as AND and XOR. Our first approach was to expand upon the gate operations within the current system, shifting towards algebraic circuits, and using graphics processing units (GPUs) to manage cryptographic operations in parallel. Then, we implemented this GPU-parallel FHE framework into a needed genomic data operation, specifically string search. We utilized popular string distance metrics (hamming distance, edit distance, set maximal matches) to ascertain the disparities between multiple genomic sequences in a secure context with all data and operations occurring under encryption. Our experimental data revealed that our GPU implementation vastly outperforms the former method, providing a 20-fold speedup for any 32-bit Boolean operation and a 14.5-fold increase for multiplications.This paper introduces unique enhancements to existing FHE cryptographic systems using GPUs and additional algorithms to quicken fundamental computations. Looking ahead, the presented framework can be further developed to accommodate more complex, real-world applications.