圖嵌入、圖表征、圖分類、圖神經(jīng)網(wǎng)絡(luò)，這篇文章將介紹你需要的圖建模論文，當(dāng)然它們都有配套實(shí)現(xiàn)的。

圖是一種非常神奇的表示方式，生活中絕大多數(shù)的現(xiàn)象或情境都能用圖來(lái)表示，例如人際關(guān)系網(wǎng)、道路交通網(wǎng)、信息互聯(lián)網(wǎng)等等。正如馬哲介紹事物具有普遍聯(lián)系性，而圖正好能捕捉這種聯(lián)系，所以用它來(lái)描述這個(gè)世界是再好不過(guò)的方法。

但圖這種結(jié)構(gòu)化數(shù)據(jù)有個(gè)麻煩的地方，我們先要有圖才能進(jìn)行后續(xù)的計(jì)算。但圖的搭建并不簡(jiǎn)單，目前也沒(méi)有比較好的自動(dòng)化方法，所以第一步還是需要挺多功夫的。只要各節(jié)點(diǎn)及邊都確定了，那么圖就是一種非常強(qiáng)大且復(fù)雜的工具，模型也能推斷出圖中的各種隱藏知識(shí)。

不同時(shí)期的圖建模

其實(shí)，我們可以將圖建模分為圖神經(jīng)網(wǎng)絡(luò)與傳統(tǒng)的圖模型。其中以前的圖建模主要借助 Graph Embedding 為不同的節(jié)點(diǎn)學(xué)習(xí)低維向量表征，這借鑒了 NLP 中詞嵌入的思想。而圖神經(jīng)網(wǎng)絡(luò)借助深度學(xué)習(xí)進(jìn)行更強(qiáng)大的圖運(yùn)算與圖表征。

Graph Embedding 算法聚焦在如何對(duì)網(wǎng)絡(luò)節(jié)點(diǎn)進(jìn)行低維向量表示，相似的節(jié)點(diǎn)在表征空間中更加接近。相比之下，GNN 最大的優(yōu)勢(shì)在于它不只可以對(duì)一個(gè)節(jié)點(diǎn)進(jìn)行語(yǔ)義表示。

例如 GNN 可以表示子圖的語(yǔ)義信息，將網(wǎng)絡(luò)中一小部分節(jié)點(diǎn)構(gòu)成的語(yǔ)義表示出來(lái)，這是以前 Graph Embedding 不容易做到的。GNN 還可以在整個(gè)圖網(wǎng)絡(luò)上進(jìn)行信息傳播、聚合等建模，也就是說(shuō)它可以把圖網(wǎng)絡(luò)當(dāng)成一個(gè)整體進(jìn)行建模。此外，GNN 對(duì)單個(gè)節(jié)點(diǎn)的表示也可以做得更好，因?yàn)樗梢愿玫亟Ｖ車?jié)點(diǎn)豐富信息。

在傳統(tǒng)圖建模中，隨機(jī)游走、最短路徑等圖方法會(huì)利用符號(hào)知識(shí)，但這些方法并沒(méi)有辦法很好地利用每個(gè)節(jié)點(diǎn)的語(yǔ)義信息。而深度學(xué)習(xí)技術(shù)更擅長(zhǎng)處理非結(jié)構(gòu)文本、圖像等數(shù)據(jù)。簡(jiǎn)言之，我們可以將 GNN 看做將深度學(xué)習(xí)技術(shù)應(yīng)用到符號(hào)表示的圖數(shù)據(jù)上，或者說(shuō)是從非結(jié)構(gòu)化數(shù)據(jù)擴(kuò)展到了結(jié)構(gòu)化數(shù)據(jù)。GNN 能夠充分融合符號(hào)表示和低維向量表示，發(fā)揮兩者優(yōu)勢(shì)。

圖建模論文與代碼

在 GitHub 的一項(xiàng)開(kāi)源工作中，開(kāi)發(fā)者收集了圖建模相關(guān)的論文與實(shí)現(xiàn)，并且從經(jīng)典的 Graph Embedding、Graph Kernel 到圖神經(jīng)網(wǎng)絡(luò)都有涉及。它們?cè)趫D嵌入、圖分類、圖表征等領(lǐng)域都是非常重要的論文。

