论文标题
示例引导了深度神经网络,用于基因表达预测的空间转录组学分析
Exemplar Guided Deep Neural Network for Spatial Transcriptomics Analysis of Gene Expression Prediction
论文作者
论文摘要
空间转录组学(ST)对于理解疾病和发展新型疗法至关重要。它测量了吞吐量低的组织载玻片中每个细粒面积(即不同的窗户)的基因表达。本文提出了一个示例引导网络(EGN),以直接从组织滑动图像的每个窗口直接准确有效地预测基因表达。我们将示例学习应用于从给定组织幻灯片图像窗口的最接近/相似示例中动态增强基因表达预测。我们的EGN框架由三个主要组成部分组成:1)构造无监督示例检索的表示空间的提取器; 2)视觉变压器(VIT)骨干以逐步提取输入窗口的表示; 3)一个示例桥接(EB)块,使用最近的示例来适应中间vit表示。最后,我们使用简单的基于注意力的预测块来完成基因表达预测任务。标准基准数据集的实验表明,与过去的最新方法(SOTA)方法相比,我们的方法的优越性。
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.