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正文
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Paper:https://arxiv.org/abs/1209.2684
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Python:https://github.com/kristyspatel/Netsimile
图神经网络
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Self-Attention Graph Pooling (ICML 2019)
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Junhyun Lee, Inyeop Lee, Jaewoo Kang
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Paper:https://arxiv.org/abs/1904.08082
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Python Reference:https://github.com/inyeoplee77/SAGPool
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Variational Recurrent Neural Networks for Graph Classification (ICLR 2019)
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Edouard Pineau, Nathan de Lara
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Paper:https://arxiv.org/abs/1902.02721
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Python Reference:https://github.com/edouardpineau/Variational-Recurrent-Neural-Networks-for-Graph-Classification
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Crystal Graph Neural Networks for Data Mining in Materials Science (Arxiv 2019)
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Takenori Yamamoto
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Paper:https://storage.googleapis.com/rimcs_cgnn/cgnn_matsci_May_27_2019.pdf
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Python Reference:https://github.com/Tony-Y/cgnn
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Explainability Techniques for Graph Convolutional Networks (ICML 2019)
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Federico Baldassarre, Hossein Azizpour
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Paper:https://128.84.21.199/pdf/1905.13686.pdf
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Python Reference:https://github.com/gn-exp/gn-exp
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Semi-Supervised Graph Classification: A Hierarchical Graph Perspective (WWW 2019)
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Jia Li, Yu Rong, Hong Cheng, Helen Meng, Wenbing Huang, and Junzhou Huang
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Paper:https://arxiv.org/pdf/1904.05003.pdf
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Python Reference:https://github.com/benedekrozemberczki/SEAL-CI
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Capsule Graph Neural Network (ICLR 2019)
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Zhang Xinyi and Lihui Chen
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Paper:https://openreview.net/forum?id=Byl8BnRcYm
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Python Reference:https://github.com/benedekrozemberczki/CapsGNN
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How Powerful are Graph Neural Networks? (ICLR 2019)
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Keyulu Xu, Weihua Hu, Jure Leskovec, Stefanie Jegelka
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Paper:https://arxiv.org/abs/1810.00826
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Python Reference:https://github.com/weihua916/powerful-gnns
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Weisfeiler and Leman Go Neural: Higher-order Graph Neural Networks (AAAI 2019)
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Christopher Morris, Martin Ritzert, Matthias Fey, William L. Hamilton, Jan Eric Lenssen, Gaurav Rattan, and Martin Grohe
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Paper:https://arxiv.org/pdf/1810.02244v2.pdf
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Python Reference:https://github.com/k-gnn/k-gnn
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Capsule Neural Networks for Graph Classification using Explicit Tensorial Graph Representations (Arxiv 2019)
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Marcelo Daniel Gutierrez Mallea, Peter Meltzer, and Peter J Bentley
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Paper:https://arxiv.org/pdf/1902.08399v1.pdf
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Python Reference:https://github.com/BraintreeLtd/PatchyCapsules
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Three-Dimensionally Embedded Graph Convolutional Network for Molecule Interpretation (Arxiv 2018)
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Hyeoncheol Cho and Insung. S. Choi
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Paper:https://arxiv.org/abs/1811.09794
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Python Reference:https://github.com/blackmints/3DGCN
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Learning Graph-Level Representations with Recurrent Neural Networks (Arxiv 2018)
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Yu Jin and Joseph F. JaJa
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Paper:https://arxiv.org/pdf/1805.07683v4.pdf
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Python Reference:https://github.com/yuj-umd/graphRNN
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Graph Capsule Convolutional Neural Networks (ICML 2018)
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Saurabh Verma and Zhi-Li Zhang
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Paper:https://arxiv.org/abs/1805.08090
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Python Reference:https://github.com/vermaMachineLearning/Graph-Capsule-CNN-Networks
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Graph Classification Using Structural Attention (KDD 2018)
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John Boaz Lee, Ryan Rossi, and Xiangnan Kong
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Paper:http://ryanrossi.com/pubs/KDD18-graph-attention-model.pdf
