PrunE: Pruning Spurious Subgraphs for Graph Out-of-Distribution Generalization

Official PyTorch implementation of "Pruning Spurious Subgraphs for Graph Out-of-Distribution Generalization"

Tianjun Yao¹, Haoxuan Li¹, Yongqiang Chen^1,2, Tongliang Liu^3,1, Le Song¹, Eric Xing^1,2, Zhiqiang Shen¹

¹Mohamed bin Zayed University of AI, ²Carnegie Mellon University, ³The University of Sydney

NeurIPS 2025

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🎯 Overview

Graph Neural Networks (GNNs) often suffer from significant performance degradation under distribution shifts. While existing methods attempt to directly identify invariant subgraphs, we propose PrunE, which takes a complementary approach by pruning spurious edges to preserve invariant structures more effectively.

Key Insight: While some spurious edges strongly correlate with labels, the majority are uninformative and easier to identify due to weak correlations. By pruning these uninformative edges, PrunE naturally preserves the invariant subgraph through ERM's inductive bias, achieving superior OOD generalization.

Why Pruning Works Better

From our case study on GOOD-Motif dataset:

• Previous methods (GSAT, CIGA, AIA) directly identify invariant edges but often misclassify edges in G_c with low probabilities
• PrunE preserves ~9/10 invariant edges vs. ~5/10 for baselines by focusing on removing spurious edges
• Even with some spurious edges remaining, better preservation of G_c leads to 24.19% performance improvement

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🚀 Key Contributions

1. Novel Pruning-Based Framework

First graph OOD method that focuses on removing spurious edges rather than directly identifying invariant ones, leading to more comprehensive preservation of invariant substructures.

2. Two Lightweight Regularization Terms

Graph Size Constraint ($\mathcal{L}_e$):

$\mathcal{L}_e = \mathbb{E}_G \left[\left(\frac{\sum_{(i,j)\in E} \tilde{A}_{ij}}{|E|} - \eta\right)^2\right]$

Excludes uninformative spurious edges by limiting total edge weights to $\eta|G|$, where $\eta \in \{0.5, 0.75, 0.85\}$.

ε-Probability Alignment ($\mathcal{L}_s$):

$\mathcal{L}_s = \mathbb{E}_G \left[\frac{1}{|\mathcal{E}_s|} \sum_{e_{ij}\in\mathcal{E}_s} |p_{ij} - \epsilon|\right]$

Suppresses spurious edge occurrence by aligning lowest $K\%$ edge probabilities to $\epsilon = \frac{1}{|E|}$.

Final Objective:

$\mathcal{L} = \mathcal{L}_{GT} + \lambda_1\mathcal{L}_e + \lambda_2\mathcal{L}_s$

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💻 Installation

Requirements

• Python ≥ 3.8
• PyTorch ≥ 2.1.2
• PyTorch Geometric ≥ 2.4.0
• CUDA 12.1 (recommended for GPU support)

Setup

# Clone the repository
git clone https://github.com/tianyao-aka/PrunE-GraphOOD.git
cd PrunE-GraphOOD

# Create conda environment
conda create -n prune python=3.8
conda activate prune

# Install PyTorch (adjust CUDA version as needed)
pip install torch==2.1.2 torchvision torchaudio --index-url https://download.pytorch.org/whl/cu121

# Install PyTorch Geometric
pip install torch-geometric==2.4.0

# Install other dependencies
pip install numpy==1.24.4 ogb==1.3.6

# Install GOOD benchmark dependencies (optional, for dataset loading)
# Follow instructions at: https://good.readthedocs.io/en/latest/installation.html

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⚡ Quick Start

Training on GOOD-Motif (Base Split)

python run.py --device 0 --batch_size 64 --dataset goodmotif --domain basis --shift covariate \
    --base_gnn gin --early_stop_epochs 50 --nhid 128 --epochs 100 --pretraining_epochs 10 \
    --nlayers 4 --edge_gnn_layers 2 --edge_gnn gin \
    --edge_uniform_penalty 0.001 --edge_prob_thres 90 --edge_budget 0.85 --edge_penalty 10 \
    --seed 1 --with_bn --dropout 0.0

Training on GOOD-HIV (Scaffold Split)

python run.py --device 0 --batch_size 64 --dataset goodhiv --domain scaffold --shift covariate \
    --base_gnn gin --early_stop_epochs 50 --nhid 128 --epochs 100 --pretraining_epochs 10 \
    --nlayers 4 --edge_gnn_layers 2 --edge_gnn gin --mol_encoder \
    --edge_uniform_penalty 0.001 --edge_prob_thres 50 --edge_budget 0.75 --edge_penalty 10 \
    --seed 1 --with_bn --dropout 0.0

Training on OGBG-Molbbbp (Scaffold Split)

python run.py --device 0 --batch_size 64 --dataset molbbbp --domain scaffold --shift covariate \
    --base_gnn gin --early_stop_epochs 50 --nhid 64 --epochs 100 \
    --nlayers 4 --edge_gnn_layers 2 --edge_gnn gin --mol_encoder \
    --edge_uniform_penalty 0.01 --edge_prob_thres 50 --edge_budget 0.85 --edge_penalty 10 \
    --seed 1 --with_bn --dropout 0.0

Key Arguments

Argument	Description	Paper Notation	Recommended Values
--edge_budget	Edge budget ratio	η in ℒ_e	{0.5, 0.75, 0.85}
--edge_prob_thres	Percentage of lowest probability edges	K in ℒ_s	{50, 70, 90}
--edge_penalty	Weight for graph size constraint	λ₁	{10, 40}
--edge_uniform_penalty	Weight for ε-probability alignment	λ₂	{0.001, 0.01, 0.1}
--edge_gnn	Subgraph selector architecture	t(·)	{gin, gcn}
--edge_gnn_layers	Number of layers in t(·)	-	{2, 3}
--mol_encoder	Use molecular encoders (for GOODHIV/OGBG)	-	flag

Domain Options

• GOOD-Motif: --domain basis or --domain size
• GOOD-HIV: --domain scaffold or --domain size
• OGBG datasets: --domain scaffold or --domain size

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📖 Citation

If you find this work useful, please cite our paper:

@inproceedings{yao2025prune,
  title={Pruning Spurious Subgraphs for Graph Out-of-Distribution Generalization},
  author={Yao, Tianjun and Li, Haoxuan and Chen, Yongqiang and Liu, Tongliang and Song, Le and Xing, Eric and Shen, Zhiqiang},
  booktitle={Advances in Neural Information Processing Systems},
  year={2025}
}