# GNN-Suite: a Graph Neural Network Benchmarking Framework for Biomedical Informatics

arXiv: https://arxiv.org/abs/2505.10711 · HTML: https://mlsanity.com/paper/2505.10711/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 59 references that are in the map.
- First posted on arXiv 15 May 2025.

## Builds on (most cited first, 18 of 18)

- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [A Comprehensive Survey on Graph Neural Networks](https://mlsanity.com/paper/1901.00596/) (2019)
- [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)
- [Graph Neural Networks: A Review of Methods and Applications](https://mlsanity.com/paper/1812.08434/) (2018)
- [Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gauges](https://mlsanity.com/paper/2104.13478/) (2021)
- [Geometric deep learning: going beyond Euclidean data](https://mlsanity.com/paper/1611.08097/) (2016)
- [QA-GNN: Reasoning with Language Models and Knowledge Graphs for Question Answering](https://mlsanity.com/paper/2104.06378/) (2021)
- [Point-GNN: Graph Neural Network for 3D Object Detection in a Point Cloud](https://mlsanity.com/paper/2003.01251/) (2020)
- [Improving Reproducibility in Machine Learning Research (A Report from the NeurIPS 2019 Reproducibility Program)](https://mlsanity.com/paper/2003.12206/) (2020)
- [PMLB: A Large Benchmark Suite for Machine Learning Evaluation and Comparison](https://mlsanity.com/paper/1703.00512/) (2017)
- [Scientific Machine Learning Benchmarks](https://mlsanity.com/paper/2110.12773/) (2021)
- [Message passing all the way up](https://mlsanity.com/paper/2202.11097/) (2022)
- [A Survey on Graph-Based Deep Learning for Computational Histopathology](https://mlsanity.com/paper/2107.00272/) (2021)
- [GNNFlow: A Distributed Framework for Continuous Temporal GNN Learning on Dynamic Graphs](https://mlsanity.com/paper/2311.17410/) (2023)
- [GNNBENCH: Fair and Productive Benchmarking for Single-GPU GNN System](https://mlsanity.com/paper/2404.04118/) (2024)

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

- [A Multimodal Human Protein Embeddings Database: DeepDrug Protein Embeddings Bank (DPEB)](https://mlsanity.com/paper/2510.22008/) (2025)
- [EdgeRefine: Privacy-Utility Balance for Graphs via Jaccard Sampling under Edge Differential Privacy](https://mlsanity.com/paper/2607.08659/) (2026)

## Abstract (arXiv)

We present GNN-Suite, a robust modular framework for constructing and benchmarking Graph Neural Network (GNN) architectures in computational biology. GNN-Suite standardises experimentation and reproducibility using the Nextflow workflow to evaluate GNN performance. We demonstrate its utility in identifying cancer-driver genes by constructing molecular networks from protein-protein interaction (PPI) data from STRING and BioGRID and annotating nodes with features from the PCAWG, PID, and COSMIC-CGC repositories. Our design enables fair comparisons among diverse GNN architectures including GAT, GAT3H, GCN, GCN2, GIN, GTN, HGCN, PHGCN, and GraphSAGE and a baseline Logistic Regression (LR) model. All GNNs were configured as standardised two-layer models and trained with uniform hyperparameters (dropout = 0.2; Adam optimiser with learning rate = 0.01; and an adjusted binary cross-entropy loss to address class imbalance) over an 80/20 train-test split for 300 epochs. Each model was evaluated over 10 independent runs with different random seeds to yield statistically robust performance metrics, with balanced accuracy (BACC) as the primary measure. Notably, GCN2 achieved the highest BACC (0.807 +/- 0.035) on a STRING-based network, although all GNN types outperformed the LR baseline, highlighting the advantage of network-based learning over feature-only approaches. Our results show that a common framework for implementing and evaluating GNN architectures aids in identifying not only the best model but also the most effective means of incorporating complementary data. By making GNN-Suite publicly available, we aim to foster reproducible research and promote improved benchmarking standards in computational biology. Future work will explore additional omics datasets and further refine network architectures to enhance predictive accuracy and interpretability in biomedical applications.