Homomorphic Encryption for Machine Learning in Medicine and Bioinformatics

Machine learning techniques are an excellent tool for the medical community to analyzing large amounts of medical and genomic data. On the other hand, ethical concerns and privacy regulations prevent the free sharing of this data. Encryption methods such as fully homomorphic encryption (FHE) provide a method evaluate over encrypted data. Using FHE, machine learning models such as deep learning, decision trees, and naive Bayes have been implemented for private prediction using medical data. FHE has also been shown to enable secure genomic algorithms, such as paternity testing, and secure application of genome-wide association studies. This survey provides an overview of fully homomorphic encryption and its applications in medicine and bioinformatics. The high-level concepts behind FHE and its history are introduced. Details on current open-source implementations are provided, as is the state of FHE for privacy-preserving techniques in machine learning and bioinformatics and future growth opportunities for FHE

ESCAPED: Efficient Secure and Private Dot Product Framework for Kernel-based Machine Learning Algorithms with Applications in Healthcare

To train sophisticated machine learning models one usually needs many training samples. Especially in healthcare settings these samples can be very expensive, meaning that one institution alone usually does not have enough on its own. Merging privacy-sensitive data from different sources is usually restricted by data security and data protection measures. This can lead to approaches that reduce data quality by putting noise onto the variables (e.g., in $\epsilon$-differential privacy) or omitting certain values (e.g., for $k$-anonymity). Other measures based on cryptographic methods can lead to very time-consuming computations, which is especially problematic for larger multi-omics data. We address this problem by introducing ESCAPED, which stands for Efficient SeCure And PrivatE Dot product framework, enabling the computation of the dot product of vectors from multiple sources on a third-party, which later trains kernel-based machine learning algorithms, while neither sacrificing privacy nor adding noise. We evaluated our framework on drug resistance prediction for HIV-infected people and multi-omics dimensionality reduction and clustering problems in precision medicine. In terms of execution time, our framework significantly outperforms the best-fitting existing approaches without sacrificing the performance of the algorithm. Even though we only show the benefit for kernel-based algorithms, our framework can open up new research opportunities for further machine learning models that require the dot product of vectors from multiple sources.Comment: AAAI 2021, Preprint version of the full paper with supplementary materia

Turbo-Aggregate: Breaking the Quadratic Aggregation Barrier in Secure Federated Learning

Federated learning is a distributed framework for training machine learning models over the data residing at mobile devices, while protecting the privacy of individual users. A major bottleneck in scaling federated learning to a large number of users is the overhead of secure model aggregation across many users. In particular, the overhead of the state-of-the-art protocols for secure model aggregation grows quadratically with the number of users. In this paper, we propose the first secure aggregation framework, named Turbo-Aggregate, that in a network with $N$ users achieves a secure aggregation overhead of $O(N\log{N})$, as opposed to $O(N^2)$, while tolerating up to a user dropout rate of $50\%$. Turbo-Aggregate employs a multi-group circular strategy for efficient model aggregation, and leverages additive secret sharing and novel coding techniques for injecting aggregation redundancy in order to handle user dropouts while guaranteeing user privacy. We experimentally demonstrate that Turbo-Aggregate achieves a total running time that grows almost linear in the number of users, and provides up to $40\times$ speedup over the state-of-the-art protocols with up to $N=200$ users. Our experiments also demonstrate the impact of model size and bandwidth on the performance of Turbo-Aggregate