dgl: A Python repository from bioannidis

For a full list of official DGL examples, see here.

DGL is an easy-to-use, high performance and scalable Python package for deep learning on graphs. DGL is framework agnostic, meaning if a deep graph model is a component of an end-to-end application, the rest of the logics can be implemented in any major frameworks, such as PyTorch, Apache MXNet or TensorFlow.

Figure: DGL Overall Architecture

DGL News

09/05/2020: We invite you to participate in the survey here to make DGL better fit for your needs. Thanks!

08/21/2020: The new v0.5.0 release includes distributed GNN training, overhauled documentation and user guide, and several more features. We have also submitted some models to the OGB leaderboard. See our release note for more details.

06/11/2020: Amazon Shanghai AI Lab and AWS Deep Engine Science team working along with academic collaborators from the University of Minnesota, The Ohio State University, and Hunan University have created the Drug Repurposing Knowledge Graph (DRKG) and a set of machine learning tools, DGL-KE, that can be used to prioritize drugs for repurposing studies. DRKG is a comprehensive biological knowledge graph that relates human genes, compounds, biological processes, drug side effects, diseases and symptoms. DRKG includes, curates, and normalizes information from six publicly available databases and data that were collected from recent publications related to Covid-19. It has 97,238 entities belonging to 13 types of entities, and 5,874,261 triplets belonging to 107 types of relations. More about the dataset is in this blogpost.

Using DGL

A data scientist may want to apply a pre-trained model to your data right away. For this you can use DGL's Application packages, formally Model Zoo. Application packages are developed for domain applications, as is the case for DGL-LifeScience. We will soon add model zoo for knowledge graph embedding learning and recommender systems. Here's how you will use a pretrained model:

from dgllife.data import Tox21
from dgllife.model import load_pretrained
from dgllife.utils import smiles_to_bigraph, CanonicalAtomFeaturizer

dataset = Tox21(smiles_to_bigraph, CanonicalAtomFeaturizer())
model = load_pretrained('GCN_Tox21') # Pretrained model loaded
model.eval()

smiles, g, label, mask = dataset[0]
feats = g.ndata.pop('h')
label_pred = model(g, feats)
print(smiles)                   # CCOc1ccc2nc(S(N)(=O)=O)sc2c1
print(label_pred[:, mask != 0]) # Mask non-existing labels
# tensor([[ 1.4190, -0.1820,  1.2974,  1.4416,  0.6914,  
# 2.0957,  0.5919,  0.7715, 1.7273,  0.2070]])

Further reading: DGL is released as a managed service on AWS SageMaker, see the medium posts for an easy trip to DGL on SageMaker(part1 and part2).

Researchers can start from the growing list of models implemented in DGL. Developing new models does not mean that you have to start from scratch. Instead, you can reuse many pre-built modules. Here is how to get a standard two-layer graph convolutional model with a pre-built GraphConv module:

from dgl.nn.pytorch import GraphConv
import torch.nn.functional as F

# build a two-layer GCN with ReLU as the activation in between
class GCN(nn.Module):
    def __init__(self, in_feats, h_feats, num_classes):
        super(GCN, self).__init__()
        self.gcn_layer1 = GraphConv(in_feats, h_feats)
        self.gcn_layer2 = GraphConv(h_feats, num_classes)
    
    def forward(self, graph, inputs):
        h = self.gcn_layer1(graph, inputs)
        h = F.relu(h)
        h = self.gcn_layer2(graph, h)
        return h

Next level down, you may want to innovate your own module. DGL offers a succinct message-passing interface (see tutorial here). Here is how Graph Attention Network (GAT) is implemented (complete codes). Of course, you can also find GAT as a module GATConv:

import torch.nn as nn
import torch.nn.functional as F

# Define a GAT layer
class GATLayer(nn.Module):
    def __init__(self, in_feats, out_feats):
        super(GATLayer, self).__init__()
        self.linear_func = nn.Linear(in_feats, out_feats, bias=False)
        self.attention_func = nn.Linear(2 * out_feats, 1, bias=False)
        
    def edge_attention(self, edges):
        concat_z = torch.cat([edges.src['z'], edges.dst['z']], dim=1)
        src_e = self.attention_func(concat_z)
        src_e = F.leaky_relu(src_e)
        return {'e': src_e}
    
