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VQGraph: A New Method to Encode and Learn from Graphs

Introduction

Graphs are complex and diverse data structures that can represent
various kinds of information, such as social networks, molecular
structures, or knowledge bases. However, learning from graphs is not
easy, as it requires models to capture the rich and subtle patterns of the
graph structure. Graph neural networks (GNNs) and multilayer
perceptrons (MLPs) are two popular models for graph learning, but they
have their own drawbacks. GNNs often suffer from two major
challenges: over-smoothing and over-fitting. Over-smoothing occurs
when the node representations become indistinguishable after multiple
layers of message passing, leading to a loss of node-specific
information. Over-fitting happens when the model memorizes the training
data and fails to generalize to unseen graphs, especially when the graph
distribution is diverse or noisy.

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To address these challenges, a team of researchers from the Peking

University, Ant Group, and Stanford University have developed a novel
model called VQGraph. VQGraph stands for Graph Vector-Quantization,
which is a technique that compresses the node representations into
discrete codes that can be efficiently processed by multilayer
perceptrons (MLPs). VQGraph aims to bridge the gap between GNNs
and MLPs and leverage the advantages of both models.

What is VQGraph?

VQGraph is a graph vector-quantization method that aims to bridge the

gap between GNNs and MLPs. It does this by introducing a novel graph
vector-quantization method that can effectively encode the structural
information of graphs into fixed-length vectors.

Key Features of VQGraph

VQGraph has several key features that make it an effective and efficient
model for graph learning. Some of these features are:

● Code compression: VQGraph transforms the node features into

discrete codes that are compact and robust. These codes can
capture the essence of the graph and enable cross-graph transfer
learning.
● Self-supervision: VQGraph trains the codebook and the vector
quantizer with contrastive learning, which is a self-supervised
technique that maximizes the agreement between similar inputs
and minimizes the confusion between dissimilar inputs. VQGraph
applies contrastive learning at both the node level and the graph
level to boost the discriminative power of the codes.
● MLP adaptation: VQGraph uses an MLP as the decoder to predict
the graph-level output from the codes. The MLP is a simple but
expressive model that can learn complex nonlinear functions from
high-dimensional inputs. The MLP can also be easily customized

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to different tasks and domains by changing its structure or

activation functions.
● Graph encoding: VQGraph can effectively encode the structural
information of graphs into fixed-length vectors. It can improve the
performance of GNNs on graph classification tasks by reducing
over-smoothing and over-fitting. It can also improve the
performance of MLPs on graph classification tasks by enhancing
generalization and expressiveness.

Capabilities/Use Case of VQGraph

VQGraph is a versatile model that can be applied to various graph

learning tasks and domains. Here are some examples of how VQGraph
can be used:

● Drug discovery: VQGraph can classify molecules or proteins

based on their properties or functions, which can help in finding
new drugs or understanding how existing drugs work.
● Social network analysis: VQGraph can analyze social networks
based on their structure or dynamics, which can help in identifying
influential nodes, communities, or patterns in the network.
● Knowledge graph completion: VQGraph can complete missing
or noisy information in knowledge graphs based on their semantics
or relations, which can help in enhancing the quality and coverage
of the knowledge graph.

How does VQGraph Work?

VQGraph works by using a variant of VQ-VAE, which is a technique that

compresses the input data into discrete codes that can be efficiently
processed by MLPs. VQGraph first learns a codebook of prototype
vectors that represent different substructures in the graphs. Then, for
each graph, it vectorizes and quantizes its adjacency matrix using the
codebook to obtain a fixed-length vector representation of the graph.

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This allows VQGraph to create a new powerful graph representation

space that is structure-aware and expressive. The codebook size can be
flexibly controlled to fit the graphs of different scales and enrich the
expressiveness of the graph representation space. As shown in Figure
below, VQGraph uses this process to encode the graphs into vectors.

source - https://github.com/YangLing0818/VQGraph

VQGraph also uses a tailored distillation objective to effectively bridge

GNNs and MLPs. The method maximizes the consistency between the
soft token assignments of GNNs and MLPs, which are obtained by
comparing the encoder output and all token embeddings. This enables
the MLP to learn both the local structural knowledge from GNNs and the
global structural context of graph data. This way, VQGraph can improve
the performance of both GNNs and MLPs on graph learning tasks.

Performance Evaluation

Extensive experiments and analyses demonstrate the strong

performance of VQGraph, where it achieves new state-of-the-art
performance on GNN-MLP distillation in both transductive and inductive
settings across seven graph datasets. VQGraph infers faster than GNNs
by 828x and also achieves accuracy improvement over GNNs and
stand-alone MLPs by 3.90% and 28.05% on average, respectively.

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source - https://arxiv.org/pdf/2308.02117.pdf

The model was evaluated on five widely used public benchmark

datasets and two large OGB datasets. VQGraph outperforms all
baselines, including teacher GNN models, across all datasets.
Specifically, VQGraph improves performance by an average of 3.90%
compared to its teacher GNN, highlighting its ability to capture superior
structural information without relying on explicit graph structure input.
Further model analysis of VQGraph is presented in Table above.

Above table shows the node classification results of VQGraph and other
models (including two state-of-the-art GNN-MLP distillation methods:
GLNN and NOSMOG) under the standard setting, where the models are
trained and tested on the same graph. The results show the accuracy of
each model, which means how well they can predict the correct labels of
the nodes. Higher accuracy means better performance.

For further information on the experiments conducted, additional

visualizations and statistical analyses, as well as ablation studies, it is
recommended to read the research paper. This will provide a more
detailed and comprehensive understanding of the subject.

How to access and use this model?

VQGraph is available on GitHub Website. The repository contains

instructions on how to install and use the model locally. To access and
use the model, you can visit the GitHub repository, clone or download
the code, and follow the instructions provided in the repository to install
and use the model on your local machine. It is recommended to contact

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the authors of the VQGraph model for more information on its licensing
and usage.

Future Work

some possible directions for future work, which are:

● Extending to more complex scenarios: The current version of

VQGraph assumes that the graphs are undirected and
unweighted, and that the node features are binary or categorical.
However, in many real-world applications, the graphs can be
directed, weighted, or attributed with continuous or
high-dimensional features. Therefore, a possible future work is to
extend VQGraph to handle these more complex scenarios and test
its performance on more diverse and challenging datasets.
● Exploring other codebook learning methods: The current
version of VQGraph uses a variant of VQ-VAE to learn the
codebook of prototype vectors that represent different
substructures in the graphs. However, there may be other methods
that can learn a better codebook that can capture more
fine-grained or hierarchical information of the graph structure.
Therefore, a possible future work is to explore other codebook
learning methods, such as discrete autoencoders, generative
adversarial networks, or reinforcement learning, and compare their
results with VQGraph.
● Investigating other applications and tasks: The current version
of VQGraph focuses on graph classification tasks, where the goal
is to predict a label for each graph based on its structure and
features. However, there may be other applications and tasks that
can benefit from VQGraph, such as graph generation, graph
matching, graph clustering, or graph embedding. Therefore, a
possible future work is to investigate how VQGraph can be applied

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or adapted to these other applications and tasks and evaluate its

performance and usefulness.

Conclusion

VQGraph is a promising new method for bridging the gap between

GNNs and MLPs by introducing a novel graph vector-quantization
method. The method has been shown to be effective in improving the
performance of both GNNs and MLPs on graph classification tasks and
is available for use by researchers and practitioners alike.
Source
research paper - https://arxiv.org/abs/2308.02117
research document - https://arxiv.org/pdf/2308.02117.pdf
GitHub Repo - https://github.com/YangLing0818/VQGraph

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