cogdl: A Python repository from icycookies

CogDL is a graph representation learning toolkit that allows researchers and developers to easily train and compare baseline or customized models for node classification, graph classification, and other important tasks in the graph domain.

We summarize the contributions of CogDL as follows:

High Efficiency: CogDL utilizes well-optimized operators to speed up training and save GPU memory of GNN models.
Easy-to-Use: CogDL provides easy-to-use APIs for running experiments with the given models and datasets using hyper-parameter search.
Extensibility: The design of CogDL makes it easy to apply GNN models to new scenarios based on our framework.
Reproducibility: CogDL provides reproducible leaderboards for state-of-the-art models on most of important tasks in the graph domain.

❗ News

The new v0.4.0 release refactors the data storage (from Data to Graph) and provides more fast operators to speed up GNN training. It also includes many self-supervised learning methods on graphs. BTW, we are glad to announce that we will give a tutorial on KDD 2021 in August. Please see this link for more details. 🎉
CogDL supports GNN models with Mixture of Experts (MoE). You can install FastMoE and try MoE GCN in CogDL now!
The new v0.3.0 release provides a fast spmm operator to speed up GNN training. We also release the first version of CogDL paper in arXiv. You can join our slack for discussion. 🎉🎉🎉

News History

The new v0.2.0 release includes easy-to-use experiment and pipeline APIs for all experiments and applications. The experiment API supports automl features of searching hyper-parameters. This release also provides OAGBert API for model inference (OAGBert is trained on large-scale academic corpus by our lab). Some features and models are added by the open source community (thanks to all the contributors 🎉).
The new v0.1.2 release includes a pre-training task, many examples, OGB datasets, some knowledge graph embedding methods, and some graph neural network models. The coverage of CogDL is increased to 80%. Some new APIs, such as Trainer and Sampler, are developed and being tested.
The new v0.1.1 release includes the knowledge link prediction task, many state-of-the-art models, and optuna support. We also have a Chinese WeChat post about the CogDL release.

Getting Started

Requirements and Installation

Python version >= 3.6
PyTorch version >= 1.7.1

Please follow the instructions here to install PyTorch (https://github.com/pytorch/pytorch#installation).

When PyTorch has been installed, cogdl can be installed using pip as follows:

pip install cogdl

Install from source via:

pip install git+https://github.com/thudm/cogdl.git

Or clone the repository and install with the following commands:

git clone git@github.com:THUDM/cogdl.git
cd cogdl
pip install -e .

Usage

API Usage

You can run all kinds of experiments through CogDL APIs, especially experiment. You can also use your own datasets and models for experiments. A quickstart example can be found in the quick_start.py. More examples are provided in the examples/.

from cogdl import experiment

# basic usage
experiment(task="node_classification", dataset="cora", model="gcn")

# set other hyper-parameters
experiment(task="node_classification", dataset="cora", model="gcn", hidden_size=32, max_epoch=200)

# run over multiple models on different seeds
experiment(task="node_classification", dataset="cora", model=["gcn", "gat"], seed=[1, 2])

# automl usage
def func_search(trial):
    return {
        "lr": trial.suggest_categorical("lr", [1e-3, 5e-3, 1e-2]),
        "hidden_size": trial.suggest_categorical("hidden_size", [32, 64, 128]),
        "dropout": trial.suggest_uniform("dropout", 0.5, 0.8),
    }

experiment(task="node_classification", dataset="cora", model="gcn", seed=[1, 2], func_search=func_search)

Some interesting applications can be used through pipeline API. An example can be found in the pipeline.py.

from cogdl import pipeline

# print the statistics of datasets
stats = pipeline("dataset-stats")
stats(["cora", "citeseer"])

# load OAGBert model and perform inference
oagbert = pipeline("oagbert")
outputs = oagbert(["CogDL is developed by KEG, Tsinghua.", "OAGBert is developed by KEG, Tsinghua."])

More details of the OAGBert usage can be found here.

Command-Line Usage

You can also use python scripts/train.py --task example_task --dataset example_dataset --model example_model to run example_model on example_data and evaluate it via example_task.

--task, downstream tasks to evaluate representation like node_classification, unsupervised_node_classification, graph_classification. More tasks can be found in the cogdl/tasks.
--dataset, dataset name to run, can be a list of datasets with space like cora citeseer ppi. Supported datasets include 'cora', 'citeseer', 'pumbed', 'ppi', 'wikipedia', 'blogcatalog', 'flickr'. More datasets can be found in the cogdl/datasets.
--model, model name to run, can be a list of models like deepwalk line prone. Supported models include 'gcn', 'gat', 'graphsage', 'deepwalk', 'node2vec', 'hope', 'grarep', 'netmf', 'netsmf', 'prone'. More models can be found in the cogdl/models.

