GNN 101

GNN 101

姚伟峰

http://www.cnblogs.com/Matrix_Yao/

• GNN 101
  • Why
    • Graph无处不在
    • Graph Intelligence helps
    • It’s the right time now!
  • What
    • 如何建模图
      • Different Types of Graph
    • 如何表示图
    • 如何计算图
    • 不同的图数据集规模
    • 不同的图任务
  • How
    • Workflow
    • 软件栈
    • SW Challenges
      • Graph Sampler
      • Scatter-Gather
      • More
  • Finishing words
  • References

Why

Graph无处不在

Graph Intelligence helps

It’s the right time now!

Gartner预测，graph技术在数据和分析创新中的使用率从2021年的10%，到2025年会增长到80%。我们目前正在经历从early adoption到early mainstream的穿越大峡谷期间，既不太早也不太晚，时间刚刚好。

What

如何建模图

A graph is an ordered pair = (, ) comprising:

• , a set of vertices (or nodes)

• ⊆{(,)|,∈}, a set of edges (or links), which are pairs of nodes

Example:

Different Types of Graph

• Are edges directed?
  
  Directed Graph vs. Undirected Graph

• Are there multiple types of nodes or multiple types of edges?
  
  Homogeneous Graph vs Heterogeneous Graph

如何表示图

不同的表示方式会指向不同的计算模式。

如何计算图

如下图所示，图的计算步骤如下：

• 遍历图中的所有结点，或者采样图中的一些结点。每次选择其中一个结点，称为目标结点(target node);

• 一个-层的GNN至少需要聚合目标结点的L-跳领域的信息。因此，我们需要以围绕目标结点构造一个L-跳的ego network。图中是一个2-跳ego network的例子，其中绿色结点是第1跳，蓝色结点是第2跳；

• 计算并更新ego-network里的每个结点的embedding。embeddings会使用到图的结构信息和结点与边的特征。

那么，这些embedding是如何计算和更新的呢？主要是使用Message Passing的计算方法。Message Passing有一些计算范式如GAS(Gather-ApplyEdge-Scatter), SAGA(Scatter-ApplyEdge-Gather-ApplyVertex)等。我们这里介绍归纳得比较全面的SAGA计算范式。假设需要计算和更新下图中的:

• Scatter
  
  Propagate message from source vertex to edge.

• ApplyEdge
  
  Transform message along each edge.

• Gather
  
  Gather transformed message to the destination vertex.

• ApplyVertex
  
  Transform the gathered output to get updated vertex.

公式如下：

分析一下，会发现，SAGA模式中ApplyEdge和ApplyVertex是传统deep learning中的NN(Neural Network)操作，我们可以复用；而Scatter和Gather是GNN新引入的操作。即，Graph Computing = Graph Ops + NN Ops。

不同的图数据集规模

• One big graph
  
  可能高达数十亿的结点，数百亿的边。

• Many small graphs

不同的图任务

• Node-level prediction
  
  预测图中结点的类别或性质

• Edge-level prediction
  
  预测图中两个结点是否存在边，以及边的类别或性质

• Graph-level prediction
  
  预测整图或子图的类别或性质

How

Workflow

以fraud detection为例：

• Tabformer数据集
  
  

• workflow
  
  

软件栈

• 计算平面

• 数据平面

SW Challenges

Graph Sampler

For many small graphs datasets, full batch training works most time. Full batch training means we can do training on whole graph;

When it comes to one large graph datasets, in many real scenarios, we meet Neighbor Explosion problem;

Neighbor Explosion:

Graph sampler comes to rescue. Only sample a fraction of target nodes, and furthermore, for each target node, we sample a sub-graph of its ego-network for training. This is called mini-batch training.

Graph sampling is triggered for each data loading. And the hops of the sampled graph equals the GNN layer number . Which means graph sampler in data loader is important in GNN training.

Challenge: How to optimize sampler both as standalone and in training pipe?

When graph comes to huge(billions of nodes, tens of billions of edges), we meet new at-scale challenges:

• How to store the huge graph across node? -> graph partition

• How to build a training system w/ not only distributed model computing but also distributed graph store and sampling?

  • How to cut the graph while minimize cross partition connections?

A possible GNN distributed training architecture:

Scatter-Gather

• Fuse adjacent graphs ops

  One common fuse pattern for GCN & GraphSAGE：
  
  

  Challenge:
  
  How to fuse more GNN patterns on different ApplyEdge and ApplyVertex,automatically?

• How to implement fused Aggregate
  
  
  
  Challenge:

  • Different graph data structures lead to different implementations in same logic operations;

  • Different graph characteristics favors different data structures;(like low-degree graphs favor COO, high-degree graphs favor CSR)

  • How to find the applicable zone for each and hide such complexity to data scientists?

More

• Inference challenge

  • GNN inference needs full batch inference, how to make it efficient?

  • Distributed inference for big graph?

  • Vector quantization for node and edge features?

  • GNN distilled to MLP?

• SW-HW co-design challenge

  • How to relief irregular memory access in scatter-gather?

  • Do we need some data flow engine for acceleration?

• …

Finishing words

“There is plenty of room at the top” 对技术人员很重要。但为避免入宝山而空返，我们更需要建立起技术架构，这就像是地图一样，只有按图索骥才能更好地探索和利用好top里的plenty of room。

References

1. Graph + AI: What’s Next? Progress in Democratizing Graph for All

2. Recent Advances in Efficient and Scalable Graph Neural Networks

3. Crossing the Chasm – Technology adoption lifecycle

4. Understanding and Bridging the Gaps in Current GNN Performance Optimizations

5. Automatic Generation of High-Performance Inference Kernels for Graph Neural Networks on Multi-Core Systems

6. Understanding GNN Computational Graph: A Coordinated Computation, IO, And Memory Perspective

7. Graphiler: A Compiler For Graph Neural Networks

8. Scatter-Add in Data Parallel Architectures

9. fuseGNN: Accelerating Graph Convolutional Neural Network Training on GPGPU

10. VQ-GNN: A Universal Framework to Scale up Graph Neural Networks using Vector Quantization

11. NeuGraph: Parallel Deep Neural Network Computation on Large Graphs

12. Completing a member knowledge graph with Graph Neural Networks

13. PinnerFormer: Sequence Modeling for User Representation at Pinterest

14. Gartner and Graph Analytics