RSTG: Robust Generation of High Quality Spatial Transcriptomics Data using Beta Divergence Based AutoEncoder

One of the key challenges in spatial transcriptomics data analysis is the lack of sufficient data to train the models. To address this shortcoming, multiple generative models have been developed to generate synthetic spatial transcriptomics samples in a controlled environment. However, these often fail at out-of-the-box generation in the presence of noise (such as outliers). To tackle this challenge, we propose RSTG (Robust Spatial Transcriptomic Generator), an autoencoder incorporating a {beta}-ELBO loss, to generate high-quality realistic spatial transcriptomic sequences. Our model uncovers the data intrinsic structure by approximating its underlying distribution through variational inference, resulting in more interpretable and robust density estimation. We validate the effectiveness of RSTG across multiple tasks, including the recovery of cellular positions in both the 2D spatial and location domains. Our method shows improved performance both qualitatively and quantitatively on multiple datasets from the dorsolateral cortex and the brain using MERFISH and Visium technologies. We further illustrate the robustness of our model to outliers by contaminating a portion of the data with possible anomalies (such as white noises, batch effects, and dropouts). Promising results show that our proposal maintains high quality and stability even when the training data are contaminated, across a variety of experimental settings and in comparison with existing approaches.