項(xiàng)目地址：https://github.com/benedekrozemberczki/awesome-graph-classification

該項(xiàng)目主要收集的論文領(lǐng)域如下所示：

1. Factorization

2. Spectral and Statistical Fingerprints

3. Graph Neural Network

4. Graph Kernels

因式分解法

Learning Graph Representation via Frequent Subgraphs (SDM 2018)

Dang Nguyen, Wei Luo, Tu Dinh Nguyen, Svetha Venkatesh, Dinh Phung

Paper：https://epubs.siam.org/doi/10.1137/1.9781611975321.35

Python：https://github.com/nphdang/GE-FSG

Anonymous Walk Embeddings (ICML 2018)

Sergey Ivanov and Evgeny Burnaev

Paper：https://arxiv.org/pdf/1805.11921.pdf

Python：https://github.com/nd7141/AWE

Graph2vec (MLGWorkshop 2017)

Annamalai Narayanan, Mahinthan Chandramohan, Lihui Chen, Yang Liu, and Santhoshkumar Saminathan

Paper：https://arxiv.org/abs/1707.05005

Python High Performance：https://github.com/benedekrozemberczki/graph2vec

Python Reference：https://github.com/MLDroid/graph2vec_tf

Subgraph2vec (MLGWorkshop 2016)

Annamalai Narayanan, Mahinthan Chandramohan, Lihui Chen, Yang Liu, and Santhoshkumar Saminathan

Paper：https://arxiv.org/abs/1606.08928

Python High Performance：https://github.com/MLDroid/subgraph2vec_gensim

Python Reference：https://github.com/MLDroid/subgraph2vec_tf

Rdf2Vec: RDF Graph Embeddings for Data Mining (ISWC 2016)

Petar Ristoski and Heiko Paulheim

Paper：https://link.springer.com/chapter/10.1007/978-3-319-46523-4_30

Python Reference：https://github.com/airobert/RDF2VecAtWebScale

Deep Graph Kernels (KDD 2015)

Pinar Yanardag and S.V.N. Vishwanathan

Paper：https://dl.acm.org/citation.cfm?id=2783417

Python Reference：https://github.com/pankajk/Deep-Graph-Kernels

Spectral and Statistical Fingerprints

A Simple Yet Effective Baseline for Non-Attribute Graph Classification (ICLR RLPM 2019)

Chen Cai, Yusu Wang

Paper：https://arxiv.org/abs/1811.03508

Python Reference：https://github.com/Chen-Cai-OSU/LDP

NetLSD (KDD 2018)

Anton Tsitsulin, Davide Mottin, Panagiotis Karras, Alex Bronstein, and Emmanuel Müller

Paper：https://arxiv.org/abs/1805.10712

Python Reference：https://github.com/xgfs/NetLSD

A Simple Baseline Algorithm for Graph Classification (Relational Representation Learning, NIPS 2018)

Nathan de Lara and Edouard Pineau

Paper：https://arxiv.org/pdf/1810.09155.pdf

Python Reference：https://github.com/edouardpineau/A-simple-baseline-algorithm-for-graph-classification

Multi-Graph Multi-Label Learning Based on Entropy (Entropy NIPS 2018)

Zixuan Zhu and Yuhai Zhao

Paper：https://github.com/TonyZZX/MultiGraph_MultiLabel_Learning/blob/master/entropy-20-00245.pdf

Python Reference：https://github.com/TonyZZX/MultiGraph_MultiLabel_Learning

Hunt For The Unique, Stable, Sparse And Fast Feature Learning On Graphs (NIPS 2017)

Saurabh Verma and Zhi-Li Zhang

Paper：https://papers.nips.cc/paper/6614-hunt-for-the-unique-stable-sparse-and-fast-feature-learning-on-graphs.pdf

Python Reference：https://github.com/vermaMachineLearning/FGSD

Joint Structure Feature Exploration and Regularization for Multi-Task Graph Classification (TKDE 2015)

