In silico generation of gene expression profiles using diffusion models

BACKGROUND: RNA-seq data is used for precision medicine (e.g., cancer predictions), which benefits from deep learning approaches to analyze complex gene expression data. However, transcriptomics datasets often have few samples compared to deep learning standards. Synthetic data generation is thus being explored to address this data scarcity. So far, only deep generative models such as Variational Autoencoders (VAEs) and Generative Adversarial Networks (GANs) have been used for this aim. Considering the recent success of diffusion models (DM) in image generation, we propose a diffusion-model-based generation pipeline that leverages the power of such generative models on transcriptomics data. RESULTS: This paper presents two state-of-the-art diffusion models (DDPM and DDIM) and achieves their adaptation in the transcriptomics field. DM-generated data of L1000 landmark genes show better predictive performance over TCGA and GTEx datasets. We also compare linear and nonlinear reconstruction methods to recover the complete transcriptome. Results show that such reconstruction methods can boost the performance of diffusion models, as well as VAEs and GANs. CONCLUSIONS: Overall, the extensive comparison of various generative models using data quality indicators shows that diffusion models rank among the best-performing methods, making them promising synthetic transcriptomics generators.