Introduction to Graph Neural Networks
Chapter 1: Foundations of Graph-Based Learning
What is Graph Data?
Limitations of Standard Neural Networks on Graphs
Common Graph Machine Learning Tasks
Representing Graphs: Adjacency and Feature Matrices
Graph Properties and Measurements
Introduction to the NetworkX Library
Hands-on: Loading and Inspecting a Graph Dataset
Chapter 2: The Message Passing Mechanism
The Neighborhood Aggregation Idea
A General GNN Layer: Aggregate and Update
Common Aggregation Functions
Update Functions and Non-Linearities
Permutation Invariance and Equivariance
Stacking Layers to Form a Deep GNN
Practice: A Simple GNN Layer with NumPy
Chapter 3: Foundational GNN Architectures
Graph Convolutional Networks (GCN)
A Spatial Interpretation of Graph Convolutions
GraphSAGE: Sampling and Aggregating Neighborhoods
Inductive Learning with GraphSAGE
Graph Attention Networks (GAT)
The Attention Mechanism in GATs
Comparing GCN, GraphSAGE, and GAT
Hands-on: Implementing a GCN from Scratch
Chapter 4: Training GNN Models
Setting up a GNN for Node Classification
Loss Functions for Graph Tasks
The Training Loop for GNNs
Data Splitting in Graphs: Transductive vs. Inductive
Evaluation Metrics for Node Classification
Overfitting and Regularization in GNNs
Practice: Training and Evaluating your GCN
Chapter 5: GNN Implementation with PyTorch Geometric
Introduction to PyTorch Geometric (PyG)
The PyG Data Object
Working with PyG Datasets
Building Models with PyG GNN Layers
Mini-Batching for Large Graphs
A Complete Training Script in PyG
Hands-on: Node Classification on the Cora Dataset with PyG
Working with PyG Datasets
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- PyTorch Geometric Documentation, PyTorch Geometric Team, 2023 - The official documentation for PyTorch Geometric, providing detailed API references and usage examples for datasets, including built-in datasets and custom dataset creation.
- TUDataset Collection, Christopher Morris, Nils M. Kriege, Franka Bause, Kristian Kersting, Petra Mutzel, Marion Neumann, 2023 - An authoritative resource for a broad collection of benchmark graph datasets, frequently used for graph classification tasks, including the ENZYMES dataset.
- Semi-Supervised Classification with Graph Convolutional Networks, Thomas N. Kipf and Max Welling, 2017 International Conference on Learning Representations (ICLR) DOI: 10.48550/arXiv.1609.02907 - Presents Graph Convolutional Networks and established the common train/validation/test splits for citation network datasets like Cora, which are foundational for node classification benchmarks.