pydgc 1.0.3

PyDGC: A Deep Graph Clustering Benchmark

DGCBench: A Deep Graph Clustering Benchmark

【Accepted by NeurIPS D&B Track 2025】

Overview | DGCBench | Installation | Tutorial | Docs | Citation

PyDGC

PyDGC, a flexible and extensible Python library for deep graph clustering (DGC), is compatible with frameworks such as PyG and OGB. It supports the easy integration of new models and datasets, facilitating the rapid development, reproduction, and fair comparison of DGC methods.

News

• 🔥2025.09.19: Our paper "DGCBench: A Deep Graph Clustering Benchmark" is accepted by NeurIPS D&B 2025.
• 2025.07: API documentation is released.
• 2025.07: PyDGC is now available on PyPI.
• 2025.05: Release source code of PyDGC.

What is DGC?

Deep graph clustering, which aims to reveal the underlying graph structure and divide the nodes into different groups, has attracted intensive attention in recent years.

More details can be found in the survey paper. Please click here to view the comprehensive archive of papers.

Timeline of representative models.

DGCBench

DGCBench encompasses 12 diverse datasets with different characteristics and 12 state-of-the-art methods from all major paradigms. By integrating them into a standardized pipeline, we ensure fair, reproducible, and comprehensive evaluations across multiple dimensions.

Features

• Integration of multiple deep graph clustering models. Supported Models
• Support for various graph datasets from PyG and OGB. Supported Datasets
• Model evaluation and visualization capabilities.
• Standardized Pipeline.

Overview of Pipeline

Installation

It is recommended to use conda to create a virtual python environment.

conda create --name DGCbench python=3.8
conda activate DGCbench

It is recommended to install GPU or CPU version of PyTorch according to the device in advance, version >=2.0.1. Then, torch_cluster, torch_sparse, torch_scatter may need to be installed according to the documentation of PyG Installation-from-Wheels.

• (Plan 1) Install with Pip

  pip install pydgc
  

• (Plan 2) Installation for local development

  git clone https://github.com/Marigoldwu/PyDGC.git
  cd PyDGC
  pip install -e .
  

Tutorial

Reproduce built-in models

Take GAE as an example. You can run the following command to reproduce the results of GAE on CORA dataset.

Create a folder dgc to store the results.

mkdir dgc
cd dgc
mkdir gae
cd gae

Copy config.yaml and run.py of GAE from our github repository to the current folder.

wget https://raw.githubusercontent.com/Marigoldwu/PyDGC/master/examples/pipelines/gae/config.yaml
wget https://raw.githubusercontent.com/Marigoldwu/PyDGC/master/examples/pipelines/gae/run.py

Run the pipeline.

python run.py

You can also specify arguments in the command line:

python run.py --dataset_name CORA -eval_each --rounds 1

Note:

• --dataset_name is the name of the dataset.
• --rounds is the number of times to run the pipeline.
• -eval_each is the flag to evaluate the model after each epoch.

Other optional arguments:

--cfg_file_path YourPath  # path of corresponding configurations file
--flag FlagContent  # Descriptions
--drop_edge float  # probability of dropping edges
--drop_feature float  # probability of dropping features
--add_edge float  # probability of adding edges
--add_noise float  # standard deviation of Gaussian Noise
-pretrain  # only run the pretraining stage in the model

Develop your own DGC model

from pydgc.models import DGCModel

class MyModel(DGCModel):
    def __init__(self, logger, cfg):
        super(MyModel).__init__(logger, cfg)
        your_model = ...  # Your model
        
        self.loss_curve = []
        self.nmi_curve = []
        self.best_embedding = None
        self.best_predicted_labels = None
        self.best_results = {'ACC': -1}
    
    def forward(self, data):
        ...  # forward process
        return something
    # If needed
    def loss(self, *args, **kwargs):
    # If needed
    def pretrain(self, data, cfg, flag):
    
    def train_model(self, data, cfg, flag):
    
    def get_embedding(self, data):
    
    def clustering(self, data):
        embedding = self.get_embedding(data)
        # clustering
        return embedding, labels_, clustering_centers
    
    def evaluate(self, data):
        embedding, predicted_labels, clustering_centers = self.clustering(data)
        ground_truth = data.y.numpy()
        metric = DGCMetric(ground_truth, predicted_labels.numpy(), embedding, data.edge_index)
        results = metric.evaluate_one_epoch(self.logger, self.cfg.evaluate)
        return embedding, predicted_labels, results

Develop your own DGC pipeline

from pydgc.pipelines import BasePipeline
from pydgc.utils import perturb_data
import MyModel  # import your own model

class MyPipeline(BasePipeline):
    def __init__(self, args):
        super(MyPipeline).__init__(args)
    
    def augmentation(self):
        self.data = perturb_data(self.data, self.cfg.dataset.augmentation)
        # other augmentations if needed
        
    def build_model(self):
        model = MyModel(self.logger, self.cfg)
        self.logger.model_info(model)
        return model

Supported Models

No.	Model	Paper	Source Code
1	GAE	Variational Graph Auto-Encoders	code
2	GAE_SSC	-	-
3	DAEGC	Attributed graph clustering: A deep attentional embedding approach	code
4	SDCN	Structural Deep Clustering Network	code
5	DFCN	Deep Fusion Clustering Network	code
6	DCRN	Deep Graph Clustering via Dual Correlation Reduction	code
7	AGC-DRR	Attributed Graph Clustering with Dual Redundancy Reduction	code
8	DGCluster	DGCLUSTER: A Neural Framework for Attributed Graph Clustering via Modularity Maximization	code
9	HSAN	Hard Sample Aware Network for Contrastive Deep Graph Clustering	code
10	CCGC	Cluster-guided Contrastive Graph Clustering Network	code
11	MAGI	Revisiting Modularity Maximization for Graph Clustering: A Contrastive Learning Perspective	code
12	NS4GC	Reliable Node Similarity Matrix Guided Contrastive Graph Clustering	code

Supported Datasets

No.	Dataset	#Samples	#Features	#Edges	#Classes	Homo. Ratio
1	Wiki	2,405	4,973	17,981	17	0.71
2	Cora	2,708	1,433	5,429	7	0.81
3	ACM	3,025	1,870	13,128	3	0.82
4	Citeseer	3,327	3,703	9,104	6	0.74
5	DBLP	4,057	334	3,528	4	0.80
6	PubMed	19,717	500	88,648	3	0.80
7	Ogbn-arXiv	169,343	128	2,315,598	40	0.65
8	USPS(3NN)	9,298	256	27,894	10	0.98
9	HHAR(3NN)	10,299	561	30,897	6	0.95
10	BlogCatalog	5,196	8,189	343,486	6	0.40
11	Flickr	7,575	12,047	479,476	9	0.24
12	Roman-empire	22,662	300	65,854	18	0.05

The 12 datasets above are benchmark datasets introduced in our paper. More Datasets will be introduced.

Citation

@inproceedings{wu2025dgcbench,
  title={{DGCB}ench:  A Deep Graph Clustering Benchmark},
  author={Benyu Wu and Yue Liu and Qiaoyu Tan and Xinwang Liu and Wei Du and Jun Wang and Guoxian Yu},
  booktitle={The Thirty-ninth Annual Conference on Neural Information Processing Systems Datasets and Benchmarks Track},
  year={2025},
  url={https://openreview.net/forum?id=dKVUUZfcW9}
}

Related Repositories

ADGC: Awesome-Deep-Graph-Clustering

Older version of this repository: A-Unified-Framework-for-Attribute-Graph-Clustering