    def message_func(self, edges):
        return {'z': edges.src['z'], 'e':edges.data['e']}
        
    def reduce_func(self, nodes):
        a = F.softmax(nodes.mailbox['e'], dim=1)
        h = torch.sum(a * nodes.mailbox['z'], dim=1)
        return {'h': h}
                               
    def forward(self, graph, h):
        z = self.linear_func(h)
        graph.ndata['z'] = z
        graph.apply_edges(self.edge_attention)
        graph.update_all(self.message_func, self.reduce_func)
        return graph.ndata.pop('h')

Performance and Scalability

Microbenchmark on speed and memory usage: While leaving tensor and autograd functions to backend frameworks (e.g. PyTorch, MXNet, and TensorFlow), DGL aggressively optimizes storage and computation with its own kernels. Here's a comparison to another popular package -- PyTorch Geometric (PyG). The short story is that raw speed is similar, but DGL has much better memory management.

Dataset	Model	Accuracy	Time PyG DGL	Memory PyG DGL
Cora	GCN GAT	81.31 ± 0.88 83.98 ± 0.52	0.478 0.666 1.608 1.399	1.1 1.1 1.2 1.1
CiteSeer	GCN GAT	70.98 ± 0.68 69.96 ± 0.53	0.490 0.674 1.606 1.399	1.1 1.1 1.3 1.1
PubMed	GCN GAT	79.00 ± 0.41 77.65 ± 0.32	0.491 0.690 1.946 1.393	1.1 1.1 1.6 1.1
Reddit	GCN	93.46 ± 0.06	OOM 28.6	OOM 11.7
Reddit-S	GCN	N/A	29.12 9.44	15.7 3.6

Table: Training time(in seconds) for 200 epochs and memory consumption(GB)

Here is another comparison of DGL on TensorFlow backend with other TF-based GNN tools (training time in seconds for one epoch):

Dateset	Model	DGL	GraphNet	tf_geometric
Core	GCN	0.0148	0.0152	0.0192
Reddit	GCN	0.1095	OOM	OOM
PubMed	GCN	0.0156	0.0553	0.0185
PPI	GCN	0.09	0.16	0.21
Cora	GAT	0.0442	n/a	0.058
PPI	GAT	0.398	n/a	0.752

High memory utilization allows DGL to push the limit of single-GPU performance, as seen in below images.

Scalability: DGL has fully leveraged multiple GPUs in both one machine and clusters for increasing training speed, and has better performance than alternatives, as seen in below images.

Further reading: Detailed comparison of DGL and other Graph alternatives can be found here.

DGL Models and Applications

DGL for research

Overall there are 30+ models implemented by using DGL:

DGL for domain applications

DGL-LifeSci, previously DGL-Chem
DGL-KE
DGL-RecSys(coming soon)

DGL for NLP/CV problems

We are currently in Beta stage. More features and improvements are coming.

Awesome Papers Using DGL

Benchmarking Graph Neural Networks, Vijay Prakash Dwivedi, Chaitanya K. Joshi, Thomas Laurent, Yoshua Bengio, Xavier Bresson
Open Graph Benchmarks: Datasets for Machine Learning on Graphs, NeurIPS'20, Weihua Hu, Matthias Fey, Marinka Zitnik, Yuxiao Dong, Hongyu Ren, Bowen Liu, Michele Catasta, Jure Leskovec
DropEdge: Towards Deep Graph Convolutional Networks on Node Classification, ICLR'20, Yu Rong, Wenbing Huang, Tingyang Xu, Junzhou Huan
Discourse-Aware Neural Extractive Text Summarization, ACL'20, Jiacheng Xu, Zhe Gan, Yu Cheng, Jingjing Liu
GCC: Graph Contrastive Coding for Graph Neural Network Pre-Training, KDD'20, Jiezhong Qiu, Qibin Chen, Yuxiao Dong, Jing Zhang, Hongxia Yang, Ming Ding, Kuansan Wang, Jie Tang
DGL-KE: Training Knowledge Graph Embeddings at Scale, SIGIR'20, Da Zheng, Xiang Song, Chao Ma, Zeyuan Tan, Zihao Ye, Jin Dong, Hao Xiong, Zheng Zhang, George Karypis
Improving Graph Neural Network Expressivity via Subgraph Isomorphism Counting, Giorgos Bouritsas, Fabrizio Frasca, Stefanos Zafeiriou, Michael M. Bronstein
INT: An Inequality Benchmark for Evaluating Generalization in Theorem Proving, Yuhuai Wu, Albert Q. Jiang, Jimmy Ba, Roger Grosse
Finding Patient Zero: Learning Contagion Source with Graph Neural Networks, Chintan Shah, Nima Dehmamy, Nicola Perra, Matteo Chinazzi, Albert-László Barabási, Alessandro Vespignani, Rose Yu
FeatGraph: A Flexible and Efficient Backend for Graph Neural Network Systems, SC'20, Yuwei Hu, Zihao Ye, Minjie Wang, Jiali Yu, Da Zheng, Mu Li, Zheng Zhang, Zhiru Zhang, Yida Wang