Shirui Pan, Jia Wu, Xingquan Zhuy, Chengqi Zhang, and Philip S. Yuz

Paper：https://ieeexplore.ieee.org/document/7302040

Java Reference：https://github.com/shiruipan/MTG

NetSimile: A Scalable Approach to Size-Independent Network Similarity (arXiv 2012)

Michele Berlingerio, Danai Koutra, Tina Eliassi-Rad, and Christos Faloutsos

Paper：https://arxiv.org/abs/1209.2684

Python：https://github.com/kristyspatel/Netsimile

圖神經(jīng)網(wǎng)絡(luò)

Self-Attention Graph Pooling (ICML 2019)

Junhyun Lee, Inyeop Lee, Jaewoo Kang

Paper：https://arxiv.org/abs/1904.08082

Python Reference：https://github.com/inyeoplee77/SAGPool

Variational Recurrent Neural Networks for Graph Classification (ICLR 2019)

Edouard Pineau, Nathan de Lara

Paper：https://arxiv.org/abs/1902.02721

Python Reference：https://github.com/edouardpineau/Variational-Recurrent-Neural-Networks-for-Graph-Classification

Crystal Graph Neural Networks for Data Mining in Materials Science (Arxiv 2019)

Takenori Yamamoto

Paper：https://storage.googleapis.com/rimcs_cgnn/cgnn_matsci_May_27_2019.pdf

Python Reference：https://github.com/Tony-Y/cgnn

Explainability Techniques for Graph Convolutional Networks (ICML 2019)

Federico Baldassarre, Hossein Azizpour

Paper：https://128.84.21.199/pdf/1905.13686.pdf

Python Reference：https://github.com/gn-exp/gn-exp

Semi-Supervised Graph Classification: A Hierarchical Graph Perspective (WWW 2019)

Jia Li, Yu Rong, Hong Cheng, Helen Meng, Wenbing Huang, and Junzhou Huang

Paper：https://arxiv.org/pdf/1904.05003.pdf

Python Reference：https://github.com/benedekrozemberczki/SEAL-CI

Capsule Graph Neural Network (ICLR 2019)

Zhang Xinyi and Lihui Chen

Paper：https://openreview.net/forum?id=Byl8BnRcYm

Python Reference：https://github.com/benedekrozemberczki/CapsGNN

How Powerful are Graph Neural Networks? (ICLR 2019)

Keyulu Xu, Weihua Hu, Jure Leskovec, Stefanie Jegelka

Paper：https://arxiv.org/abs/1810.00826

Python Reference：https://github.com/weihua916/powerful-gnns

Weisfeiler and Leman Go Neural: Higher-order Graph Neural Networks (AAAI 2019)

Christopher Morris, Martin Ritzert, Matthias Fey, William L. Hamilton, Jan Eric Lenssen, Gaurav Rattan, and Martin Grohe

Paper：https://arxiv.org/pdf/1810.02244v2.pdf

Python Reference：https://github.com/k-gnn/k-gnn

Capsule Neural Networks for Graph Classification using Explicit Tensorial Graph Representations (Arxiv 2019)

Marcelo Daniel Gutierrez Mallea, Peter Meltzer, and Peter J Bentley

Paper：https://arxiv.org/pdf/1902.08399v1.pdf

Python Reference：https://github.com/BraintreeLtd/PatchyCapsules

Three-Dimensionally Embedded Graph Convolutional Network for Molecule Interpretation (Arxiv 2018)

Hyeoncheol Cho and Insung. S. Choi

Paper：https://arxiv.org/abs/1811.09794

Python Reference：https://github.com/blackmints/3DGCN

Learning Graph-Level Representations with Recurrent Neural Networks (Arxiv 2018)

Yu Jin and Joseph F. JaJa

Paper：https://arxiv.org/pdf/1805.07683v4.pdf

Python Reference：https://github.com/yuj-umd/graphRNN

Graph Capsule Convolutional Neural Networks (ICML 2018)

