Biological data science is an emerging field facing multiple challenges for hosting, sharing, computing on, and interacting with large data sets. Privacy regulations and concerns about the risks of leaking sensitive personal health and genomic data add another layer of complexity to the problem. Recent advances in cryptography over the last five years have yielded a tool, homomorphic encryption, which can be used to encrypt data in such a way that storage can be outsourced to an untrusted cloud, and the data can be computed on in a meaningful way in encrypted form, without access to decryption keys. This paper introduces homomorphic encryption to the bioinformatics community, and presents an informal “manual” for using the Simple Encrypted Arithmetic Library (SEAL), which we have made publicly available for bioinformatic, genomic, and other research purposes.

Lattice-based cryptography offers some of the most attractive primitives believed to be resistant to quantum computers. Following increasing interest from both companies and government agencies in building quantum computers, a number of works have proposed instantiations of practical post-quantum key exchange protocols based on hard problems in ideal lattices, mainly based on the Ring Learning With Errors (R-LWE) problem. While ideal lattices facilitate major efficiency and storage benefits over their non-ideal counterparts, the additional ring structure that enables these advantages also raises concerns about the assumed difficulty of the underlying problems. Thus, a question of significant interest to cryptographers, and especially to those currently placing bets on primitives that will withstand quantum adversaries, is how much of an advantage the additional ring structure actually gives in practice. Despite conventional wisdom that generic lattices might be too slow and unwieldy, we demonstrate that LWE-based key exchange is quite practical: our constant time implementation requires around 1.3ms computation time for each party; compared to the recent NewHope R-LWE scheme, communication sizes increase by a factor of 4.7x, but remain under 12 KiB in each direction. Our protocol is competitive when used for serving web pages over TLS; when partnered with ECDSA signatures, latencies increase by less than a factor of 1.6x, and (even under heavy load) server throughput only decreases by factors of 1.5x and 1.2x when serving typical 1 KiB and 100 KiB pages, respectively. To achieve these practical results, our protocol takes advantage of several innovations. These include techniques to optimize communication bandwidth, dynamic generation of public parameters (which also offers additional security against backdoors), carefully chosen error distributions, and tight security parameters.

Applying machine learning to a problem which involves medical, financial, or other types of sensitive data, not only requires accurate predictions but also careful attention to maintaining data privacy and security. Legal and ethical requirements may prevent the use of cloud-based machine learning solutions for such tasks. In this work, we will present a method to convert learned neural networks to CryptoNets, neural networks that can be applied to encrypted data. This allows a data owner to send their data in an encrypted form to a cloud service that hosts the network. The encryption ensures that the data remains confidential since the cloud does not have access to the keys needed to decrypt it. Nevertheless, we will show that the cloud service is capable of applying the neural network to the encrypted data to make encrypted predictions, and also return them in encrypted form. These encrypted predictions can be sent back to the owner of the secret key who can decrypt them. Therefore, the cloud service does not gain any information about the raw data nor about the prediction it made. We demonstrate CryptoNets on the MNIST optical character recognition tasks. CryptoNets achieve 99% accuracy and can make around 59000 predictions per hour on a single PC. Therefore, they allow high throughput, accurate, and private predictions.

Abstract Decision trees and random forests are common classifiers with widespread use. In this paper, we develop two protocols for privately evaluating decision trees and random forests. We operate in the standard two-party setting where the server holds a model (either a tree or a forest), and the client holds an input (a feature vector). At the conclusion of the protocol, the client learns only the model’s output on its input and a few generic parameters concerning the model; the server learns nothing. The first protocol we develop provides security against semi-honest adversaries. We then give an extension of the semi-honest protocol that is robust against malicious adversaries. We implement both protocols and show that both variants are able to process trees with several hundred decision nodes in just a few seconds and a modest amount of bandwidth. Compared to previous semi-honest protocols for private decision tree evaluation, we demonstrate a tenfold improvement in computation and bandwidth.

Lattice-based cryptographic primitives are believed to offer resilience against attacks by quantum computers. We demonstrate the practicality of post-quantum key exchange by constructing cipher suites for the Transport Layer Security (TLS) protocol that provide key exchange based on the ring learning with errors (R-LWE) problem, we accompany these cipher suites with a rigorous proof of security. Our approach ties lattice-based key exchange together with traditional authentication using RSA or elliptic curve digital signatures: the post-quantum key exchange provides forward secrecy against future quantum attackers, while authentication can be provided using RSA keys that are issued by today's commercial certificate authorities, smoothing the path to adoption. Our cryptographically secure implementation, aimed at the 128-bit security level, reveals that the performance price when switching from non-quantum-safe key exchange is not too high. With our R-LWE cipher suites integrated into the Open SSL library and using the Apache web server on a 2-core desktop computer, we could serve 506 RLWE-ECDSA-AES128-GCM-SHA256 HTTPS connections per second for a 10 KiB payload. Compared to elliptic curve Diffie-Hellman, this means an 8 KiB increased handshake size and a reduction in throughput of only 21%. This demonstrates that provably secure post-quantum key-exchange can already be considered practical.

Cloud computing sparked interest in Verifiable Computation protocols, which allow a weak client to securely outsource computations to remote parties. Recent work has dramatically reduced the client's cost to verify the correctness of their results, but the overhead to produce proofs remains largely impractical. Geppetto introduces complementary techniques for reducing prover overhead and increasing prover flexibility. With Multi QAPs, Geppetto reduces the cost of sharing state between computations (e.g, For MapReduce) or within a single computation by up to two orders of magnitude. Via a careful choice of cryptographic primitives, Geppetto's instantiation of bounded proof bootstrapping improves on prior bootstrapped systems by up to five orders of magnitude, albeit at some cost in universality. Geppetto also efficiently verifies the correct execution of proprietary (i.e, Secret) algorithms. Finally, Geppetto's use of energy-saving circuits brings the prover's costs more in line with the program's actual (rather than worst-case) execution time. Geppetto is implemented in a full-fledged, scalable compiler and runtime that consume LLVM code generated from a variety of source C programs and cryptographic libraries.