想要了解图或图神经网络？没有比看论文更好的方式（代号Eden手机版）

机器之心编辑

参与：思源

图嵌入、图表征、图分类、图神经网络，这篇文章将介绍你需要的图建模论文，当然它们都有配套实现的。

图是一种非常神奇的表示方式，生活中绝大多数的现象或情境都能用图来表示，例如人际关系网、道路交通网、信息互联网等等。正如马哲介绍事物具有普遍联系性，而图正好能捕捉这种联系，所以用它来描述这个世界是再好不过的方法。

但图这种结构化数据有个麻烦的地方，我们先要有图才能进行后续的计算。但图的搭建并不简单，目前也没有比较好的自动化方法，所以第一步还是需要挺多功夫的。只要各节点及边都确定了，那么图就是一种非常强大且复杂的工具，模型也能推断出图中的各种隐藏知识。

不同时期的图建模

其实，我们可以将图建模分为图神经网络与传统的图模型。其中以前的图建模主要借助 Graph Embedding 为不同的节点学习低维向量表征，这借鉴了 NLP 中词嵌入的思想。而图神经网络借助深度学习进行更强大的图运算与图表征。

Graph Embedding 算法聚焦在如何对网络节点进行低维向量表示，相似的节点在表征空间中更加接近。相比之下，GNN 最大的优势在于它不只可以对一个节点进行语义表示。

例如 GNN 可以表示子图的语义信息，将网络中一小部分节点构成的语义表示出来，这是以前 Graph Embedding 不容易做到的。GNN 还可以在整个图网络上进行信息传播、聚合等建模，也就是说它可以把图网络当成一个整体进行建模。此外，GNN 对单个节点的表示也可以做得更好，因为它可以更好地建模周围节点丰富信息。

在传统图建模中，随机游走、最短路径等图方法会利用符号知识，但这些方法并没有办法很好地利用每个节点的语义信息。而深度学习技术更擅长处理非结构文本、图像等数据。简言之，我们可以将 GNN 看做将深度学习技术应用到符号表示的图数据上，或者说是从非结构化数据扩展到了结构化数据。GNN 能够充分融合符号表示和低维向量表示，发挥两者优势。

图建模论文与代码

在 GitHub 的一项开源工作中，开发者收集了图建模相关的论文与实现，并且从经典的 Graph Embedding、Graph Kernel 到图神经网络都有涉及。它们在图嵌入、图分类、图表征等领域都是非常重要的论文。

项目地址：https://github.com/benedekrozemberczki/awesome-graph-classification

该项目主要收集的论文领域如下所示：

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

图神经网络

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 Gärtner, 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

不同时期的图建模

图建模论文与代码

在的一项开源工作中，开发者收集了图建模相关的论文与实现，并且从经典的 Graph Embedding、Graph Kernel 到图神经网络都有涉及。它们在图嵌入、图分类、图表征等领域都是非常重要的论文。

项目地址：benedekrozemberczki/awesome-graph-classification

该项目主要收集的论文领域如下所示：

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：nphdang/GE-FSG

· Anonymous Walk Embeddings (ICML 2018)

· Sergey Ivanov and Evgeny Burnaev

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

· Python：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：benedekrozemberczki/graph2vec

· Python Reference：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：MLDroid/subgraph2vec_gensim

· Python Reference：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：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：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：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：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：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:// .com/TonyZZX/MultiGraph_MultiLabel_Learning/blob/master/entropy-20-00245.pdf

· Python Reference：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:// .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:// .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:// .com/kristyspatel/Netsimile

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