Saurabh Verma and Zhi-Li Zhang

Paper：https://arxiv.org/abs/1805.08090

Python Reference：https://github.com/vermaMachineLearning/Graph-Capsule-CNN-Networks

Graph Classification Using Structural Attention (KDD 2018)

John Boaz Lee, Ryan Rossi, and Xiangnan Kong

Paper：http://ryanrossi.com/pubs/KDD18-graph-attention-model.pdf

Python Pytorch Reference：https://github.com/benedekrozemberczki/GAM

Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation (NIPS 2018)

Jiaxuan You, Bowen Liu, Rex Ying, Vijay Pande, and Jure Leskovec

Paper：https://arxiv.org/abs/1806.02473

Python Reference：https://github.com/bowenliu16/rl_graph_generation

Hierarchical Graph Representation Learning with Differentiable Pooling (NIPS 2018)

Zhitao Ying, Jiaxuan You, Christopher Morris, Xiang Ren, Will Hamilton and Jure Leskovec

Paper：http://papers.nips.cc/paper/7729-hierarchical-graph-representation-learning-with-differentiable-pooling.pdf

Python Reference：https://github.com/rusty1s/pytorch_geometric

Contextual Graph Markov Model: A Deep and Generative Approach to Graph Processing (ICML 2018)

Davide Bacciu, Federico Errica, and Alessio Micheli

Paper：https://arxiv.org/pdf/1805.10636.pdf

Python Reference：https://github.com/diningphil/CGMM

MolGAN: An Implicit Generative Model for Small Molecular Graphs (ICML 2018)

Nicola De Cao and Thomas Kipf

Paper：https://arxiv.org/pdf/1805.11973.pdf

Python Reference：https://github.com/nicola-decao/MolGAN

Deeply Learning Molecular Structure-Property Relationships Using Graph Attention Neural Network (2018)

Seongok Ryu, Jaechang Lim, and Woo Youn Kim

Paper：https://arxiv.org/abs/1805.10988

Python Reference：https://github.com/SeongokRyu/Molecular-GAT

Compound-protein Interaction Prediction with End-to-end Learning of Neural Networks for Graphs and Sequences (Bioinformatics 2018)

Masashi Tsubaki, Kentaro Tomii, and Jun Sese

Paper：https://academic.oup.com/bioinformatics/article/35/2/309/5050020

Python Reference：https://github.com/masashitsubaki/CPI_prediction

Python Reference：https://github.com/masashitsubaki/GNN_molecules

Python Alternative：https://github.com/xnuohz/GCNDTI

Learning Graph Distances with Message Passing Neural Networks (ICPR 2018)

Pau Riba, Andreas Fischer, Josep Llados, and Alicia Fornes

Paper：https://ieeexplore.ieee.org/abstract/document/8545310

Python Reference：https://github.com/priba/siamese_ged

Edge Attention-based Multi-Relational Graph Convolutional Networks (2018)

Chao Shang, Qinqing Liu, Ko-Shin Chen, Jiangwen Sun, Jin Lu, Jinfeng Yi and Jinbo Bi

Paper：https://arxiv.org/abs/1802.04944v1

Python Reference：https://github.com/Luckick/EAGCN

Commonsense Knowledge Aware Conversation Generation with Graph Attention (IJCAI-ECAI 2018)

Hao Zhou, Tom Yang, Minlie Huang, Haizhou Zhao, Jingfang Xu and Xiaoyan Zhu

Paper：http://coai.cs.tsinghua.edu.cn/hml/media/files/2018_commonsense_ZhouHao_3_TYVQ7Iq.pdf

Python Reference：https://github.com/tuxchow/ccm

Residual Gated Graph ConvNets (ICLR 2018)

Xavier Bresson and Thomas Laurent

Paper：https://arxiv.org/pdf/1711.07553v2.pdf

Python Pytorch Reference：https://github.com/xbresson/spatial_graph_convnets

An End-to-End Deep Learning Architecture for Graph Classification (AAAI 2018)

