# A New Graph Node Classification Benchmark: Learning Structure from Histology Cell Graphs

arXiv: https://arxiv.org/abs/2211.06292 · HTML: https://mlsanity.com/paper/2211.06292/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 22 of its 41 references that are in the map.
- First posted on arXiv 11 Nov 2022.

## Builds on (most cited first, 22 of 22)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [Simplifying Graph Convolutional Networks](https://mlsanity.com/paper/1902.07153/) (2019)
- [Deep Graph Infomax](https://mlsanity.com/paper/1809.10341/) (2018)
- [Pitfalls of Graph Neural Network Evaluation](https://mlsanity.com/paper/1811.05868/) (2018)
- [Revisiting Semi-Supervised Learning with Graph Embeddings](https://mlsanity.com/paper/1603.08861/) (2016)
- [How Attentive are Graph Attention Networks?](https://mlsanity.com/paper/2105.14491/) (2021)
- [GraphSAINT: Graph Sampling Based Inductive Learning Method](https://mlsanity.com/paper/1907.04931/) (2019)
- [Cluster-GCN: An Efficient Algorithm for Training Deep and Large Graph Convolutional Networks](https://mlsanity.com/paper/1905.07953/) (2019)
- [Quantifying the Carbon Emissions of Machine Learning](https://mlsanity.com/paper/1910.09700/) (2019)
- [SIGN: Scalable Inception Graph Neural Networks](https://mlsanity.com/paper/2004.11198/) (2020)
- [Pathomic Fusion: An Integrated Framework for Fusing Histopathology and Genomic Features for Cancer Diagnosis and Prognosis](https://mlsanity.com/paper/1912.08937/) (2019)
- [Predicting multicellular function through multi-layer tissue networks](https://mlsanity.com/paper/1707.04638/) (2017)
- [Decoupling the Depth and Scope of Graph Neural Networks](https://mlsanity.com/paper/2201.07858/) (2022)
- [CGC-Net: Cell Graph Convolutional Network for Grading of Colorectal Cancer Histology Images](https://mlsanity.com/paper/1909.01068/) (2019)
- [SlideGraph+: Whole Slide Image Level Graphs to Predict HER2Status in Breast Cancer](https://mlsanity.com/paper/2110.06042/) (2021)
- [Histographs: Graphs in Histopathology](https://mlsanity.com/paper/1908.05020/) (2019)

## Built on by (most cited first, 2 of 2)

- [Robust Subgraph Learning by Monitoring Early Training Representations](https://mlsanity.com/paper/2403.09901/) (2024)
- [Context-aware Skin Cancer Epithelial Cell Classification with Scalable Graph Transformers](https://mlsanity.com/paper/2602.15783/) (2026)

## Abstract (arXiv)

We introduce a new benchmark dataset, Placenta, for node classification in an underexplored domain: predicting microanatomical tissue structures from cell graphs in placenta histology whole slide images. This problem is uniquely challenging for graph learning for a few reasons. Cell graphs are large (>1 million nodes per image), node features are varied (64-dimensions of 11 types of cells), class labels are imbalanced (9 classes ranging from 0.21% of the data to 40.0%), and cellular communities cluster into heterogeneously distributed tissues of widely varying sizes (from 11 nodes to 44,671 nodes for a single structure). Here, we release a dataset consisting of two cell graphs from two placenta histology images totalling 2,395,747 nodes, 799,745 of which have ground truth labels. We present inductive benchmark results for 7 scalable models and show how the unique qualities of cell graphs can help drive the development of novel graph neural network architectures.