论文标题

GNN如何从大规模医学图像中促进CNNS的挖掘几何信息

How GNNs Facilitate CNNs in Mining Geometric Information from Large-Scale Medical Images

论文作者

Shen, Yiqing, Zhou, Bingxin, Xiong, Xinye, Gao, Ruitian, Wang, Yu Guang

论文摘要

Gigapixel Medical图像提供了大量的数据,包括形态学纹理和空间信息。由于组织学的数据量表较大,​​深度学习方法作为提取器起着越来越重要的作用。现有的解决方案在很大程度上依赖卷积神经网络(CNN)进行全局像素级分析,从而使潜在的局部几何结构(例如肿瘤微环境中的细胞之间的相互作用均未探索。事实证明,医学图像中的拓扑结构与肿瘤进化密切相关,可以很好地以图为特征。为了获得下游肿瘤学任务的更全面的表示,我们提出了一个融合框架,以增强CNN捕获的全局图像级表示,并使用图形神经网络(GNN)学习的细胞级空间信息的几何形状。融合层优化了全局图像和单元格图的协作特征之间的集成。已经开发了两种融合策略:一种具有MLP的融合策略,这很简单,但通过微调有效,而Transformer获得了融合多个网络的冠军。我们评估了从大型患者群体和胃癌策划的组织学数据集的融合策略,以完成三个生物标志物预测任务。两种型号的表现都优于普通CNN或GNN,在各种网络骨架上达到了超过5%的AUC提高。实验结果在医学图像分析中将图像水平的形态特征与细胞空间关系相结合的必要性。代码可在https://github.com/yiqings/hegnnenhancecnn上找到。

Gigapixel medical images provide massive data, both morphological textures and spatial information, to be mined. Due to the large data scale in histology, deep learning methods play an increasingly significant role as feature extractors. Existing solutions heavily rely on convolutional neural networks (CNNs) for global pixel-level analysis, leaving the underlying local geometric structure such as the interaction between cells in the tumor microenvironment unexplored. The topological structure in medical images, as proven to be closely related to tumor evolution, can be well characterized by graphs. To obtain a more comprehensive representation for downstream oncology tasks, we propose a fusion framework for enhancing the global image-level representation captured by CNNs with the geometry of cell-level spatial information learned by graph neural networks (GNN). The fusion layer optimizes an integration between collaborative features of global images and cell graphs. Two fusion strategies have been developed: one with MLP which is simple but turns out efficient through fine-tuning, and the other with Transformer gains a champion in fusing multiple networks. We evaluate our fusion strategies on histology datasets curated from large patient cohorts of colorectal and gastric cancers for three biomarker prediction tasks. Both two models outperform plain CNNs or GNNs, reaching a consistent AUC improvement of more than 5% on various network backbones. The experimental results yield the necessity for combining image-level morphological features with cell spatial relations in medical image analysis. Codes are available at https://github.com/yiqings/HEGnnEnhanceCnn.

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