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GraphSlim

Online Demo

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. We will reply as soon as possible :)

Prepare Environments

CUDA and PyTorch

Check torch 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

# 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.

Use As Project

cd graphslim
python train_all.py -xxx xx

Run python configs.py --help to get all command line options.

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

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.<main_args/dataset_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.<agent_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.<evaluator_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

<main_args>: dataset, method, setting, reduction_rate, seed, aggpreprocess, eval_whole, run_reduction
<attack_args>: attack, ptb_r
<dataset_args>: pre_norm, save_path, split, threshold
<agent_args>: 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
<evaluator_args>: final_eval_model, eval_epochs, lr, weight_decay

See more details in

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 is deployed online using streamlit. But it also can be initiated using:

cd interface
python -m streamlit run vis_graphslim.py

to activate the interface. Please satisfy the dependency in 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.