Terminologies |
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xxxi | |
1 Basic concepts of Graphs |
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xxxi | |
2 Machine Learning on Graphs |
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xxxii | |
3 Graph Neural Networks |
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xxxii | |
Notations |
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xxxv | |
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1 Representation Learning |
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3 | (14) |
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1.1 Representation Learning: An Introduction |
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3 | (2) |
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1.2 Representation Learning in Different Areas |
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5 | (9) |
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1.2.1 Representation Learning for Image Processing |
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5 | (3) |
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1.2.2 Representation Learning for Speech Recognition |
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8 | (2) |
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1.2.3 Representation Learning for Natural Language Processing |
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10 | (3) |
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1.2.4 Representation Learning for Networks |
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13 | (1) |
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14 | (3) |
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2 Graph Representation Learning |
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17 | (10) |
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2.1 Graph Representation Learning: An Introduction |
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17 | (2) |
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2.2 Traditional Graph Embedding |
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19 | (1) |
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2.3 Modem Graph Embedding |
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20 | (5) |
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2.3.1 Structure-Property Preserving Graph Representation Learning |
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20 | (3) |
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2.3.2 Graph Representation Learning with Side Information |
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23 | (1) |
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2.3.3 Advanced Information Preserving Graph Representation Learning |
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24 | (1) |
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2.4 Graph Neural Networks |
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25 | (1) |
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26 | (1) |
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27 | (14) |
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3.1 Graph Neural Networks: An Introduction |
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28 | (1) |
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3.2 Graph Neural Networks: Overview |
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29 | (7) |
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3.2.1 Graph Neural Networks: Foundations |
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29 | (2) |
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3.2.2 Graph Neural Networks: Frontiers |
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31 | (2) |
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3.2.3 Graph Neural Networks: Applications |
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33 | (2) |
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3.2.4 Graph Neural Networks: Organization |
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35 | (1) |
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36 | (5) |
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Part II Foundations of Graph Neural Networks |
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4 Graph Neural Networks for Node Classification |
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41 | (22) |
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4.1 Background and Problem Definition |
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41 | (1) |
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4.2 Supervised Graph Neural Networks |
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42 | (12) |
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4.2.1 General Framework of Graph Neural Networks |
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43 | (1) |
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4.2.2 Graph Convolutional Networks |
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44 | (2) |
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4.2.3 Graph Attention Networks |
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46 | (2) |
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4.2.4 Neural Message Passing Networks |
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48 | (1) |
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4.2.5 Continuous Graph Neural Networks |
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48 | (3) |
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4.2.6 Multi-Scale Spectral Graph Convolutional Networks |
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51 | (3) |
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4.3 Unsupervised Graph Neural Networks |
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54 | (5) |
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4.3.1 Variational Graph Auto-Encoders |
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54 | (3) |
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57 | (2) |
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4.4 Over-smoothing Problem |
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59 | (2) |
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61 | (2) |
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5 The Expressive Power of Graph Neural Networks |
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63 | (36) |
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63 | (4) |
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5.2 Graph Representation Learning and Problem Formulation |
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67 | (3) |
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5.3 The Power of Message Passing Graph Neural Networks |
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70 | (7) |
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5.3.1 Preliminaries: Neural Networks for Sets |
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70 | (1) |
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5.3.2 Message Passing Graph Neural Networks |
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71 | (1) |
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5.3.3 The Expressive Power of MP-GNN |
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72 | (3) |
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5.3.4 MP-GNN with the Power of the 1-WL Test |
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75 | (2) |
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5.4 Graph Neural Networks Architectures that are more Powerful than 1-WL Test |
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77 | (20) |
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5.4.1 Limitations of MP-GNN |
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77 | (2) |
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5.4.2 Injecting Random Attributes |
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79 | (7) |
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5.4.3 Injecting Deterministic Distance Attributes |
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86 | (6) |
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5.4.4 Higher-order Graph Neural Networks |
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92 | (5) |
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97 | (2) |
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6 Graph Neural Networks: Scalability |
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99 | (22) |