BP-Transformer: Modelling Long-Range Context via Binary Partitioning., Zihao Ye, Qipeng Guo, Quan Gan, Xipeng Qiu, Zheng Zhang
OptiMol: Optimization of Binding Affinities in Chemical Space for Drug Discovery, Jacques Boitreaud,Vincent Mallet, Carlos Oliver, Jérôme Waldispühl
JAKET: Joint Pre-training of Knowledge Graph and Language Understanding, Donghan Yu, Chenguang Zhu, Yiming Yang, Michael Zeng
Architectural Implications of Graph Neural Networks, Zhihui Zhang, Jingwen Leng, Lingxiao Ma, Youshan Miao, Chao Li, Minyi Guo
Combining Reinforcement Learning and Constraint Programming for Combinatorial Optimization, Quentin Cappart, Thierry Moisan, Louis-Martin Rousseau1, Isabeau Prémont-Schwarz, and Andre Cire
Sparse Graph Attention Networks, Yang Ye, Shihao Ji
On Self-Distilling Graph Neural Network, Yuzhao Chen, Yatao Bian, Xi Xiao, Yu Rong, Tingyang Xu, Junzhou Huang
Learning Robust Node Representations on Graphs, Xu Chen, Ya Zhang, Ivor Tsang, and Yuangang Pan
Recurrent Event Network: Autoregressive Structure Inference over Temporal Knowledge Graphs, Woojeong Jin, Meng Qu, Xisen Jin, Xiang Ren
Graph Neural Ordinary Differential Equations, Michael Poli, Stefano Massaroli, Junyoung Park, Atsushi Yamashita, Hajime Asama, Jinkyoo Park
FusedMM: A Unified SDDMM-SpMM Kernel for Graph Embedding and Graph Neural Networks, Md. Khaledur Rahman, Majedul Haque Sujon, , Ariful Azad
An Efficient Neighborhood-based Interaction Model for Recommendation on Heterogeneous Graph, KDD'20 Jiarui Jin, Jiarui Qin, Yuchen Fang, Kounianhua Du, Weinan Zhang, Yong Yu, Zheng Zhang, Alexander J. Smola
Learning Interaction Models of Structured Neighborhood on Heterogeneous Information Network, Jiarui Jin, Kounianhua Du, Weinan Zhang, Jiarui Qin, Yuchen Fang, Yong Yu, Zheng Zhang, Alexander J. Smola
Graphein - a Python Library for Geometric Deep Learning and Network Analysis on Protein Structures, Arian R. Jamasb, Pietro Lió, Tom L. Blundell
Graph Policy Gradients for Large Scale Robot Control, Arbaaz Khan, Ekaterina Tolstaya, Alejandro Ribeiro, Vijay Kumar
Heterogeneous Molecular Graph Neural Networks for Predicting Molecule Properties, Zeren Shui, George Karypis
Could Graph Neural Networks Learn Better Molecular Representation for Drug Discovery? A Comparison Study of Descriptor-based and Graph-based Models, Dejun Jiang, Zhenxing Wu, Chang-Yu Hsieh, Guangyong Chen, Ben Liao, Zhe Wang, Chao Shen, Dongsheng Cao, Jian Wu, Tingjun Hou
Principal Neighbourhood Aggregation for Graph Nets, Gabriele Corso, Luca Cavalleri, Dominique Beaini, Pietro Liò, Petar Veličković
Collective Multi-type Entity Alignment Between Knowledge Graphs, Qi Zhu, Hao Wei, Bunyamin Sisman, Da Zheng, Christos Faloutsos, Xin Luna Dong, Jiawei Han
Graph Representation Forecasting of Patient's Medical Conditions: towards A Digital Twin, Pietro Barbiero, Ramon Viñas Torné, Pietro Lió
Relational Graph Learning on Visual and Kinematics Embeddings for Accurate Gesture Recognition in Robotic Surgery, Yong-Hao Long, Jie-Ying Wu, Bo Lu, Yue-Ming Jin, Mathias Unberath, Yun-Hui Liu, Pheng-Ann Heng and Qi Dou
Dark Reciprocal-Rank: Boosting Graph-Convolutional Self-Localization Network via Teacher-to-student Knowledge Transfer, Takeda Koji, Tanaka Kanji