Muhan Zhang, Zhicheng Cui, Marion Neumann and Yixin Chen

Paper：https://www.cse.wustl.edu/~muhan/papers/AAAI_2018_DGCNN.pdf

Python Tensorflow Reference：https://github.com/muhanzhang/DGCNN

Python Pytorch Reference：https://github.com/muhanzhang/pytorch_DGCNN

MATLAB Reference：https://github.com/muhanzhang/DGCNN

Python Alternative：https://github.com/leftthomas/DGCNN

Python Alternative：https://github.com/hitlic/DGCNN-tensorflow

SGR: Self-Supervised Spectral Graph Representation Learning (KDD DLDay 2018)

Anton Tsitsulin, Davide Mottin, Panagiotis Karra, Alex Bronstein and Emmanueal Müller

Paper：https://arxiv.org/abs/1807.02839

Python Reference：http://mott.in/publications/others/sgr/

Deep Learning with Topological Signatures (NIPS 2017)

Christoph Hofer, Roland Kwitt, Marc Niethammer, and Andreas Uhl

paper：https://arxiv.org/abs/1707.04041

Python Reference：https://github.com/c-hofer/nips2017

Dynamic Edge-Conditioned Filters in Convolutional Neural Networks on Graphs (CVPR 2017)

Martin Simonovsky and Nikos Komodakis

paper：https://arxiv.org/pdf/1704.02901v3.pdf

Python Reference：https://github.com/mys007/ecc

Deriving Neural Architectures from Sequence and Graph Kernels (ICML 2017)

Tao Lei, Wengong Jin, Regina Barzilay, and Tommi Jaakkola

Paper：https://arxiv.org/abs/1705.09037

Python Reference：https://github.com/taolei87/icml17_knn

Protein Interface Prediction using Graph Convolutional Networks (NIPS 2017)

Alex Fout, Jonathon Byrd, Basir Shariat and Asa Ben-Hur

Paper：https://papers.nips.cc/paper/7231-protein-interface-prediction-using-graph-convolutional-networks

Python Reference：https://github.com/fouticus/pipgcn

Graph Classification with 2D Convolutional Neural Networks (2017)

Antoine J.-P. Tixier, Giannis Nikolentzos, Polykarpos Meladianos and Michalis Vazirgiannis

Paper：https://arxiv.org/abs/1708.02218

Python Reference：https://github.com/Tixierae/graph_2D_CNN

CayleyNets: Graph Convolutional Neural Networks with Complex Rational Spectral Filters (IEEE TSP 2017)

Ron Levie, Federico Monti, Xavier Bresson, Michael M. Bronstein

Paper：https://arxiv.org/pdf/1705.07664v2.pdf

Python Reference：https://github.com/fmonti/CayleyNet

Semi-supervised Learning of Hierarchical Representations of Molecules Using Neural Message Passing (2017)

Hai Nguyen, Shin-ichi Maeda, Kenta Oono

Paper：https://arxiv.org/pdf/1711.10168.pdf

Python Reference：https://github.com/pfnet-research/hierarchical-molecular-learning

Kernel Graph Convolutional Neural Networks (2017)

Giannis Nikolentzos, Polykarpos Meladianos, Antoine Jean-Pierre Tixier, Konstantinos Skianis, Michalis Vazirgiannis

Paper：https://arxiv.org/pdf/1710.10689.pdf

Python Reference：https://github.com/giannisnik/cnn-graph-classification

Deep Topology Classification: A New Approach For Massive Graph Classification (IEEE Big Data 2016)

Stephen Bonner, John Brennan, Georgios Theodoropoulos, Ibad Kureshi, Andrew Stephen McGough

Paper：https://ieeexplore.ieee.org/document/7840988/

Python Reference：https://github.com/sbonner0/DeepTopologyClassification

Learning Convolutional Neural Networks for Graphs (ICML 2016)

Mathias Niepert, Mohamed Ahmed, Konstantin Kutzkov

Paper：https://arxiv.org/abs/1605.05273

Python Reference：https://github.com/tvayer/PSCN

Gated Graph Sequence Neural Networks (ICLR 2016)