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100 | (1) |
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101 | (1) |
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101 | (14) |
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103 | (3) |
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6.3.2 Layer-wise Sampling |
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106 | (5) |
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6.3.3 Graph-wise Sampling |
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111 | (4) |
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6.4 Applications of Large-scale Graph Neural Networks on Recommendation Systems |
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115 | (3) |
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6.4.1 Item-item Recommendation |
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116 | (1) |
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6.4.2 User-item Recommendation |
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116 | (2) |
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118 | (3) |
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7 Interpretability in Graph Neural Networks |
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121 | (28) |
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7.1 Background: Interpretability in Deep Models |
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121 | (7) |
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7.1.1 Definition of Interpretability and Interpretation |
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122 | (1) |
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7.1.2 The Value of Interpretation |
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123 | (1) |
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7.1.3 Traditional Interpretation Methods |
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124 | (3) |
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7.1.4 Opportunities and Challenges |
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127 | (1) |
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7.2 Explanation Methods for Graph Neural Networks |
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128 | (10) |
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128 | (2) |
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7.2.2 Approximation-Based Explanation |
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130 | (4) |
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7.2.3 Relevance-Propagation Based Explanation |
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134 | (1) |
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7.2.4 Perturbation-Based Approaches |
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135 | (2) |
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7.2.5 Generative Explanation |
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137 | (1) |
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7.3 Interpretable Modeling on Graph Neural Networks |
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138 | (5) |
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7.3.1 GNN-Based Attention Models |
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138 | (3) |
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7.3.2 Disentangled Representation Learning on Graphs |
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141 | (2) |
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7.4 Evaluation of Graph Neural Networks Explanations |
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143 | (3) |
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143 | (2) |
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145 | (1) |
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146 | (3) |
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8 Graph Neural Networks: Adversarial Robustness |
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149 | (30) |
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149 | (3) |
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8.2 Limitations of Graph Neural Networks: Adversarial Examples |
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152 | (8) |
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8.2.1 Categorization of Adversarial Attacks |
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152 | (4) |
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8.2.2 The Effect of Perturbations and Some Insights |
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156 | (3) |
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8.2.3 Discussion and Future Directions |
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159 | (1) |
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8.3 Provable Robustness: Certificates for Graph Neural Networks |
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160 | (5) |
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8.3.1 Model-Specific Certificates |
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160 | (3) |
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8.3.2 Model-Agnostic Certificates |
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163 | (2) |
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8.3.3 Advanced Certification and Discussion |
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165 | (1) |
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8.4 Improving Robustness of Graph Neural Networks |
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165 | (7) |
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8.4.1 Improving the Graph |
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166 | (1) |
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8.4.2 Improving the Training Procedure |
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167 | (3) |
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8.4.3 Improving the Graph Neural Networks' Architecture |
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170 | (1) |
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8.4.4 Discussion and Future Directions |
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171 | (1) |
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8.5 Proper Evaluation in the View of Robustness |
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172 | (3) |
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175 | (4) |
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Part III Frontiers of Graph Neural Networks |
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9 Graph Neural Networks: Graph Classification |
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179 | (16) |
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179 | (1) |
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9.2 Graph neural networks for graph classification: Classic works and modern architectures |
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180 | (6) |
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181 | (3) |
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9.2.2 Spectral approaches |
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184 | (2) |
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9.3 Pooling layers: Learning graph-level outputs from node-level outputs |
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186 | (3) |
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9.3.1 Attention-based pooling layers |
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187 | (1) |
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9.3.2 Cluster-based pooling layers |
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187 | (1) |
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9.3.3 Other pooling layers |
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188 | (1) |
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9.4 Limitations of graph neural networks and higher-order layers for graph classification |
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189 | (2) |
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9.4.1 Overcoming limitations |
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190 | (1) |
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9.5 Applications of graph neural networks for graph classification |
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191 | (1) |
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192 | (1) |
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192 | (3) |