Graph InfoClust: Leveraging Cluster-Level Node Information For Unsupervised Graph Representation Learning, Costas Mavromatis, George Karypis
GraphSeam: Supervised Graph Learning Framework for Semantic UV Mapping, Fatemeh Teimury, Bruno Roy, Juan Sebastian Casallas, David macdonald, Mark Coates
Comprehensive Study on Molecular Supervised Learning with Graph Neural Networks, Doyeong Hwang, Soojung Yang, Yongchan Kwon, Kyung Hoon Lee, Grace Lee, Hanseok Jo, Seyeol Yoon, and Seongok Ryu
A graph auto-encoder model for miRNA-disease associations prediction, Zhengwei Li, Jiashu Li, Ru Nie, Zhu-Hong You, Wenzheng Bao
Graph convolutional regression of cardiac depolarization from sparse endocardial maps, STACOM 2020 workshop, Felix Meister, Tiziano Passerini, Chloé Audigier, Èric Lluch, Viorel Mihalef, Hiroshi Ashikaga, Andreas Maier, Henry Halperin, Tommaso Mansi
AttnIO: Knowledge Graph Exploration with In-and-Out Attention Flow for Knowledge-Grounded Dialogue, EMNLP'20, Jaehun Jung, Bokyung Son, Sungwon Lyu
Learning from Non-Binary Constituency Trees via Tensor Decomposition, COLING'20, Daniele Castellana, Davide Bacciu
Inducing Alignment Structure with Gated Graph Attention Networks for Sentence Matching, Peng Cui, Le Hu, Yuanchao Liu
Enhancing Extractive Text Summarization with Topic-Aware Graph Neural Networks, COLING'20, Peng Cui, Le Hu, Yuanchao Liu
Double Graph Based Reasoning for Document-level Relation Extraction, EMNLP'20, Shuang Zeng, Runxin Xu, Baobao Chang, Lei Li
Systematic Generalization on gSCAN with Language Conditioned Embedding, AACL-IJCNLP'20, Tong Gao, Qi Huang, Raymond J. Mooney
Automatic selection of clustering algorithms using supervised graph embedding, Noy Cohen-Shapira, Lior Rokach
Improving Learning to Branch via Reinforcement Learning, Haoran Sun, Wenbo Chen, Hui Li, Le Song
A Practical Guide to Graph Neural Networks, Issac Ronald Ward, Jack Joyner, Casey Lickfold, Stash Rowe, Yulan Guo, Mohammed Bennamoun, code
APAN: Asynchronous Propagation Attention Network for Real-time Temporal Graph Embedding, SIGMOD'21, Xuhong Wang, Ding Lyu, Mengjian Li, Yang Xia, Qi Yang, Xinwen Wang, Xinguang Wang, Ping Cui, Yupu Yang, Bowen Sun, Zhenyu Guo, Junkui Li
Uncertainty-Matching Graph Neural Networks to Defend Against Poisoning Attacks, Uday Shankar Shanthamallu, Jayaraman J. Thiagarajan, Andreas Spanias
Computing Graph Neural Networks: A Survey from Algorithms to Accelerators, Sergi Abadal, Akshay Jain, Robert Guirado, Jorge López-Alonso, Eduard Alarcón
NHK_STRL at WNUT-2020 Task 2: GATs with Syntactic Dependencies as Edges and CTC-based Loss for Text Classification, Yuki Yasuda, Taichi Ishiwatari, Taro Miyazaki, Jun Goto
Relation-aware Graph Attention Networks with Relational Position Encodings for Emotion Recognition in Conversations, Taichi Ishiwatari, Yuki Yasuda, Taro Miyazaki, Jun Goto
PGM-Explainer: Probabilistic Graphical Model Explanations for Graph Neural Networks, Minh N. Vu, My T. Thai
A Generalization of Transformer Networks to Graphs, Vijay Prakash Dwivedi, Xavier Bresson
Discourse-Aware Neural Extractive Text Summarization, ACL'20, Jiacheng Xu, Zhe Gan, Yu Cheng, Jingjing Liu
Learning Robust Node Representations on Graphs, Xu Chen, Ya Zhang, Ivor Tsang, Yuangang Pan

