Private Computation of Phylogenetic Trees Based on Quantum Technologies

Abstract

Individuals' privacy and legal regulations demand genomic data be handled and studied with highly secure privacy-preserving techniques. In this work, we propose a feasible Secure Multiparty Computation (SMC) system assisted with quantum cryptographic protocols that is designed to compute a phylogenetic tree from a set of private genome sequences. This system significantly improves the privacy and security of the computation thanks to three quantum cryptographic protocols that provide enhanced security against quantum computer attacks. This system adapts several distance-based methods (Unweighted Pair Group Method with Arithmetic mean, Neighbour-Joining, Fitch-Margoliash) into a private setting where the sequences owned by each party are not disclosed to the other members present in the protocol. We theoretically evaluate the performance and privacy guarantees of the system through a complexity analysis and security proof and give an extensive explanation about the implementation details and cryptographic protocols. We also implement a quantum-assisted secure phylogenetic tree computation based on the Libscapi implementation of the Yao, the PHYLIP library and simulated keys of two quantum systems: Quantum Oblivious Key Distribution and Quantum Key Distribution. This demonstrates its effectiveness and practicality. We benchmark this implementation against a classical-only solution and we conclude that both approaches render similar execution times, the only difference being the time overhead taken by the oblivious key management system of the quantum-assisted approach.

Quantum Oblivious Transfer: A Short Review

“…However, quantum hacking techniques pose a security threat to these protocols. Santos et al [ 19 ] gave a brief description of how two common techniques (faked-state and trojan-horses attacks) break the security of assumption-based BBCS protocols ( , and ). In summary, a faked-state attack allows the receiver to avoid the security guarantees enforced by the assumptions and effectively receive both messages and .…”

“…More recently, the first direct quantum protocol for a generalization of oblivious transfer known as oblivious linear evaluation was proposed [ 17 ]. In addition, quantum versions of oblivious transfer have recently been applied to SMC systems in the field of genomics medicine [ 18 , 19 ]. Developing efficient and secure OT primitives is essential not only from a theoretical perspective but also from a practical one.…”

“…When used in SMC systems, OTs mask every input bit [ 20 ] or mask the computation at every boolean circuit gate [ 21 ]. Regarding OT generation, a genomics use case [ 18 , 19 ] with three parties based on the Yao protocol [ 20 ] requires the execution of ∼12 million OTs. Hopefully, quantum OT approaches can be extended through classical methods [ 22 , 23 ], increasing the amount of OT produced.…”

“…This was recently initiated by Santos et al [ 33 ], where the authors theoretically compared different classical OT approaches with the quantum BBCS (Bennett–Brassard–Crépeau–Skubiszewska) protocol in the hybrid model (defined in Section 4.2 ). In addition, in subsequent work, Santos et al [ 19 ] experimentally compared the efficiency impact of classical and quantum OT protocols on an SMC system.…”

Quantum oblivious transfer: a short review

“…More recently, the first direct quantum protocol for a generalization of oblivious transfer known as oblivious linear evaluation was proposed [SMV22]. Also, quantum versions of oblivious transfer have recently been applied to SMC systems in the field of genomics medicine [SGPM21,SGPM22]. Developing efficient and secure OT primitives is essential not only from a theoretical perspective but also from a practical one.…”