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10 Graph Neural Networks: Link Prediction |
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195 | (30) |
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195 | (2) |
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10.2 Traditional Link Prediction Methods |
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197 | (6) |
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197 | (3) |
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10.2.2 Latent-Feature Methods |
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200 | (3) |
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10.2.3 Content-Based Methods |
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203 | (1) |
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10.3 GNN Methods for Link Prediction |
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203 | (8) |
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10.3.1 Node-Based Methods |
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203 | (3) |
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10.3.2 Subgraph-Based Methods |
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206 | (3) |
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10.3.3 Comparing Node-Based Methods and Subgraph-Based Methods |
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209 | (2) |
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10.4 Theory for Link Prediction |
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211 | (9) |
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10.4.1 y-Decaying Heuristic Theory |
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211 | (6) |
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217 | (3) |
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220 | (5) |
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10.5.1 Accelerating Subgraph-Based Methods |
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220 | (1) |
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10.5.2 Designing More Powerful Labeling Tricks |
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221 | (1) |
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10.5.3 Understanding When to Use One-Hot Features |
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222 | (3) |
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11 Graph Neural Networks: Graph Generation |
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225 | (26) |
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225 | (1) |
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11.2 Classic Graph Generative Models |
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226 | (3) |
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226 | (2) |
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11.2.2 Stochastic Block Model |
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228 | (1) |
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11.3 Deep Graph Generative Models |
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229 | (21) |
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11.3.1 Representing Graphs |
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230 | (1) |
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11.3.2 Variational Auto-Encoder Methods |
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230 | (6) |
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11.3.3 Deep Autoregressive Methods |
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236 | (8) |
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11.3.4 Generative Adversarial Methods |
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244 | (6) |
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250 | (1) |
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12 Graph Neural Networks: Graph Transformation |
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251 | (26) |
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12.1 Problem Formulation of Graph Transformation |
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252 | (1) |
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12.2 Node-level Transformation |
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253 | (3) |
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12.2.1 Definition of Node-level Transformation |
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253 | (1) |
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12.2.2 Interaction Networks |
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253 | (1) |
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12.2.3 Spatio-Temporal Convolution Recurrent Neural Networks |
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254 | (2) |
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12.3 Edge-level Transformation |
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256 | (5) |
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12.3.1 Definition of Edge-level Transformation |
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256 | (1) |
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12.3.2 Graph Transformation Generative Adversarial Networks |
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257 | (2) |
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12.3.3 Multi-scale Graph Transformation Networks |
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259 | (1) |
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12.3.4 Graph Transformation Policy Networks |
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260 | (1) |
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12.4 Node-Edge Co-Transformation |
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261 | (10) |
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12.4.1 Definition of Node-Edge Co-Transformation |
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261 | (5) |
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12.4.2 Editing-based Node-Edge Co-Transformation |
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266 | (5) |
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12.5 Other Graph-based Transformations |
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271 | (4) |
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12.5.1 Sequence-to-Graph Transformation |
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271 | (1) |
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12.5.2 Graph-to-Sequence Transformation |
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272 | (1) |
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12.5.3 Context-to-Graph Transformation |
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273 | (2) |
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275 | (2) |
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13 Graph Neural Networks: Graph Matching |
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277 | (20) |
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278 | (1) |
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13.2 Graph Matching Learning |
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279 | (9) |
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13.2.1 Problem Definition |
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280 | (2) |
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13.2.2 Deep Learning based Models |
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282 | (2) |
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13.2.3 Graph Neural Network based Models |
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284 | (4) |
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13.3 Graph Similarity Learning |
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288 | (7) |
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13.3.1 Problem Definition |
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288 | (2) |
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13.3.2 Graph-Graph Regression Tasks |
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290 | (3) |
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13.3.3 Graph-Graph Classification Tasks |
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293 | (2) |
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295 | (2) |
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14 Graph Neural Networks: Graph Structure Learning |
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297 | (26) |
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297 | (2) |
