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

arXiv: https://arxiv.org/abs/2406.04377 · HTML: https://mlsanity.com/paper/2406.04377/

## Key facts

- Cited by 7 papers in the map (data through 14 Oct 2026).
- Placed in Mamba for medical image analysis, one of 10 directions in State-space sequence models (S4, Mamba).
- Builds on 23 of its 61 references that are in the map.
- First posted on arXiv 5 Jun 2024.

## Placed in

- State-space sequence models (S4, Mamba) / [Mamba for medical image analysis](https://mlsanity.com/ssm/mamba-for-medical-image-analysis/)

## Builds on (most cited first, 23 of 23)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [Efficiently Modeling Long Sequences with Structured State Spaces](https://mlsanity.com/paper/2111.00396/) (2021)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Big Bird: Transformers for Longer Sequences](https://mlsanity.com/paper/2007.14062/) (2020)
- [Rethinking Attention with Performers](https://mlsanity.com/paper/2009.14794/) (2020)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classification](https://mlsanity.com/paper/2106.00908/) (2021)
- [DeepGCNs: Can GCNs Go as Deep as CNNs?](https://mlsanity.com/paper/1904.03751/) (2019)
- [HoVer-Net: Simultaneous Segmentation and Classification of Nuclei in Multi-Tissue Histology Images](https://mlsanity.com/paper/1812.06499/) (2018)
- [DeepSurv: Personalized Treatment Recommender System Using A Cox Proportional Hazards Deep Neural Network](https://mlsanity.com/paper/1606.00931/) (2016)
- [Long Range Graph Benchmark](https://mlsanity.com/paper/2206.08164/) (2022)
- [Whole Slide Images based Cancer Survival Prediction using Attention Guided Deep Multiple Instance Learning Networks](https://mlsanity.com/paper/2009.11169/) (2020)
- [Graph-Mamba: Towards Long-Range Graph Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2402.00789/) (2024)
- [Whole Slide Images are 2D Point Clouds: Context-Aware Survival Prediction using Patch-based Graph Convolutional Networks](https://mlsanity.com/paper/2107.13048/) (2021)
- [MambaMIL: Enhancing Long Sequence Modeling with Sequence Reordering in Computational Pathology](https://mlsanity.com/paper/2403.06800/) (2024)
- [A graph-transformer for whole slide image classification](https://mlsanity.com/paper/2205.09671/) (2022)
- [Dynamic Graph Representation with Knowledge-aware Attention for Histopathology Whole Slide Image Analysis](https://mlsanity.com/paper/2403.07719/) (2024)
- [Demystifying Oversmoothing in Attention-Based Graph Neural Networks](https://mlsanity.com/paper/2305.16102/) (2023)
- [A Personalized Diagnostic Generation Framework Based on Multi-source Heterogeneous Data](https://mlsanity.com/paper/2110.13677/) (2021)

## Built on by (most cited first, 7 of 7)

- [Classification of Gleason Grading in Prostate Cancer Histopathology Images Using Deep Learning Techniques: YOLO, Vision Transformers, and Vision Mamba](https://mlsanity.com/paper/2409.17122/) (2024)
- [Exploring Graph Mamba: A Comprehensive Survey on State-Space Models for Graph Learning](https://mlsanity.com/paper/2412.18322/) (2024)
- [GAMDTP: Dynamic Trajectory Prediction with Graph Attention Mamba Network](https://mlsanity.com/paper/2504.04862/) (2025)
- [SlideMamba: Entropy-Based Adaptive Fusion of GNN and Mamba for Enhanced Representation Learning in Digital Pathology](https://mlsanity.com/paper/2509.21239/) (2025)
- [XtraLight-MedMamba for Classification of Neoplastic Tubular Adenomas](https://mlsanity.com/paper/2602.04819/) (2026)
- [Graph Mamba Survival Analysis Based on Topology-Aware ordering](https://mlsanity.com/paper/2606.02602/) (2026)
- [Semantic-Aware Subgraph State Space Model for WSI Classification in Histopathology](https://mlsanity.com/paper/2609.03689/) (2026)

## Abstract (arXiv)

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.