A Transformer-Based Deep Diffusion Model for Bulk RNA-Seq Deconvolution

Background: Bulk RNA-seq is a cost-effective method for measuring average gene expression in tissue samples, but its lack of single-cell resolution limits the understanding of cellular heterogeneity. Computational deconvolution aims to infer cell-type proportions from bulk RNA-seq data; however, the accuracy of existing methods needs improvement, especially in complex tissues. Methods: In this study, we introduce DiffFormer, a novel deconvolution model that, for the first time, integrates a conditional diffusion model with a Transformer architecture. We systematically evaluated DiffFormer on four pseudo-bulk datasets and validated it on a gold-standard real-world dataset with FACS-based ground truth. Results: DiffFormer demonstrated consistent and strong performance across all test datasets, outperforming existing methods and a baseline MLP-based diffusion model (DiffMLP). For instance, on the pbmc3k dataset, DiffFormer reduced the Root Mean Square Error (RMSE) from 0.1060 to 0.0120 compared to DiffMLP. This advantage was further confirmed on the real-world dataset, where DiffFormer achieved the highest Pearson Correlation Coefficient (PCC). Conclusions: This work provides a high-precision, reproducible tool for cellular deconvolution. Crucially, the direct comparison with an MLP-based diffusion model provides definitive evidence that the Transformer architecture is key to its success, highlighting the potential of such models for solving complex bioinformatics problems.