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14.2 Traditional Graph Structure Learning |
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299 | (4) |
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14.2.1 Unsupervised Graph Structure Learning |
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299 | (2) |
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14.2.2 Supervised Graph Structure Learning |
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301 | (2) |
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14.3 Graph Structure Learning for Graph Neural Networks |
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303 | (16) |
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14.3.1 Joint Graph Structure and Representation Learning |
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304 | (13) |
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14.3.2 Connections to Other Problems |
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317 | (2) |
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319 | (1) |
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14.4.1 Robust Graph Structure Learning |
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319 | (1) |
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14.4.2 Scalable Graph Structure Learning |
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320 | (1) |
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14.4.3 Graph Structure Learning for Heterogeneous Graphs |
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320 | (1) |
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320 | (3) |
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15 Dynamic Graph Neural Networks |
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323 | (28) |
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323 | (2) |
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15.2 Background and Notation |
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325 | (6) |
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15.2.1 Graph Neural Networks |
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325 | (2) |
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327 | (3) |
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15.2.3 Encoder-Decoder Framework and Model Training |
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330 | (1) |
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15.3 Categories of Dynamic Graphs |
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331 | (4) |
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15.3.1 Discrete vs. Continues |
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331 | (2) |
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15.3.2 Types of Evolution |
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333 | (1) |
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15.3.3 Prediction Problems, Interpolation, and Extrapolation |
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334 | (1) |
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15.4 Modeling Dynamic Graphs with Graph Neural Networks |
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335 | (8) |
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15.4.1 Conversion to Static Graphs |
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335 | (2) |
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15.4.2 Graph Neural Networks for DTDGs |
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337 | (3) |
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15.4.3 Graph Neural Networks for CTDGs |
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340 | (3) |
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343 | (5) |
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15.5.1 Skeleton-based Human Activity Recognition |
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343 | (2) |
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15.5.2 Traffic Forecasting |
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345 | (1) |
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15.5.3 Temporal Knowledge Graph Completion |
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346 | (2) |
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348 | (3) |
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16 Heterogeneous Graph Neural Networks |
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351 | (20) |
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16.1 Introduction to HGNNs |
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351 | (5) |
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16.1.1 Basic Concepts of Heterogeneous Graphs |
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353 | (1) |
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16.1.2 Challenges of HG Embedding |
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354 | (1) |
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16.1.3 Brief Overview of Current Development |
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355 | (1) |
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356 | (4) |
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16.2.1 Decomposition-based Methods |
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357 | (1) |
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16.2.2 Random Walk-based Methods |
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358 | (2) |
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360 | (6) |
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16.3.1 Message Passing-based Methods (HGNNs) |
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360 | (3) |
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16.3.2 Encoder-decoder-based Methods |
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363 | (1) |
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16.3.3 Adversarial-based Methods |
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364 | (2) |
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366 | (1) |
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367 | (4) |
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16.5.1 Structures and Properties Preservation |
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367 | (1) |
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16.5.2 Deeper Exploration |
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367 | (1) |
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368 | (1) |
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369 | (2) |
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17 Graph Neural Networks: AutoML |
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371 | (20) |
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372 | (4) |
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17.1.1 Notations of AutoGNN |
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373 | (2) |
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17.1.2 Problem Definition of AutoGNN |
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375 | (1) |
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17.1.3 Challenges in AutoGNN |
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375 | (1) |
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376 | (6) |
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17.2.1 Architecture Search Space |
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377 | (3) |
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17.2.2 Training Hyperparameter Search Space |
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380 | (1) |
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17.2.3 Efficient Search Space |
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381 | (1) |
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382 | (5) |
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382 | (1) |
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17.3.2 Evolutionary Search |
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382 | (1) |
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17.3.3 Reinforcement Learning Based Search |
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383 | (2) |
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17.3.4 Differentiable Search |
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385 | (1) |
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17.3.5 Efficient Performance Estimation |
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386 | (1) |
