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https://github.com/Emory-Melody/GraphSlim
A Python library for graph reduction including condensation, coarsening, and sparsification.
https://github.com/Emory-Melody/GraphSlim
Last synced: 24 days ago
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A Python library for graph reduction including condensation, coarsening, and sparsification.
- Host: GitHub
- URL: https://github.com/Emory-Melody/GraphSlim
- Owner: Emory-Melody
- Created: 2024-02-20T15:23:04.000Z (11 months ago)
- Default Branch: main
- Last Pushed: 2024-12-19T21:03:14.000Z (about 1 month ago)
- Last Synced: 2024-12-19T22:23:35.712Z (about 1 month ago)
- Language: Python
- Homepage:
- Size: 8 MB
- Stars: 15
- Watchers: 2
- Forks: 4
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- Graph-Condensation-Papers - GraphSlim
README
# GraphSlim
[](https://graphslim.readthedocs.io/en/latest/?badge=latest)
**[Documentation](https://graphslim.readthedocs.io/en/latest/?badge=latest)** |
**[Benchmark Paper](https://arxiv.org/abs/2406.16715)** |
**[Benchmark Scripts](https://github.com/Emory-Melody/GraphSlim/tree/main/benchmark)** |
**[Survey Paper](https://arxiv.org/pdf/2402.03358)** |
**[Paper Collection](https://github.com/Emory-Melody/awesome-graph-reduction)** |
**[Web Interface](https://graphslim-vis.streamlit.app/)**
**[Online Demo](https://colab.research.google.com/drive/1LLG9PYOPnmLCAr0ow0ogRYI8DvLGPk7d?usp=sharing)**
# Features
GraphSlim is a PyTorch library for graph reduction. It takes graph of PyG format as input and outputs a reduced graph
preserving **properties or performance** of the original graph.
* Covering representative methods of all 3 graph reduction strategies: Sparsification, Coarsening and Condensation.
* Different reduction strategies can be easily combined in one run.
* Unified evaluation tools including Grid Search and NAS.
* Support evasion and poisoning attacks on the input graph by DeepRobust.
# Guidance
* Please first prepare the environments.
* If you are new to GraphSlim, we highly suggest you first run the examples in the `examples` folder.
* If you have any questions or suggestions regarding this library, feel free to create an
issue [here](https://github.com/Emory-Melody/GraphSlim/issues). We will reply as soon as possible :)
# Prepare Environments
## CUDA and PyTorch
Check [torch previous versions](https://pytorch.org/get-started/previous-versions/).
We test this repo in `torch 1.13.1` and `torch 2.1.2` with `CUDA 12.4`.
## Install from requirements
Please choose from `requirements_torch1+.txt (for torch 1.\*)` and `requirements.txt (for torch2.*)` at your convenience.
## Install from pip
```shell
# choose one version from https://data.pyg.org/whl/ based on your environment
pip install torch_scatter torch_sparse -f https://data.pyg.org/whl/torch-${TORCH}+${CUDA}.html
pip install graphslim
```
## Recommended way to download 'torch_sparse' and `torch_scatter`
It's usually faster and easy to download from .whl file. See details in `install_torch_sparse.sh`
# Examples
```
python examples/train_coreset.py
python examples/train_coarsen.py
python examples/train_gcond.py
```
See more examples in **[Benchmark Scripts](https://github.com/Emory-Melody/GraphSlim/tree/main/benchmark)**.
# Use As Project
```shell
cd graphslim
python train_all.py -xxx xx
```
Run `python configs.py --help` to get all command line options.
```shell
Options:
-D, --dataset TEXT [default: cora]
-G, --gpu_id INTEGER gpu id start from 0, -1 means cpu [default:
0]
--setting [trans|ind] transductive or inductive setting
--split TEXT only support public split now, do not change
it [default: fixed]
--run_reduction INTEGER repeat times of reduction [default: 3]
--run_eval INTEGER repeat times of final evaluations [default:
10]
--run_inter_eval INTEGER repeat times of intermediate evaluations
[default: 5]
--eval_interval INTEGER [default: 100]
-H, --hidden INTEGER [default: 256]
--eval_epochs, --ee INTEGER [default: 300]
--eval_model, --em [GCN|GAT|SGC|APPNP|Cheby|GraphSage|GAT|SGFormer]
[default: GCN]
--condense_model [GCN|GAT|SGC|APPNP|Cheby|GraphSage|GAT]
[default: SGC]
-E, --epochs INTEGER number of reduction epochs [default: 1000]
--lr FLOAT [default: 0.01]
--weight_decay, --wd INTEGER [default: 0]
--pre_norm BOOLEAN pre-normalize features, forced true for
arxiv, flickr and reddit [default: True]
--outer_loop INTEGER [default: 10]
--inner_loop INTEGER [default: 1]
-R, --reduction_rate FLOAT -1 means use representative reduction rate;
reduction rate of training set, defined as
(number of nodes in small graph)/(number of
nodes in original graph) [default: -1.0]
-S, --seed INTEGER Random seed [default: 1]
--nlayers INTEGER number of GNN layers of condensed model
[default: 2]
-V, --verbose
--init [variation_neighborhoods|variation_edges|variation_cliques|heavy_edge|algebraic_JC|affinity_GS|kron|vng|clustering|averaging|cent_d|cent_p|kcenter|herding|random]
