Creating Artificial Human Genomes Using Generative Models

PLOS Genetics

Generative models have shown breakthroughs in a wide spectrum of domains due to recent advancements in machine learning algorithms and increased computational power. Despite these impressive achievements, the ability of generative models to create realistic synthetic data is still under-exploited in genetics and absent from population genetics. Yet a known limitation in the field is the reduced access to many genetic databases due to concerns about violations of individual privacy, although they would provide a rich resource for data mining and integration towards advancing genetic studies. In this study, we demonstrated that deep generative adversarial networks (GANs) and restricted Boltzmann machines (RBMs) can be trained to learn the complex distributions of real genomic datasets and generate novel high-quality artificial genomes (AGs) with none to little privacy loss. We show that our generated AGs replicate characteristics of the source dataset such as allele frequencies, linka...

2020

Generative Adversarial Network (GAN) and its variants have shown promising results in generating synthetic data. However, the issues with GANs are: (i) the learning happens around the training samples and the model often ends up remembering them, consequently, compromising the privacy of individual samples - this becomes a major concern when GANs are applied to training data including personally identifiable information, (ii) the randomness in generated data - there is no control over the specificity of generated samples. To address these issues, we propose imdpGAN-an information maximizing differentially private Generative Adversarial Network. It is an end-to-end framework that simultaneously achieves privacy protection and learns latent representations. With experiments on MNIST dataset, we show that imdpGAN preserves the privacy of the individual data point, and learns latent codes to control the specificity of the generated samples. We perform binary classification on digit pair...

Privacy is an important concern for our society where sharing data with partners or releasing data to the public is a frequent occurrence. Some of the techniques that are being used to achieve privacy are to remove identifiers, alter quasi-identifiers, and perturb values. Unfortunately, these approaches suffer from two limitations. First, it has been shown that private information can still be leaked if attackers possess some background knowledge or other information sources. Second, they do not take into account the adverse impact these methods will have on the utility of the released data. In this paper, we propose a method that meets both requirements. Our method, called table-GAN, uses generative ad-versarial networks (GANs) to synthesize fake tables that are statistically similar to the original table yet do not incur information leakage. We show that the machine learning models trained using our synthetic tables exhibit performance that is similar to that of models trained using the original table for unknown testing cases. We call this property model compatibility. We believe that anonymization/perturbation/synthesis methods without model compatibility are of little value. We used four real-world datasets from four different domains for our experiments and conducted in-depth comparisons with state-of-the-art anonymization, perturbation , and generation techniques. Throughout our experiments, only our method consistently shows balance between privacy level and model compatibility.

Information Sciences, 2022

Deep learning models have demonstrated superior performance in several real-world application problems such as image classification and speech processing. However, creating these models in sensitive domains like healthcare typically requires addressing certain privacy challenges that bring unique concerns. One effective way to handle such private data concerns is to generate realistic synthetic data that can provide practically acceptable data quality as well as be used to improve model performance. To tackle this challenge, we develop a differentially private framework for synthetic data generation using Rényi differential privacy. Our approach builds on convolutional autoencoders and convolutional generative adversarial networks to preserve critical characteristics of the generated synthetic data. In addition, our model can capture the temporal information and feature correlations present in the original data. We demonstrate that our model outperforms existing state-of-the-art models under the same privacy budget using several publicly available benchmark medical datasets in both supervised and unsupervised settings. The source code of this work is available at https://github.com/astorfi/differentially-private-cgan.

2019

Machine learning has the potential to assist many communities in using the large datasets that are becoming more and more available. Unfortunately, much of that potential is not being realized because it would require sharing data in a way that compromises privacy. In this paper, we investigate a method for ensuring (differential) privacy of the generator of the Generative Adversarial Nets (GAN) framework. The resulting model can be used for generating synthetic data on which algorithms can be trained and validated, and on which competitions can be conducted, without compromising the privacy of the original dataset. Our method modifies the Private Aggregation of Teacher Ensembles (PATE) framework and applies it to GANs. Our modified framework (which we call PATE-GAN) allows us to tightly bound the influence of any individual sample on the model, resulting in tight differential privacy guarantees and thus an improved performance over models with the same guarantees. We also look at m...