Installation

DGL should work on

all Linux distributions no earlier than Ubuntu 16.04
macOS X
Windows 10

DGL requires Python 3.6 or later.

Right now, DGL works on PyTorch 1.5.0+, MXNet 1.6+, and TensorFlow 2.3+.

Using anaconda

conda install -c dglteam dgl           # cpu version
conda install -c dglteam dgl-cuda9.2   # CUDA 9.2
conda install -c dglteam dgl-cuda10.1  # CUDA 10.1
conda install -c dglteam dgl-cuda10.2  # CUDA 10.2
conda install -c dglteam dgl-cuda11.0  # CUDA 11.0

Using pip

	Latest Nightly Build Version	Stable Version
CPU	`pip install --pre dgl`	`pip install dgl`
CUDA 9.2	`pip install --pre dgl-cu92`	`pip install dgl-cu92`
CUDA 10.1	`pip install --pre dgl-cu101`	`pip install dgl-cu101`
CUDA 10.2	`pip install --pre dgl-cu102`	`pip install dgl-cu102`
CUDA 11.0	`pip install --pre dgl-cu110`	`pip install dgl-cu110`

Built from source code

Refer to the guide here.

DGL Major Releases

Releases	Date	Features
v0.4.3	03/31/2020	- TensorFlow support - DGL-KE - DGL-LifeSci - Heterograph sampling APIs (experimental)
v0.4.2	01/24/2020	- Heterograph support - TensorFlow support (experimental) - MXNet GNN modules
v0.3.1	08/23/2019	- APIs for GNN modules - Model zoo (DGL-Chem) - New installation
v0.2	03/09/2019	- Graph sampling APIs - Speed improvement
v0.1	12/07/2018	- Basic DGL APIs - PyTorch and MXNet support - GNN model examples and tutorials

New to Deep Learning and Graph Deep Learning?

Check out the open source book Dive into Deep Learning.

For those who are new to graph neural network, please see the basic of DGL.

For audience who are looking for more advanced, realistic, and end-to-end examples, please see model tutorials.

Contributing

Please let us know if you encounter a bug or have any suggestions by filing an issue.

We welcome all contributions from bug fixes to new features and extensions.

We expect all contributions discussed in the issue tracker and going through PRs. Please refer to our contribution guide.

Cite

If you use DGL in a scientific publication, we would appreciate citations to the following paper:

@article{wang2019dgl,
    title={Deep Graph Library: A Graph-Centric, Highly-Performant Package for Graph Neural Networks},
    author={Minjie Wang and Da Zheng and Zihao Ye and Quan Gan and Mufei Li and Xiang Song and Jinjing Zhou and Chao Ma and Lingfan Yu and Yu Gai and Tianjun Xiao and Tong He and George Karypis and Jinyang Li and Zheng Zhang},
    year={2019},
    journal={arXiv preprint arXiv:1909.01315}
}

The Team

DGL is developed and maintained by NYU, NYU Shanghai, AWS Shanghai AI Lab, and AWS MXNet Science Team.

License

DGL uses Apache License 2.0.

bioannidis/dgl