features initialization methods
-M, --method [variation_neighborhoods|variation_edges|variation_cliques|heavy_edge|algebraic_JC|affinity_GS|kron|vng|clustering|averaging|gcond|doscond|gcondx|doscondx|sfgc|msgc|disco|sgdd|gcsntk|geom|cent_d|cent_p|kcenter|herding|random]
[default: kcenter]
--activation [sigmoid|tanh|relu|linear|softplus|leakyrelu|relu6|elu]
activation function when do NAS [default:
relu]
-A, --attack [random_adj|metattack|random_feat]
corruption method
-P, --ptb_r FLOAT perturbation rate for corruptions [default:
0.25]
--aggpreprocess use aggregation for coreset methods
--dis_metric TEXT distance metric for all condensation
methods,ours means metric used in GCond
paper [default: ours]
--lr_adj FLOAT [default: 0.0001]
--lr_feat FLOAT [default: 0.0001]
--threshold INTEGER sparsificaiton threshold before evaluation
[default: 0]
--dropout FLOAT [default: 0.0]
--ntrans INTEGER number of transformations in SGC and APPNP
[default: 1]
--with_bn
--no_buff skip the buffer generation and use existing
in geom,sfgc
--batch_adj INTEGER batch size for msgc [default: 1]
--alpha FLOAT for appnp [default: 0.1]
--mx_size INTEGER for gcsntk methods, avoid SVD error
[default: 100]
--save_path, --sp TEXT save path for synthetic graph [default:
../checkpoints]
-W, --eval_whole if run on whole graph
--help Show this message and exit.
```
# Use As Package
```python
from graphslim.dataset import *
from graphslim.evaluation import *
from graphslim.condensation import GCond
from graphslim.config import cli
args = cli(standalone_mode=False)
# customize args here
args.reduction_rate = 0.5
args.device = 'cuda:0'
# add more args. here
graph = get_dataset('cora', args=args)
# To reproduce the benchmark, use our args and graph class
# To use your own args and graph format, please ensure the args and graph class has the required attributes
# create an agent of one reduction algorithm
# add more args. here
agent = GCond(setting='trans', data=graph, args=args)
# reduce the graph
reduced_graph = agent.reduce(graph, verbose=True)
# create an evaluator
# add more args. here
evaluator = Evaluator(args)
# evaluate the reduced graph on a GNN model
res_mean, res_std = evaluator.evaluate(reduced_graph, model_type='GCN')
```
All parameters can be divided into
```shell
: dataset, method, setting, reduction_rate, seed, aggpreprocess, eval_whole, run_reduction
: attack, ptb_r
: pre_norm, save_path, split, threshold
: init, eval_interval, eval_epochs, eval_model, condense_model, epochs, lr, weight_decay, outer_loop, inner_loop, nlayers, method, activation, dropout, ntrans, with_bn, no_buff, batch_adj, alpha, mx_size, dis_metric, lr_adj, lr_feat
: final_eval_model, eval_epochs, lr, weight_decay
```
See more details
in [](https://graphslim.readthedocs.io/en/latest/?badge=latest)
# Customization
* To implement a new reduction algorithm, you need to create a new class in `sparsification` or `coarsening`
or `condensation` and inherit the `Base` class.
* To implement a new dataset, you need to create a new class in `dataset/loader.py` and inherit the `TransAndInd` class.
* To implement a new evaluation metric, you need to create a new function in `evaluation/eval_agent.py`.
* To implement a new GNN model, you need to create a new class in `models` and inherit the `Base` class.
* To customize sparsification before evaluation, please modify the function `sparsify` in `evaluation/utils.py`.
# Web Interface
Our [web application](https://graphslim-vis.streamlit.app/) is deployed online using [streamlit](https://streamlit.io/).
But it also can be initiated using:
```bash
cd interface
python -m streamlit run vis_graphslim.py
```
to activate the interface. Please satisfy the dependency in [interface/requirements.txt](interface/requirements.txt).
# TODO
- [ ] Add sparsification algorithms like Spanner
- [ ] Add latest condensation methods
- [ ] Support more datasets
- [ ] Present full results in a website
# Limitations
* The GEOM and SFGC are not fully implemented in the current version due to disk space limit. We set the number of
experts to 20 currently. If you have over 100GB disk space, you can set the number of experts to 1000 to reproduce the
If you have over 100GB disk space, you can set the number of experts to 200 to reproduce the results in the paper.
# Acknowledgement
Some of the algorithms are referred to paper authors' implementations and other packages.
[SCAL](https://github.com/szzhang17/Scaling-Up-Graph-Neural-Networks-Via-Graph-Coarsening)
[Sparsification](https://github.com/yuhanchan/sparsification)
[GCOND](https://github.com/ChandlerBang/GCond)
[GCSNTK](https://github.com/WANGLin0126/GCSNTK)
[SFGC](https://github.com/Amanda-Zheng/SFGC)
[GEOM](https://github.com/NUS-HPC-AI-Lab/GEOM/tree/main)
[DeepRobust](https://github.com/DSE-MSU/DeepRobust)