Exemplar Guided Deep Neural Network for Spatial Transcriptomics Analysis of Gene Expression Prediction

Spatial transcriptomics (ST) is essential for understanding diseases and developing novel treatments. It measures gene expression of each fine-grained area (i.e., different windows) in the tissue slide with low throughput. This paper proposes an Exemplar Guided Network (EGN) to accurately and efficiently predict gene expression directly from each window of a tissue slide image. We apply exemplar learning to dynamically boost gene expression prediction from nearest/similar exemplars of a given tissue slide image window. Our EGN framework composes of three main components: 1) an extractor to structure a representation space for unsupervised exemplar retrievals; 2) a vision transformer (ViT) backbone to progressively extract representations of the input window; and 3) an Exemplar Bridging (EB) block to adaptively revise the intermediate ViT representations by using the nearest exemplars. Finally, we complete the gene expression prediction task with a simple attention-based prediction block. Experiments on standard benchmark datasets indicate the superiority of our approach when comparing with the past state-of-the-art (SOTA) methods.

ISG: I can See Your Gene Expression

This paper aims to predict gene expression from a histology slide image precisely. Such a slide image has a large resolution and sparsely distributed textures. These obstruct extracting and interpreting discriminative features from the slide image for diverse gene types prediction. Existing gene expression methods mainly use general components to filter textureless regions, extract features, and aggregate features uniformly across regions. However, they ignore gaps and interactions between different image regions and are therefore inferior in the gene expression task. Instead, we present ISG framework that harnesses interactions among discriminative features from texture-abundant regions by three new modules: 1) a Shannon Selection module, based on the Shannon information content and Solomonoff's theory, to filter out textureless image regions; 2) a Feature Extraction network to extract expressive low-dimensional feature representations for efficient region interactions among a high-resolution image; 3) a Dual Attention network attends to regions with desired gene expression features and aggregates them for the prediction task. Extensive experiments on standard benchmark datasets show that the proposed ISG framework outperforms state-of-the-art methods significantly.