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Python Pytorch Reference:https://github.com/benedekrozemberczki/GAM
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Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation (NIPS 2018)
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Jiaxuan You, Bowen Liu, Rex Ying, Vijay Pande, and Jure Leskovec
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Paper:https://arxiv.org/abs/1806.02473
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Python Reference:https://github.com/bowenliu16/rl_graph_generation
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Hierarchical Graph Representation Learning with Differentiable Pooling (NIPS 2018)
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Zhitao Ying, Jiaxuan You, Christopher Morris, Xiang Ren, Will Hamilton and Jure Leskovec
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Paper:http://papers.nips.cc/paper/7729-hierarchical-graph-representation-learning-with-differentiable-pooling.pdf
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Python Reference:https://github.com/rusty1s/pytorch_geometric
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Contextual Graph Markov Model: A Deep and Generative Approach to Graph Processing (ICML 2018)
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Davide Bacciu, Federico Errica, and Alessio Micheli
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Paper:https://arxiv.org/pdf/1805.10636.pdf
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Python Reference:https://github.com/diningphil/CGMM
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MolGAN: An Implicit Generative Model for Small Molecular Graphs (ICML 2018)
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Nicola De Cao and Thomas Kipf
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Paper:https://arxiv.org/pdf/1805.11973.pdf
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Python Reference:https://github.com/nicola-decao/MolGAN
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Deeply Learning Molecular Structure-Property Relationships Using Graph Attention Neural Network (2018)
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Seongok Ryu, Jaechang Lim, and Woo Youn Kim
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Paper:https://arxiv.org/abs/1805.10988
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Python Reference:https://github.com/SeongokRyu/Molecular-GAT
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Compound-protein Interaction Prediction with End-to-end Learning of Neural Networks for Graphs and Sequences (Bioinformatics 2018)
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Masashi Tsubaki, Kentaro Tomii, and Jun Sese
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Paper:https://academic.oup.com/bioinformatics/article/35/2/309/5050020
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Python Reference:https://github.com/masashitsubaki/CPI_prediction
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Python Reference:https://github.com/masashitsubaki/GNN_molecules
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Python Alternative:https://github.com/xnuohz/GCNDTI
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Learning Graph Distances with Message Passing Neural Networks (ICPR 2018)
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Pau Riba, Andreas Fischer, Josep Llados, and Alicia Fornes
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Paper:https://ieeexplore.ieee.org/abstract/document/8545310
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Python Reference:https://github.com/priba/siamese_ged
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Edge Attention-based Multi-Relational Graph Convolutional Networks (2018)
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Chao Shang, Qinqing Liu, Ko-Shin Chen, Jiangwen Sun, Jin Lu, Jinfeng Yi and Jinbo Bi
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Paper:https://arxiv.org/abs/1802.04944v1
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Python Reference:https://github.com/Luckick/EAGCN
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Commonsense Knowledge Aware Conversation Generation with Graph Attention (IJCAI-ECAI 2018)
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Hao Zhou, Tom Yang, Minlie Huang, Haizhou Zhao, Jingfang Xu and Xiaoyan Zhu
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Paper:http://coai.cs.tsinghua.edu.cn/hml/media/files/2018_commonsense_ZhouHao_3_TYVQ7Iq.pdf
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Python Reference:https://github.com/tuxchow/ccm
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Residual Gated Graph ConvNets (ICLR 2018)
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Xavier Bresson and Thomas Laurent
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Paper:https://arxiv.org/pdf/1711.07553v2.pdf
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Python Pytorch Reference:https://github.com/xbresson/spatial_graph_convnets
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An End-to-End Deep Learning Architecture for Graph Classification (AAAI 2018)
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Muhan Zhang, Zhicheng Cui, Marion Neumann and Yixin Chen
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Paper:https://www.cse.wustl.edu/~muhan/papers/AAAI_2018_DGCNN.pdf
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Python Tensorflow Reference:https://github.com/muhanzhang/DGCNN
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Python Pytorch Reference:https://github.com/muhanzhang/pytorch_DGCNN
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MATLAB Reference:https://github.com/muhanzhang/DGCNN