Proceedings 2022 Network and Distributed System Security Symposium

The availability of genomic data is essential to progress in biomedical research, personalized medicine, etc. However, its extreme sensitivity makes it problematic, if not outright impossible, to publish or share it. As a result, several initiatives have been launched to experiment with synthetic genomic data, e.g., using generative models to learn the underlying distribution of the real data and generate artificial datasets that preserve its salient characteristics without exposing it. This paper provides the first evaluation of both utility and privacy protection of six state-of-the-art models for generating synthetic genomic data. We assess the performance of the synthetic data on several common tasks, such as allele population statistics and linkage disequilibrium. We then measure privacy through the lens of membership inference attacks, i.e., inferring whether a record was part of the training data. Our experiments show that no single approach to generate synthetic genomic data yields both high utility and strong privacy across the board. Also, the size and nature of the training dataset matter. Moreover, 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. Looking forward, our techniques can be used by practitioners to assess the risks of deploying synthetic genomic data in the wild and serve as a benchmark for future work.

arXiv (Cornell University), 2021

Generative Adversarial Networks (GANs) are gaining increasing attention as a means for synthesising data. So far much of this work has been applied to use cases outside of the data confidentiality domain with a common application being the production of artificial images. Here we consider the potential application of GANs for the purpose of generating synthetic census microdata. We employ a battery of utility metrics and a disclosure risk metric (the Targeted Correct Attribution Probability) to compare the data produced by tabular GANs with those produced using orthodox data synthesis methods.

Biocomputing 2020, 2019

Typical personal medical data contains sensitive information about individuals. Storing or sharing the personal medical data is thus often risky. For example, a short DNA sequence can provide information that can not only identify an individual, but also his or her relatives. Nonetheless, most countries and researchers agree on the necessity of collecting personal medical data. This stems from the fact that medical data, including genomic data, are an indispensable resource for further research and development regarding disease prevention and treatment. To prevent personal medical data from being misused, techniques to reliably preserve sensitive information should be developed for real world application. In this paper, we propose a framework called anonymized generative adversarial networks (AnomiGAN), to improve the maintenance of privacy of personal medical data, while also maintaining high prediction performance. We compared our method to state-of-the-art techniques and observed that our method preserves the same level of privacy as differential privacy (DP), but had better prediction results. We also observed that there is a trade-off between privacy and performance results depending on the degree of preservation of the original data. Here, we provide a mathematical overview of our proposed model and demonstrate its validation using UCI machine learning repository datasets in order to highlight its utility in practice. Experimentally, our approach delivers a better performance compared to that of the DP approach.

The transcriptome is the most extensive and standardized among all biological data, but its lack of inherent structure impedes the application of deep learning tools. This study resolves the neighborhood relationship of protein-coding genes through uniform manifold approximation and projection (UMAP) of high-quality gene expression data. The resultant transcriptome image is conducive to classification tasks and generative learning. Convolutional neural networks (CNNs) trained with full or partial transcriptome images differentiate normal versus lung squamous cell carcinoma (LUSC) and LUSC versus lung adenocarcinoma (LUAD) with over 96% accuracy, comparable to XGBoost. Meanwhile, the generative adversarial network (GAN) model trained with 93 TcgaTargetGtex transcriptome classes synthesizes highly realistic and diverse tissue/cancer-specific transcriptome images. Comparative analysis of GAN-synthesized LUSC and LUAD transcriptome images show selective retention and enhancement of epit...

The generation of synthetic medical data has become a focal point for researchers, driven by the increasing demand for privacy-preserving solutions. While existing generative methods heavily rely on real datasets for training, access to such data is often restricted. In contrast, statistical information about these datasets is more readily available, yet current methods struggle to generate tabular data solely from statistical inputs. This study addresses the gaps by introducing a novel approach that converts statistical data into tabular datasets using a modified Generative Adversarial Network (GAN) architecture. A custom loss function was incorporated into the training process to enhance the quality of the generated data. The proposed method is evaluated using fidelity and utility metrics, achieving "Good" similarity and "Excellent" utility scores. While the generated data may not fully replace real databases, it demonstrates satisfactory performance for training machine-learning algorithms. This work provides a promising solution for synthetic data generation when real datasets are inaccessible, with potential applications in medical data privacy and beyond.