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ArXiv Preprint

Genomic data provides researchers with an invaluable source of information to advance progress in biomedical research, personalized medicine, and drug development. At the same time, however, this data is extremely sensitive, which makes data sharing, and consequently availability, problematic if not outright impossible. As a result, organizations have begun to experiment with sharing synthetic data, which should mirror the real data's salient characteristics, without exposing it. In this paper, we provide the first evaluation of the utility and the privacy protection of five state-of-the-art models for generating synthetic genomic data. First, we assess the performance of the synthetic data on a number of common tasks, such as allele and population statistics as well as linkage disequilibrium and principal component analysis. Then, we study the susceptibility of the data to membership inference attacks, i.e., inferring whether a target record was part of the data used to train the model producing the synthetic dataset. Overall, there is no single approach for generating synthetic genomic data that performs well across the board. We show how the size and the nature of the training dataset matter, especially in the case of generative models. While some combinations of datasets and models produce synthetic data with distributions close to the real data, there often are target data points that are vulnerable to membership inference. Our measurement framework can be used by practitioners to assess the risks of deploying synthetic genomic data in the wild, and will serve as a benchmark tool for researchers and practitioners in the future.

Bristena Oprisanu, Georgi Ganev, Emiliano De Cristofaro