M2ORT: Many-To-One Regression Transformer for Spatial Transcriptomics Prediction from Histopathology Images

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Abstract

The advancement of Spatial Transcriptomics (ST) has facilitated the spatially-aware profiling of gene expressions based on histopathology images. Although ST data offers valuable insights into the micro-environment of tumors, its acquisition cost remains expensive. Therefore, directly predicting the ST expressions from digital pathology images is desired. Current methods usually adopt existing regression backbones for this task, which ignore the inherent multi-scale hierarchical data structure of digital pathology images. To address this limit, we propose M2ORT, a many-to-one regression Transformer that can accommodate the hierarchical structure of the pathology images through a decoupled multi-scale feature extractor. Different from traditional models that are trained with one-to-one image-label pairs, M2ORT accepts multiple pathology images of different magnifications at a time to jointly predict the gene expressions at their corresponding common ST spot, aiming at learning a many-to-one relationship through training. We have tested M2ORT on three public ST datasets and the experimental results show that M2ORT can achieve state-of-the-art performance with fewer parameters and floating-point operations (FLOPs). The code is available at: https://github.com/Dootmaan/M2ORT/.

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