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Python Alternative:https://github.com/leftthomas/DGCNN
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Python Alternative:https://github.com/hitlic/DGCNN-tensorflow
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SGR: Self-Supervised Spectral Graph Representation Learning (KDD DLDay 2018)
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Anton Tsitsulin, Davide Mottin, Panagiotis Karra, Alex Bronstein and Emmanueal Müller
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Paper:https://arxiv.org/abs/1807.02839
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Python Reference:http://mott.in/publications/others/sgr/
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Deep Learning with Topological Signatures (NIPS 2017)
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Christoph Hofer, Roland Kwitt, Marc Niethammer, and Andreas Uhl
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paper:https://arxiv.org/abs/1707.04041
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Python Reference:https://github.com/c-hofer/nips2017
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Dynamic Edge-Conditioned Filters in Convolutional Neural Networks on Graphs (CVPR 2017)
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Martin Simonovsky and Nikos Komodakis
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paper:https://arxiv.org/pdf/1704.02901v3.pdf
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Python Reference:https://github.com/mys007/ecc
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Deriving Neural Architectures from Sequence and Graph Kernels (ICML 2017)
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Tao Lei, Wengong Jin, Regina Barzilay, and Tommi Jaakkola
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Paper:https://arxiv.org/abs/1705.09037
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Python Reference:https://github.com/taolei87/icml17_knn
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Protein Interface Prediction using Graph Convolutional Networks (NIPS 2017)
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Alex Fout, Jonathon Byrd, Basir Shariat and Asa Ben-Hur
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Paper:https://papers.nips.cc/paper/7231-protein-interface-prediction-using-graph-convolutional-networks
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Python Reference:https://github.com/fouticus/pipgcn
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Graph Classification with 2D Convolutional Neural Networks (2017)
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Antoine J.-P. Tixier, Giannis Nikolentzos, Polykarpos Meladianos and Michalis Vazirgiannis
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Paper:https://arxiv.org/abs/1708.02218
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Python Reference:https://github.com/Tixierae/graph_2D_CNN
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CayleyNets: Graph Convolutional Neural Networks with Complex Rational Spectral Filters (IEEE TSP 2017)
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Ron Levie, Federico Monti, Xavier Bresson, Michael M. Bronstein
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Paper:https://arxiv.org/pdf/1705.07664v2.pdf
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Python Reference:https://github.com/fmonti/CayleyNet
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Semi-supervised Learning of Hierarchical Representations of Molecules Using Neural Message Passing (2017)
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Hai Nguyen, Shin-ichi Maeda, Kenta Oono
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Paper:https://arxiv.org/pdf/1711.10168.pdf
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Python Reference:https://github.com/pfnet-research/hierarchical-molecular-learning
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Kernel Graph Convolutional Neural Networks (2017)
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Giannis Nikolentzos, Polykarpos Meladianos, Antoine Jean-Pierre Tixier, Konstantinos Skianis, Michalis Vazirgiannis
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Paper:https://arxiv.org/pdf/1710.10689.pdf
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Python Reference:https://github.com/giannisnik/cnn-graph-classification
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Deep Topology Classification: A New Approach For Massive Graph Classification (IEEE Big Data 2016)
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Stephen Bonner, John Brennan, Georgios Theodoropoulos, Ibad Kureshi, Andrew Stephen McGough
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Paper:https://ieeexplore.ieee.org/document/7840988/
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Python Reference:https://github.com/sbonner0/DeepTopologyClassification
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Learning Convolutional Neural Networks for Graphs (ICML 2016)
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Mathias Niepert, Mohamed Ahmed, Konstantin Kutzkov
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Paper:https://arxiv.org/abs/1605.05273
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Python Reference:https://github.com/tvayer/PSCN
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Gated Graph Sequence Neural Networks (ICLR 2016)
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Yujia Li, Daniel Tarlow, Marc Brockschmidt, Richard Zemel
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Paper:https://arxiv.org/abs/1511.05493
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Python TensorFlow:https://github.com/bdqnghi/ggnn.tensorflow
