BioGAN: Enhancing Transcriptomic Data Generation with Biological Knowledge

The advancement of computational genomics has significantly enhanced the use of data-driven solutions in disease prediction and precision medicine. Yet, challenges such as data scarcity, privacy constraints, and biases persist. Synthetic data generation offers a promising solution to these issues. However, existing approaches based on generative artificial intelligence often fail to incorporate biological knowledge, limiting the realism and utility of generated samples. In this work, we present BioGAN, a novel generative framework that, for the first time, incorporates graph neural networks into a generative adversarial network architecture for transcriptomic data generation. By leveraging gene regulatory and co-expression networks, our model preserves biological properties in the generated transcriptomic profiles. We validate its effectiveness on E. coli and human gene expression datasets through extensive experiments using unsupervised and supervised evaluation metrics. The results demonstrate that incorporating a priori biological knowledge is an effective strategy for enhancing both the quality and utility of synthetic transcriptomic data. On human data, BioGAN achieves a 4.3% improvement in precision and an up to 2.6% higher correlation with real profiles compared to state-of-the-art models. In downstream disease and tissue classification tasks, our synthetic data improves prediction performance by an average of 5.7%. Results on E. coli further confirm BioGAN's robustness, showing consistently strong recall and predictive utility.