Scalable Privacy-Preserving Distributed Learning

Secure Discovery of Genetic Relatives across Large-Scale and Distributed Genomic Datasets

Finding relatives within a study cohort is a necessary step in many genomic studies. However, when the cohort is distributed across multiple entities subject to data-sharing restrictions, performing this step often becomes infeasible. Developing a privacy-preserving solution for this task is challenging due to the significant burden of estimating kinship between all pairs of individuals across datasets. We introduce SF-Relate, a practical and secure federated algorithm for identifying genetic relatives across data silos. SF-Relate vastly reduces the number of individual pairs to compare while maintaining accurate detection through a novel locality-sensitive hashing approach. We assign individuals who are likely to be related together into buckets and then test relationships only between individuals in matching buckets across parties. To this end, we construct an effective hash function that captures identity-by-descent (IBD) segments in genetic sequences, which, along with a new bucketing strategy, enable accurate and practical private relative detection. To guarantee privacy, we introduce an efficient algorithm based on multiparty homomorphic encryption (MHE) to allow data holders to cooperatively compute the relatedness coefficients between individuals, and to further classify their degrees of relatedness, all without sharing any private data. We demonstrate the accuracy and practical runtimes of SF-Relate on the UK Biobank and All of Us datasets. On a dataset of 200K individuals split between two parties, SF-Relate detects 94.9% of third-degree relatives, and 99.9% of second-degree or closer relatives, within 15 hours of runtime. Our work enables secure identification of relatives across large-scale genomic datasets.

Encrypted federated learning for secure decentralized collaboration in cancer image analysis

Artificial intelligence (AI) has a multitude of applications in cancer research and oncology. However, the training of AI systems is impeded by the limited availability of large datasets due to data protection requirements and other regulatory obstacles. Federated and swarm learning represent possible solutions to this problem by collaboratively training AI models while avoiding data transfer. However, in these decentralized methods, weight updates are still transferred to the aggregation server for merging the models. This leaves the possibility for a breach of data privacy, for example by model inversion or membership inference attacks by untrusted servers. Somewhat-homomorphically-encrypted federated learning (SHEFL) is a solution to this problem because only encrypted weights are transferred, and model updates are performed in the encrypted space. Here, we demonstrate the first successful implementation of SHEFL in a range of clinically relevant tasks in cancer image analysis on multicentric datasets in radiology and histopathology. We show that SHEFL enables the training of AI models which outperform locally trained models and perform on par with models which are centrally trained. In the future, SHEFL can enable multiple institutions to co-train AI models without forsaking data governance and without ever transmitting any decryptable data to untrusted servers.

Scalable and Privacy-Preserving Federated Principal Component Analysis

Principal component analysis (PCA) is an essential algorithm for dimensionality reduction in many data science domains. We address the problem of performing a federated PCA on private data distributed among multiple data providers while ensuring data confidentiality. Our solution, SF-PCA, is an end-to-end secure system that preserves the confidentiality of both the original data and all intermediate results in a passive-adversary model with up to all-but-one colluding parties. SF-PCA jointly leverages multiparty homomorphic encryption, interactive protocols, and edge computing to efficiently interleave computations on local cleartext data with operations on collectively encrypted data. SF-PCA obtains results as accurate as non-secure centralized solutions, independently of the data distribution among the parties. It scales linearly or better with the dataset dimensions and with the number of data providers. SF-PCA is more precise than existing approaches that approximate the solution by combining local analysis results, and between 3x and 250x faster than privacy-preserving alternatives based solely on secure multiparty computation or homomorphic encryption. Our work demonstrates the practical applicability of secure and federated PCA on private distributed datasets.

Privacy-preserving Decentralized Federated Learning over Time-varying Communication Graph

Establishing how a set of learners can provide privacy-preserving federated learning in a fully decentralized (peer-to-peer, no coordinator) manner is an open problem. We propose the first privacy-preserving consensus-based algorithm for the distributed learners to achieve decentralized global model aggregation in an environment of high mobility, where participating learners and the communication graph between them may vary during the learning process. In particular, whenever the communication graph changes, the Metropolis-Hastings method [69] is applied to update the weighted adjacency matrix based on the current communication topology. In addition, the Shamir’s secret sharing scheme [61] is integrated to facilitate privacy in reaching consensus of the global model. The paper establishes the correctness and privacy properties of the proposed algorithm. The computational efficiency is evaluated by a simulation built on a federated learning framework with a real-world dataset.

Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption

Using real-world evidence in biomedical research, an indispensable complement to clinical trials, requires access to large quantities of patient data that are typically held separately by multiple healthcare institutions. We propose FAMHE, a novel federated analytics system that, based on multiparty homomorphic encryption (MHE), enables privacy-preserving analyses of distributed datasets by yielding highly accurate results without revealing any intermediate data. We demonstrate the applicability of FAMHE to essential biomedical analysis tasks, including Kaplan-Meier survival analysis in oncology and genome-wide association studies in medical genetics. Using our system, we accurately and efficiently reproduce two published centralized studies in a federated setting, enabling biomedical insights that are not possible from individual institutions alone. Our work represents a necessary key step towards overcoming the privacy hurdle in enabling multi-centric scientific collaborations.

Existing approaches to sharing of distributed medical data either provide only limited protection of patients’ privacy or sacrifice the accuracy of results. Here, the authors propose a federated analytics system, based on multiparty homomorphic encryption (MHE), to overcome these issues.

Multiparty Homomorphic Encryption from Ring-Learning-with-Errors

We propose and evaluate a secure-multiparty-computation (MPC) solution in the semi-honest model with dishonest majority that is based on multiparty homomorphic encryption (MHE). To support our solution, we introduce a multiparty version of the Brakerski-Fan-Vercauteren homomorphic cryptosystem and implement it in an open-source library. MHE-based MPC solutions have several advantages: Their transcript is public, their o~ine phase is compact, and their circuit-evaluation procedure is noninteractive. By exploiting these properties, the communication complexity of MPC tasks is reduced from quadratic to linear in the number of parties, thus enabling secure computation among potentially thousands of parties and in a broad variety of computing paradigms, from the traditional peer-to-peer setting to cloud-outsourcing and smart-contract technologies. MHE-based approaches can also outperform the state-of-the-art solutions, even for a small number of parties. We demonstrate this for three circuits: private input selection with application to private-information retrieval, component-wise vector multiplication with application to private-set intersection, and Beaver multiplication triples generation. For the first circuit, privately selecting one input among eight thousand parties’ (of 32 KB each) requires only 1.31 MB of communication per party and completes in 61.7 seconds. For the second circuit with eight parties, our approach is 8.6 times faster and requires 39.3 times less communication than the current methods. For the third circuit and ten parties, our approach generates 20 times more triples per second while requiring 136 times less communication per-triple than an approach based on oblivious transfer. We implemented our scheme in the Lattigo library and open-sourced the code at github.com/ldsec/lattigo.