Yujia Li, Daniel Tarlow, Marc Brockschmidt, Richard Zemel

Paper：https://arxiv.org/abs/1511.05493

Python TensorFlow：https://github.com/bdqnghi/ggnn.tensorflow

Python PyTorch：https://github.com/JamesChuanggg/ggnn.pytorch

Python Reference：https://github.com/YunjaeChoi/ggnnmols

Convolutional Networks on Graphs for Learning Molecular Fingerprints (NIPS 2015)

David Duvenaud, Dougal Maclaurin, Jorge Aguilera-Iparraguirre, Rafael Gómez-Bombarelli, Timothy Hirzel, Alán Aspuru-Guzik, and Ryan P. Adams

Paper：https://papers.nips.cc/paper/5954-convolutional-networks-on-graphs-for-learning-molecular-fingerprints.pdf

Python Reference：https://github.com/fllinares/neural_fingerprints_tf

Python Reference：https://github.com/jacklin18/neural-fingerprint-in-GNN

Python Reference：https://github.com/HIPS/neural-fingerprint

Python Reference：https://github.com/debbiemarkslab/neural-fingerprint-theano

Graph Kernels

Message Passing Graph Kernels (2018)

Giannis Nikolentzos, Michalis Vazirgiannis

Paper：https://arxiv.org/pdf/1808.02510.pdf

Python Reference：https://github.com/giannisnik/message_passing_graph_kernels

Matching Node Embeddings for Graph Similarity (AAAI 2017)

Giannis Nikolentzos, Polykarpos Meladianos, and Michalis Vazirgiannis

Paper：https://aaai.org/ocs/index.php/AAAI/AAAI17/paper/view/14494

Global Weisfeiler-Lehman Graph Kernels (2017)

Christopher Morris, Kristian Kersting and Petra Mutzel

Paper：https://arxiv.org/pdf/1703.02379.pdf

C++ Reference：https://github.com/chrsmrrs/glocalwl

On Valid Optimal Assignment Kernels and Applications to Graph Classification (2016)

Nils Kriege, Pierre-Louis Giscard, Richard Wilson

Paper：https://arxiv.org/pdf/1606.01141.pdf

Java Reference：https://github.com/nlskrg/optimal_assignment_kernels

Efficient Comparison of Massive Graphs Through The Use Of ‘Graph Fingerprints’ (MLGWorkshop 2016)

Stephen Bonner, John Brennan, and A. Stephen McGough

Paper：http://dro.dur.ac.uk/19773/1/19773.pdf?DDD10+lzdh59+d700tmt

python Reference：https://github.com/sbonner0/GraphFingerprintComparison

The Multiscale Laplacian Graph Kernel (NIPS 2016)

Risi Kondor and Horace Pan

Paper：https://arxiv.org/abs/1603.06186

C++ Reference：https://github.com/horacepan/MLGkernel

Faster Kernels for Graphs with Continuous Attributes (ICDM 2016)

Christopher Morris, Nils M. Kriege, Kristian Kersting and Petra Mutzel

Paper：https://arxiv.org/abs/1610.00064

Python Reference：https://github.com/chrsmrrs/hashgraphkernel

Propagation Kernels: Efficient Graph Kernels From Propagated Information (Machine Learning 2016)

Neumann, Marion and Garnett, Roman and Bauckhage, Christian and Kersting, Kristian

Paper：https://link.springer.com/article/10.1007/s10994-015-5517-9

Matlab Reference：https://github.com/marionmari/propagation_kernels

Halting Random Walk Kernels (NIPS 2015)

Mahito Sugiyama and Karsten M. Borgward

Paper：https://pdfs.semanticscholar.org/79ba/8bcfbf9496834fdc22a1f7c96d26d776cd6c.pdf

C++ Reference：https://github.com/BorgwardtLab/graph-kernels

Scalable Kernels for Graphs with Continuous Attributes (NIPS 2013)

Aasa Feragen, Niklas Kasenburg, Jens Petersen, Marleen de Bruijne and Karsten Borgwardt