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Python PyTorch:https://github.com/JamesChuanggg/ggnn.pytorch
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Python Reference:https://github.com/YunjaeChoi/ggnnmols
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Convolutional Networks on Graphs for Learning Molecular Fingerprints (NIPS 2015)
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David Duvenaud, Dougal Maclaurin, Jorge Aguilera-Iparraguirre, Rafael Gómez-Bombarelli, Timothy Hirzel, Alán Aspuru-Guzik, and Ryan P. Adams
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Paper:https://papers.nips.cc/paper/5954-convolutional-networks-on-graphs-for-learning-molecular-fingerprints.pdf
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Python Reference:https://github.com/fllinares/neural_fingerprints_tf
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Python Reference:https://github.com/jacklin18/neural-fingerprint-in-GNN
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Python Reference:https://github.com/HIPS/neural-fingerprint
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Python Reference:https://github.com/debbiemarkslab/neural-fingerprint-theano
Graph Kernels
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Message Passing Graph Kernels (2018)
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Giannis Nikolentzos, Michalis Vazirgiannis
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Paper:https://arxiv.org/pdf/1808.02510.pdf
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Python Reference:https://github.com/giannisnik/message_passing_graph_kernels
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Matching Node Embeddings for Graph Similarity (AAAI 2017)
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Giannis Nikolentzos, Polykarpos Meladianos, and Michalis Vazirgiannis
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Paper:https://aaai.org/ocs/index.php/AAAI/AAAI17/paper/view/14494
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Global Weisfeiler-Lehman Graph Kernels (2017)
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Christopher Morris, Kristian Kersting and Petra Mutzel
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Paper:https://arxiv.org/pdf/1703.02379.pdf
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C++ Reference:https://github.com/chrsmrrs/glocalwl
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On Valid Optimal Assignment Kernels and Applications to Graph Classification (2016)
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Nils Kriege, Pierre-Louis Giscard, Richard Wilson
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Paper:https://arxiv.org/pdf/1606.01141.pdf
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Java Reference:https://github.com/nlskrg/optimal_assignment_kernels
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Efficient Comparison of Massive Graphs Through The Use Of ‘Graph Fingerprints’ (MLGWorkshop 2016)
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Stephen Bonner, John Brennan, and A. Stephen McGough
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Paper:http://dro.dur.ac.uk/19773/1/19773.pdf?DDD10+lzdh59+d700tmt
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python Reference:https://github.com/sbonner0/GraphFingerprintComparison
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The Multiscale Laplacian Graph Kernel (NIPS 2016)
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Risi Kondor and Horace Pan
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Paper:https://arxiv.org/abs/1603.06186
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C++ Reference:https://github.com/horacepan/MLGkernel
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Faster Kernels for Graphs with Continuous Attributes (ICDM 2016)
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Christopher Morris, Nils M. Kriege, Kristian Kersting and Petra Mutzel
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Paper:https://arxiv.org/abs/1610.00064
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Python Reference:https://github.com/chrsmrrs/hashgraphkernel
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Propagation Kernels: Efficient Graph Kernels From Propagated Information (Machine Learning 2016)
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Neumann, Marion and Garnett, Roman and Bauckhage, Christian and Kersting, Kristian
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Paper:https://link.springer.com/article/10.1007/s10994-015-5517-9
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Matlab Reference:https://github.com/marionmari/propagation_kernels
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Halting Random Walk Kernels (NIPS 2015)
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Mahito Sugiyama and Karsten M. Borgward
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Paper:https://pdfs.semanticscholar.org/79ba/8bcfbf9496834fdc22a1f7c96d26d776cd6c.pdf
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C++ Reference:https://github.com/BorgwardtLab/graph-kernels
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Scalable Kernels for Graphs with Continuous Attributes (NIPS 2013)
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Aasa Feragen, Niklas Kasenburg, Jens Petersen, Marleen de Bruijne and Karsten Borgwardt
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Paper:https://papers.nips.cc/paper/5155-scalable-kernels-for-graphs-with-continuous-attributes.pdf
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Subgraph Matching Kernels for Attributed Graphs (ICML 2012)
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Nils Kriege and Petra Mutzel
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Paper:https://arxiv.org/abs/1206.6483
