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正文

  • 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

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 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

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一个人可以走的很快,但一群人才能走的更远!不论你是正从事IT行业的老鸟或是对IT行业感兴趣的新人,都欢迎加入我们的的圈子(技术交流、学习资源、职场吐槽、大厂内推、面试辅导),让我们一起学习成长!
运用到实际当中去,这时候可以搞点实战案例来学习。

六、面试资料

我们学习Python必然是为了找到高薪的工作,下面这些面试题是来自阿里、腾讯、字节等一线互联网大厂最新的面试资料,并且有阿里大佬给出了权威的解答,刷完这一套面试资料相信大家都能找到满意的工作。

网上学习资料一大堆,但如果学到的知识不成体系,遇到问题时只是浅尝辄止,不再深入研究,那么很难做到真正的技术提升。

需要这份系统化的资料的朋友,可以添加V获取:vip1024c (备注python)
[外链图片转存中…(img-VxRMbGeb-1713591997313)]

一个人可以走的很快,但一群人才能走的更远!不论你是正从事IT行业的老鸟或是对IT行业感兴趣的新人,都欢迎加入我们的的圈子(技术交流、学习资源、职场吐槽、大厂内推、面试辅导),让我们一起学习成长!

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