Variational Clustering and Denoising of Spatial Transcriptomics

Spatial transcriptomics data provides a unique opportunity to investigate both gene expression and spatial structure in tissues at the same time. However, incorporating spatial information to accurately identify spatial domains is difficult due to factors such as high-dimensionality, sparsity, noise, and dropout events. To address these issues, we introduce vGraphST, a novel graph-based deep learning approach tailored for spatial transcriptomics data. Our method combines auto-encoder and contrastive learning techniques to process high-dimensional data and generate meaningful low-dimensional embeddings. Additionally, we use continuous distributions instead of discrete values in both the latent space and the denoised gene expression space. Specifically, Gaussian distributions are used to model the latent space, while zero-inflated Poisson distributions are used to model the denoised gene expression space. Experimental results demonstrate the effectiveness of vGraphST in accurately representing and analyzing spatial transcriptomics data. When compared to other methods using the DLPFC dataset, vGraphST achieves an average Adjusted Rand Index (ARI) of 0.58, demonstrating its superiority in segmenting spatial domains and recognizing biologically relevant spatiotemporal patterns.