For example, if you want to run LINE, NetMF on Wikipedia with unsupervised node classification task, with 5 different seeds:

$ python scripts/train.py --task unsupervised_node_classification --dataset wikipedia --model line netmf --seed 0 1 2 3 4

Expected output:

Variant	Micro-F1 0.1	Micro-F1 0.3	Micro-F1 0.5	Micro-F1 0.7	Micro-F1 0.9
('wikipedia', 'line')	0.4069±0.0011	0.4071±0.0010	0.4055±0.0013	0.4054±0.0020	0.4080±0.0042
('wikipedia', 'netmf')	0.4551±0.0024	0.4932±0.0022	0.5046±0.0017	0.5084±0.0057	0.5125±0.0035

If you have ANY difficulties to get things working in the above steps, feel free to open an issue. You can expect a reply within 24 hours.

❗ FAQ

How to contribute to CogDL?

If you have a well-performed algorithm and are willing to implement it in our toolkit to help more people, you can first open an issue and then create a pull request, detailed information can be found here.

Before committing your modification, please first run pre-commit install to setup the git hook for checking code format and style using black and flake8. Then the pre-commit will run automatically on git commit! Detailed information of pre-commit can be found here.

How to enable fast GNN training?

CogDL provides a fast sparse matrix-matrix multiplication operator called [GE-SpMM](https://arxiv.org/abs/2007.03179) to speed up training of GNN models on the GPU. You can set `fast_spmm=True` in the API usage or `--fast-spmm` in the command-line usage to enable this feature. Note that this feature is still in testing and may not work under some versions of CUDA.

How to run parallel experiments with GPUs on several models?

If you want to run parallel experiments on your server with multiple GPUs on multiple models, GCN and GAT, on the Cora dataset:

$ python scripts/parallel_train.py --task node_classification --dataset cora --model gcn gat --device-id 0 1 --seed 0 1 2 3 4

Expected output:

Variant	Acc
('cora', 'gcn')	0.8236±0.0033
('cora', 'gat')	0.8262±0.0032

How to use docker container?

You might also opt to use a Docker container. There is an image available in this repo that you can build with the Torch and CUDA versions available in your system. To build the docker image just run:

docker build --build-arg CUDA=YOUR_CUDA_VERSION --build-arg TORCH=YOUR_TORCH_VERSION --tag cogdl .

Where YOUR_CUDA_VERSION should be cuxxx representing your cuda version (or just cpu) and YOUR_TORCH_VERSION should be the version of PyTorch you want to use. For example, to run with CUDA 10.1 and PyTorch 1.7.1 you can run:

docker build --build-arg CUDA=cu101 --build-arg TORCH=1.7.1 --tag cogdl .

Then you can start the container by running:

docker run -it -v cogdl:/cogdl cogdl /bin/bash

And then clone your fork or this repository into the cogdl folder:

git clone https://github.com/THUDM/cogdl /cogdl

How to use models from other libraries?

If you are familiar with other popular graph libraries, you can implement your own model in CogDL using modules from PyTorch Geometric (PyG), and Deep Graph Library (DGL). For the installation of these two libraries, you can follow the instructions from PyG (https://github.com/rusty1s/pytorch_geometric/#installation), and DGL (https://docs.dgl.ai/install/index.html). For the quick-start usage of how to use layers of PyG, you can find some examples in the [examples/pytorch_geometric](https://github.com/THUDM/cogdl/tree/master/examples/pytorch_geometric/).

How to make a successful pull request with unit test

To have a successful pull request, you need to have at least (1) your model implementation and (2) a unit test.

You might be confused why your pull request was rejected because of 'Coverage decreased ...' issue even though your model is working fine locally. This is because you have not included a unit test, which essentially runs through the extra lines of code you added. The Travis CI service used by Github conducts all unit tests on the code you committed and checks how many lines of the code have been checked by the unit tests, and if a significant portion of your code has not been checked (insufficient coverage), the pull request is rejected.

So how do you do a unit test?

Let's say you implement a GNN model in a script models/nn/abcgnn.py that does the task of node classification. Then, you need to add a unit test inside the script tests/tasks/test_node_classification.py (or whatever relevant task your model does).
To add the unit test, you simply add a function test_abcgnn_cora() (just follow the format of the other unit tests already in the script), fill it with required arguments and the last line in the function 'assert 0 <= ret["Acc"] <= 1' is the very basic sanity check conducted by the unit test.
After modifying tests/tasks/test_node_classification.py, commit it together with your models/nn/abcgnn.py and your pull request should pass.

CogDL Team

CogDL is developed and maintained by Tsinghua, BAAI, DAMO Academy, and ZHIPU.AI.

The core development team can be reached at cogdlteam@gmail.com.

Citing CogDL

Please cite our paper if you find our code or results useful for your research:

@article{cen2021cogdl,
    title={CogDL: An Extensive Toolkit for Deep Learning on Graphs},
    author={Yukuo Cen and Zhenyu Hou and Yan Wang and Qibin Chen and Yizhen Luo and Xingcheng Yao and Aohan Zeng and Shiguang Guo and Peng Zhang and Guohao Dai and Yu Wang and Chang Zhou and Hongxia Yang and Jie Tang},
    journal={arXiv preprint arXiv:2103.00959},
    year={2021}
}

icycookies/cogdl