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387 | (4) |
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18 Graph Neural Networks: Self-supervised Learning |
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391 | (32) |
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392 | (1) |
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18.2 Self-supervised Learning |
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393 | (2) |
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18.3 Applying SSL to Graph Neural Networks: Categorizing Training Strategies, Loss Functions and Pretext Tasks |
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395 | (8) |
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18.3.1 Training Strategies |
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396 | (3) |
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399 | (3) |
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402 | (1) |
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18.4 Node-level SSL Pretext Tasks |
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403 | (5) |
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18.4.1 Structure-based Pretext Tasks |
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403 | (1) |
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18.4.2 Feature-based Pretext Tasks |
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404 | (2) |
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18.4.3 Hybrid Pretext Tasks |
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406 | (2) |
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18.5 Graph-level SSL Pretext Tasks |
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408 | (9) |
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18.5.1 Structure-based Pretext Tasks |
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408 | (5) |
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18.5.2 Feature-based Pretext Tasks |
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413 | (1) |
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18.5.3 Hybrid Pretext Tasks |
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414 | (3) |
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18.6 Node-graph-level SSL Pretext Tasks |
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417 | (1) |
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418 | (1) |
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419 | (4) |
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Part IV Broad and Emerging Applications with Graph Neural Networks |
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19 Graph Neural Networks in Modern Recommender Systems |
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423 | (24) |
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19.1 Graph Neural Networks for Recommender System in Practice |
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423 | (8) |
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423 | (5) |
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19.1.2 Classic Approaches to Predict User-Item Preference |
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428 | (1) |
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19.1.3 Item Recommendation in user-item Recommender Systems: a Bipartite Graph Perspective |
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429 | (2) |
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19.2 Case Study 1: Dynamic Graph Neural Networks Learning |
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431 | (7) |
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19.2.1 Dynamic Sequential Graph |
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431 | (1) |
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19.2.2 DSGL: Dynamic Sequential Graph Learning |
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432 | (3) |
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435 | (1) |
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19.2.4 Experiments and Discussions |
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436 | (2) |
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19.3 Case Study 2: Device-Cloud Collaborative Learning for Graph Neural Networks |
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438 | (6) |
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19.3.1 The proposed framework |
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438 | (4) |
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19.3.2 Experiments and Discussions |
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442 | (2) |
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444 | (3) |
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20 Graph Neural Networks in Computer Vision |
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447 | (16) |
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448 | (1) |
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20.2 Representing Vision as Graphs |
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448 | (3) |
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20.2.1 Visual Node representation |
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448 | (2) |
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20.2.2 Visual Edge representation |
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450 | (1) |
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451 | (3) |
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451 | (2) |
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20.3.2 Image Classification |
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453 | (1) |
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454 | (3) |
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20.4.1 Video Action Recognition |
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454 | (2) |
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20.4.2 Temporal Action Localization |
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456 | (1) |
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20.5 Other Related Work: Cross-media |
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457 | (3) |
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457 | (1) |
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20.5.2 Visual Question Answering |
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458 | (1) |
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20.5.3 Cross-Media Retrieval |
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459 | (1) |
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20.6 Frontiers for Graph Neural Networks on Computer Vision |
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460 | (2) |
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20.6.1 Advanced Graph Neural Networks for Computer Vision |
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460 | (1) |
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20.6.2 Broader Area of Graph Neural Networks on Computer Vision |
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461 | (1) |
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462 | (1) |
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21 Graph Neural Networks in Natural Language Processing |
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463 | (20) |
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463 | (3) |
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21.2 Modeling Text as Graphs |
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466 | (4) |
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21.2.1 Graph Representations in Natural Language Processing |
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|
466 | (2) |
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21.2.2 Tackling Natural Language Processing Tasks from a Graph Perspective |
|
|
468 | (2) |
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21.3 Case Study 1: Graph-based Text Clustering and Matching |
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|
470 | (5) |
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21.3.1 Graph-based Clustering for Hot Events Discovery and Organization |
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|
470 | (3) |
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21.3.2 Long Document Matching with Graph Decomposition and Convolution |
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|
473 | (2) |
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21.4 Case Study 2: Graph-based Multi-Hop Reading Comprehension |