Paper：https://papers.nips.cc/paper/5155-scalable-kernels-for-graphs-with-continuous-attributes.pdf

Subgraph Matching Kernels for Attributed Graphs (ICML 2012)

Nils Kriege and Petra Mutzel

Paper：https://arxiv.org/abs/1206.6483

Python Reference：https://github.com/mockingbird2/GraphKernelBenchmark

Nested Subtree Hash Kernels for Large-Scale Graph Classification over Streams (ICDM 2012)

Bin Li, Xingquan Zhu, Lianhua Chi, Chengqi Zhang

Paper：https://ieeexplore.ieee.org/document/6413884/

Python Reference：https://github.com/benedekrozemberczki/NestedSubtreeHash

Weisfeiler-Lehman Graph Kernels (JMLR 2011)

Nino Shervashidze, Pascal Schweitzer, Erik Jan van Leeuwen, Kurt Mehlhorn, and Karsten M. Borgwardt

Paper：http://www.jmlr.org/papers/volume12/shervashidze11a/shervashidze11a.pdf

Python Reference：https://github.com/jajupmochi/py-graph

Python Reference：https://github.com/deeplego/wl-graph-kernels

C++ Reference：https://github.com/BorgwardtLab/graph-kernels

Fast Neighborhood Subgraph Pairwise Distance Kernel (ICML 2010)

Fabrizio Costa and Kurt De Grave

Paper：https://icml.cc/Conferences/2010/papers/347.pdf

C++ Reference：https://github.com/benedekrozemberczki/awesome-graph-classification/blob/master/www.bioinf.uni-freiburg.de/~costa/EDeNcpp.tgz

Python Reference：https://github.com/fabriziocosta/EDeN

A Linear-time Graph Kernel (ICDM 2009)

Shohei Hido and Hisashi Kashima

Paper：https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=5360243

Python Reference：https://github.com/hgascon/adagio

Weisfeiler-Lehman Subtree Kernels (NIPS 2009)

Nino Shervashidze, Pascal Schweitzer, Erik Jan van Leeuwen, Kurt Mehlhorn, and Karsten M. Borgwardt

Paper：http://papers.nips.cc/paper/3813-fast-subtree-kernels-on-graphs.pdf

Python Reference：https://github.com/jajupmochi/py-graph

Python Reference：https://github.com/deeplego/wl-graph-kernels

C++ Reference：https://github.com/BorgwardtLab/graph-kernels

Fast Computation of Graph Kernels (NIPS 2006)

S. V. N. Vishwanathan, Karsten M. Borgwardt, and Nicol N. Schraudolph

Paper：http://www.dbs.ifi.lmu.de/Publikationen/Papers/VisBorSch06.pdf

Python Reference：https://github.com/jajupmochi/py-graph

C++ Reference：https://github.com/BorgwardtLab/graph-kernels

Shortest-Path Kernels on Graphs (ICDM 2005)

Karsten M. Borgwardt and Hans-Peter Kriegel

Paper：https://www.ethz.ch/content/dam/ethz/special-interest/bsse/borgwardt-lab/documents/papers/BorKri05.pdf

C++ Reference：https://github.com/KitwareMedical/ITKTubeTK

Cyclic Pattern Kernels For Predictive Graph Mining (KDD 2004)

Tamás Horváth, Thomas G?rtner, and Stefan Wrobel

Paper：http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.332.6158&rep=rep1&type=pdf

Python Reference：https://github.com/jajupmochi/py-graph

Extensions of Marginalized Graph Kernels (ICML 2004)

Pierre Mahe, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, and Jean-Philippe Vert

Paper：http://members.cbio.mines-paristech.fr/~jvert/publi/04icml/icmlMod.pdf

Python Reference：https://github.com/jajupmochi/py-graph

Marginalized Kernels Between Labeled Graphs (ICML 2003)

Hisashi Kashima, Koji Tsuda, and Akihiro Inokuchi

Paper：https://pdfs.semanticscholar.org/2dfd/92c808487049ab4c9b45db77e9055b9da5a2.pdf

Python Reference：https://github.com/jajupmochi/py-graph