Combining Graph Neural Network and Mamba to Capture Local and Global Tissue Spatial Relationships in Whole Slide Images

In computational pathology, extracting spatial features from gigapixel whole slide images (WSIs) is a fundamental task, but due to their large size, WSIs are typically segmented into smaller tiles. A critical aspect of this analysis is aggregating information from these tiles to make predictions at the WSI level. We introduce a model that combines a message-passing graph neural network (GNN) with a state space model (Mamba) to capture both local and global spatial relationships among the tiles in WSIs. The model's effectiveness was demonstrated in predicting progression-free survival among patients with early-stage lung adenocarcinomas (LUAD). We compared the model with other state-of-the-art methods for tile-level information aggregation in WSIs, including tile-level information summary statistics-based aggregation, multiple instance learning (MIL)-based aggregation, GNN-based aggregation, and GNN-transformer-based aggregation. Additional experiments showed the impact of different types of node features and different tile sampling strategies on the model performance. This work can be easily extended to any WSI-based analysis. Code: https://github.com/rina-ding/gat-mamba.

Improving mitosis detection on histopathology images using large vision-language models

In certain types of cancerous tissue, mitotic count has been shown to be associated with tumor proliferation, poor prognosis, and therapeutic resistance. Due to the high inter-rater variability of mitotic counting by pathologists, convolutional neural networks (CNNs) have been employed to reduce the subjectivity of mitosis detection in hematoxylin and eosin (H&E)-stained whole slide images. However, most existing models have performance that lags behind expert panel review and only incorporate visual information. In this work, we demonstrate that pre-trained large-scale vision-language models that leverage both visual features and natural language improve mitosis detection accuracy. We formulate the mitosis detection task as an image captioning task and a visual question answering (VQA) task by including metadata such as tumor and scanner types as context. The effectiveness of our pipeline is demonstrated via comparison with various baseline models using 9,501 mitotic figures and 11,051 hard negatives (non-mitotic figures that are difficult to characterize) from the publicly available Mitosis Domain Generalization Challenge (MIDOG22) dataset.