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Python Reference:https://github.com/mockingbird2/GraphKernelBenchmark
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Nested Subtree Hash Kernels for Large-Scale Graph Classification over Streams (ICDM 2012)
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Bin Li, Xingquan Zhu, Lianhua Chi, Chengqi Zhang
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Paper:https://ieeexplore.ieee.org/document/6413884/
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Python Reference:https://github.com/benedekrozemberczki/NestedSubtreeHash
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Weisfeiler-Lehman Graph Kernels (JMLR 2011)
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Nino Shervashidze, Pascal Schweitzer, Erik Jan van Leeuwen, Kurt Mehlhorn, and Karsten M. Borgwardt
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Paper:http://www.jmlr.org/papers/volume12/shervashidze11a/shervashidze11a.pdf
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Python Reference:https://github.com/jajupmochi/py-graph
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Python Reference:https://github.com/deeplego/wl-graph-kernels
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C++ Reference:https://github.com/BorgwardtLab/graph-kernels
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Fast Neighborhood Subgraph Pairwise Distance Kernel (ICML 2010)
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Fabrizio Costa and Kurt De Grave
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Paper:https://icml.cc/Conferences/2010/papers/347.pdf
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C++ Reference:https://github.com/benedekrozemberczki/awesome-graph-classification/blob/master/www.bioinf.uni-freiburg.de/~costa/EDeNcpp.tgz
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Python Reference:https://github.com/fabriziocosta/EDeN
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A Linear-time Graph Kernel (ICDM 2009)
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Shohei Hido and Hisashi Kashima
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Paper:https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=5360243
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Python Reference:https://github.com/hgascon/adagio
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Weisfeiler-Lehman Subtree Kernels (NIPS 2009)
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Nino Shervashidze, Pascal Schweitzer, Erik Jan van Leeuwen, Kurt Mehlhorn, and Karsten M. Borgwardt
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Paper:http://papers.nips.cc/paper/3813-fast-subtree-kernels-on-graphs.pdf
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Python Reference:https://github.com/jajupmochi/py-graph
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Python Reference:https://github.com/deeplego/wl-graph-kernels
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C++ Reference:https://github.com/BorgwardtLab/graph-kernels
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Fast Computation of Graph Kernels (NIPS 2006)
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S. V. N. Vishwanathan, Karsten M. Borgwardt, and Nicol N. Schraudolph
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Paper:http://www.dbs.ifi.lmu.de/Publikationen/Papers/VisBorSch06.pdf
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Python Reference:https://github.com/jajupmochi/py-graph
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C++ Reference:https://github.com/BorgwardtLab/graph-kernels
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Shortest-Path Kernels on Graphs (ICDM 2005)
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Karsten M. Borgwardt and Hans-Peter Kriegel
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Paper:https://www.ethz.ch/content/dam/ethz/special-interest/bsse/borgwardt-lab/documents/papers/BorKri05.pdf
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C++ Reference:https://github.com/KitwareMedical/ITKTubeTK
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Cyclic Pattern Kernels For Predictive Graph Mining (KDD 2004)
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Tamás Horváth, Thomas Gärtner, and Stefan Wrobel
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Paper:http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.332.6158&rep=rep1&type=pdf
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Python Reference:https://github.com/jajupmochi/py-graph
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Extensions of Marginalized Graph Kernels (ICML 2004)
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Pierre Mahe, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, and Jean-Philippe Vert
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Paper:http://members.cbio.mines-paristech.fr/~jvert/publi/04icml/icmlMod.pdf
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Python Reference:https://github.com/jajupmochi/py-graph
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Marginalized Kernels Between Labeled Graphs (ICML 2003)
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Hisashi Kashima, Koji Tsuda, and Akihiro Inokuchi
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Paper:https://pdfs.semanticscholar.org/2dfd/92c808487049ab4c9b45db77e9055b9da5a2.pdf
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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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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)
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)
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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!