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|
475 | (4) |
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|
479 | (1) |
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|
480 | (3) |
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22 Graph Neural Networks in Program Analysis |
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|
483 | (16) |
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|
|
483 | (1) |
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22.2 Machine Learning in Program Analysis |
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|
484 | (2) |
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22.3 A Graph Represention of Programs |
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|
486 | (3) |
|
22.4 Graph Neural Networks for Program Graphs |
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|
489 | (2) |
|
22.5 Case Study 1: Detecting Variable Misuse Bugs |
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|
491 | (2) |
|
22.6 Case Study 2: Predicting Types in Dynamically Typed Languages |
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|
493 | (2) |
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|
495 | (4) |
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23 Graph Neural Networks in Software Mining |
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|
499 | (18) |
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|
499 | (1) |
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23.2 Modeling Software as a Graph |
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|
500 | (3) |
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23.2.1 Macro versus Micro Representations |
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|
501 | (2) |
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23.2.2 Combining the Macro- and Micro-level |
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|
503 | (1) |
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23.3 Relevant Software Mining Tasks |
|
|
503 | (1) |
|
23.4 Example Software Mining Task: Source Code Summarization |
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|
504 | (8) |
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23.4.1 Primer GNN-based Code Summarization |
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|
505 | (5) |
|
23.4.2 Directions for Improvement |
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|
510 | (2) |
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|
512 | (5) |
|
24 GNN-based Biomedical Knowledge Graph Mining in Drug Development |
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|
517 | (24) |
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|
|
|
517 | (1) |
|
24.2 Existing Biomedical Knowledge Graphs |
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|
518 | (5) |
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24.3 Inference on Knowledge Graphs |
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|
523 | (5) |
|
24.3.1 Conventional KG inference techniques |
|
|
523 | (1) |
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24.3.2 GNN-based KG inference techniques |
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|
524 | (4) |
|
24.4 KG-based hypothesis generation in computational drug development |
|
|
528 | (3) |
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24.4.1 A machine learning framework for KG-based drug repurposing |
|
|
529 | (1) |
|
24.4.2 Application of KG-based drug repurposing in COVID-19 |
|
|
530 | (1) |
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|
531 | (10) |
|
24.5.1 KG quality control |
|
|
532 | (1) |
|
24.5.2 Scalable inference |
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|
533 | (1) |
|
24.5.3 Coupling KGs with other biomedical data |
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|
533 | (8) |
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25 Graph Neural Networks in Predicting Protein Function and Interactions |
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|
541 | (16) |
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25.1 From Protein Interactions to Function: An Introduction |
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|
541 | (6) |
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25.1.1 Enter Stage Left: Protein-Protein Interaction Networks |
|
|
542 | (1) |
|
25.1.2 Problem Formulation(s), Assumptions, and Noise: A Historical Perspective |
|
|
543 | (1) |
|
25.1.3 Shallow Machine Learning Models over the Years |
|
|
543 | (1) |
|
25.1.4 Enter Stage Right: Graph Neural Networks |
|
|
544 | (3) |
|
25.2 Highlighted Case Studies |
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|
547 | (8) |
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25.2.1 Case Study 1: Prediction of Protein-Protein and Protein-Drug Interactions: The Link Prediction Problem |
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|
547 | (2) |
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25.2.2 Case Study 2: Prediction of Protein Function and Functionally-important Residues |
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|
549 | (4) |
|
25.2.3 Case Study 3: From Representation Learning to Multirelational Link Prediction in Biological Networks with Graph Autoencoders |
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|
553 | (2) |
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|
555 | (2) |
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26 Graph Neural Networks in Anomaly Detection |
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|
557 | (22) |
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|
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|
557 | (4) |
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|
561 | (3) |
|
26.2.1 Data-specific issues |
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|
561 | (2) |
|
26.2.2 Task-specific Issues |
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|
563 | (1) |
|
26.2.3 Model-specific Issues |
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|
563 | (1) |
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|
564 | (4) |
|
26.3.1 Graph Construction and Transformation |
|
|
564 | (1) |
|
26.3.2 Graph Representation Learning |
|
|
565 | (2) |
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|
567 | (1) |
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|
568 | (1) |
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|
568 | (9) |
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26.5.1 Case Study 1: Graph Embeddings for Malicious Accounts Detection |
|
|
569 | (1) |
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26.5.2 Case Study 2: Hierarchical Attention Mechanism based Cash-out User Detection |
|
|
570 | (2) |
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26.5.3 Case Study 3: Attentional Heterogeneous Graph Neural Networks for Malicious Program Detection |
|
|
572 | (1) |
|
26.5.4 Case Study 4: Graph Matching Framework to Learn the Program Representation and Similarity Metric via Graph Neural Networks for Unknown Malicious Program Detection |
|
|
573 | (2) |
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26.5.5 Case Study 5: Anomaly Detection in Dynamic Graph Using Attention-based Temporal GCN |
|
|
575 | (1) |
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26.5.6 Case Study 6: GCN-based Anti-Spam for Spam Review Detection |
|
|
576 | (1) |
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|
577 | (2) |
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27 Graph Neural Networks in Urban Intelligence |
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|
579 | (16) |
|
|
|
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27.1 Graph Neural Networks for Urban Intelligence |
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|
580 | (15) |
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|
580 | (1) |
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27.1.2 Application scenarios in urban intelligence |
|
|
581 | (3) |
|
27.1.3 Representing urban systems as graphs |
|
|
584 | (2) |
|
27.1.4 Case Study 1: Graph Neural Networksin urban configuration and transportation |
|
|
586 | (3) |
|
27.1.5 Case Study 2: Graph Neural Networks in urban anomaly and event detection |
|
|
589 | (1) |
|
27.1.6 Case Study 3: Graph Neural Networks in urban human behavior inference |
|
|
590 | (2) |
|
|
592 | (3) |
References |
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595 | |