Towards Biologically Plausible and Private Gene Expression Data
  Generation
Dingfan Chen Marie Oestreich Tejumade Afonja Raouf Kerkouche Matthias Becker Mario Fritz
Generative models trained with Differential Privacy (DP) are becoming
increasingly prominent in the creation of synthetic data for downstream
applications. Existing literature, however, primarily focuses on basic
benchmarking datasets and tends to report promising results only for elementary
metrics and relatively simple data distributions. In this paper, we initiate a
systematic analysis of how DP generative models perform in their natural
application scenarios, specifically focusing on real-world gene expression
data. We conduct a comprehensive analysis of five representative DP generation
methods, examining them from various angles, such as downstream utility,
statistical properties, and biological plausibility. Our extensive evaluation
illuminates the unique characteristics of each DP generation method, offering
critical insights into the strengths and weaknesses of each approach, and
uncovering intriguing possibilities for future developments. Perhaps
surprisingly, our analysis reveals that most methods are capable of achieving
seemingly reasonable downstream utility, according to the standard evaluation
metrics considered in existing literature. Nevertheless, we find that none of
the DP methods are able to accurately capture the biological characteristics of
the real dataset. This observation suggests a potential over-optimistic
assessment of current methodologies in this field and underscores a pressing
need for future enhancements in model design.