More Like this

1. Identity-Aware Graph Neural Networks

   You, Jiaxuan; Gomes-Selman, Jonathan; Ying, Rex; Leskovec, Jure. (January 2021, Conference on Artificial Intelligence (AAAI))

   null (Ed.)

   Message passing Graph Neural Networks (GNNs) provide a powerful modeling framework for relational data. However, the expressive power of existing GNNs is upper-bounded by the 1-Weisfeiler-Lehman (1-WL) graph isomorphism test, which means GNNs that are not able to predict node clustering coefficients and shortest path distances, and cannot differentiate between different d regular graphs. Here we develop a class of message passing GNNs, named Identity-aware Graph Neural Networks (ID-GNNs), with greater expressive power than the 1-WL test. ID-GNN offers a minimal but powerful solution to limitations of existing GNNs. ID-GNN extends existing GNN architectures by inductively considering nodes’ identities during message passing. To embed a given node, IDGNN first extracts the ego network centered at the node, then conducts rounds of heterogeneous message passing, where different sets of parameters are applied to the center node than to other surrounding nodes in the ego network. We further propose a simplified but faster version of ID-GNN that injects node identity information as augmented node features. Altogether, both versions of ID GNN represent general extensions of message passing GNNs, where experiments show that transforming existing GNNs to ID-GNNs yields on average 40% accuracy improvement on challenging node, edge, and graph property prediction tasks; 3% accuracy improvement on node and graph classification benchmarks; and 15% ROC AUC improvement on real-world link prediction tasks. Additionally, ID-GNNs demonstrate improved or comparable performance over other task-specific graph networks. 

   more » « less
2. Identity-aware Graph Neural Networks

   You, Jiaxuan; Gomes-Selman, Jonathan; Ying, Rex; Leskovec, Jure (January 2021, Proceedings of the AAAI Conference on Artificial Intelligence)

   null (Ed.)

   Message passing Graph Neural Networks (GNNs) provide a powerful modeling framework for relational data. However, the expressive power of existing GNNs is upper-bounded by the 1-Weisfeiler-Lehman (1-WL) graph isomorphism test, which means GNNs that are not able to predict node clustering coefficients and shortest path distances, and cannot differentiate between different d-regular graphs. Here we develop a class of message passing GNNs, named Identity-aware Graph Neural Networks (ID-GNNs), with greater expressive power than the 1-WL test. ID-GNN offers a minimal but powerful solution to limitations of existing GNNs. ID-GNN extends existing GNN architectures by inductively considering nodes’ identities during message passing. To embed a given node, IDGNN first extracts the ego network centered at the node, then conducts rounds of heterogeneous message passing, where different sets of parameters are applied to the center node than to other surrounding nodes in the ego network. We further propose a simplified but faster version of ID-GNN that injects node identity information as augmented node features. Altogether, both versions of ID-GNN represent general extensions of message passing GNNs, where experiments show that transforming existing GNNs to ID-GNNs yields on average 40% accuracy improvement on challenging node, edge, and graph property prediction tasks; 3% accuracy improvement on node and graph classification benchmarks; and 15% ROC AUC improvement on real-world link prediction tasks. Additionally, ID-GNNs demonstrate improved or comparable performance over other task-specific graph networks. 

   more » « less
3. Motif-Based Graph Representation Learning with Application to Chemical Molecules

   https://doi.org/10.3390/informatics10010008  

   Wang, Yifei; Chen, Shiyang; Chen, Guobin; Shurberg, Ethan; Liu, Hang; Hong, Pengyu (March 2023, Informatics)

   This work considers the task of representation learning on the attributed relational graph (ARG). Both the nodes and edges in an ARG are associated with attributes/features allowing ARGs to encode rich structural information widely observed in real applications. Existing graph neural networks offer limited ability to capture complex interactions within local structural contexts, which hinders them from taking advantage of the expression power of ARGs. We propose motif convolution module (MCM), a new motif-based graph representation learning technique to better utilize local structural information. The ability to handle continuous edge and node features is one of MCM’s advantages over existing motif-based models. MCM builds a motif vocabulary in an unsupervised way and deploys a novel motif convolution operation to extract the local structural context of individual nodes, which is then used to learn higher level node representations via multilayer perceptron and/or message passing in graph neural networks. When compared with other graph learning approaches to classifying synthetic graphs, our approach is substantially better at capturing structural context. We also demonstrate the performance and explainability advantages of our approach by applying it to several molecular benchmarks. 

   more » « less
4. VQ-GNN: A Universal Framework to Scale up Graph Neural Networks using Vector Quantization

   Ding, Mucong; Kong, Kezhi; Li, Jingling; Zhu, Chen; Dickerson, John P; Huang, Furong; Goldstein, Tom (January 2021, Advances in Neural Information Processing Systems 34)

   Most state-of-the-art Graph Neural Networks (GNNs) can be defined as a form of graph convolution which can be realized by message passing between direct neighbors or beyond. To scale such GNNs to large graphs, various neighbor-, layer-, or subgraph-sampling techniques are proposed to alleviate the "neighbor explosion" problem by considering only a small subset of messages passed to the nodes in a mini-batch. However, sampling-based methods are difficult to apply to GNNs that utilize many-hops-away or global context each layer, show unstable performance for different tasks and datasets, and do not speed up model inference. We propose a principled and fundamentally different approach, VQ-GNN, a universal framework to scale up any convolution-based GNNs using Vector Quantization (VQ) without compromising the performance. In contrast to sampling-based techniques, our approach can effectively preserve all the messages passed to a mini-batch of nodes by learning and updating a small number of quantized reference vectors of global node representations, using VQ within each GNN layer. Our framework avoids the "neighbor explosion" problem of GNNs using quantized representations combined with a low-rank version of the graph convolution matrix. We show that such a compact low-rank version of the gigantic convolution matrix is sufficient both theoretically and experimentally. In company with VQ, we design a novel approximated message passing algorithm and a nontrivial back-propagation rule for our framework. Experiments on various types of GNN backbones demonstrate the scalability and competitive performance of our framework on large-graph node classification and link prediction benchmarks. 

   more » « less
5. Graph Compression Networks

   https://doi.org/10.1109/BigData52589.2021.9671652  

   Guo, Ting; Zhu, Xingquan; Wang, Yang; Chen, Fang (December 2021, Proc. of the 2021 IEEE International Conference on Big Data (Big Data))

   Graphs/Networks are common in real-world applications where data have rich content and complex relationships. The increasing popularity also motivates many network learning algorithms, such as community detection, clustering, classification, and embedding learning, etc.. In reality, the large network volumes often hider a direct use of learning algorithms to the graphs. As a result, it is desirable to have the flexibility to condense a network to an arbitrary size, with well-preserved network topology and node content information. In this paper, we propose a graph compression network (GEN) to achieve network compression and embedding at the same time. Our theme is to leverage the network topology to find node mappings, such that densely connected nodes, including their node content, are compressed as a new node, with a latent vector (i.e. embedding) being learned to represent the compressed node. In addition to compression learning, we also develop a novel encoding-decoding framework, using feature diffusion process, to "decompress" the condensed network. Different from traditional graph convolution which uses direct-neighbor message passing, our decompression advocates high-order message passing within compressed nodes to learning feature representation for all nodes in the network. A unique strength of GEN is that it leverages the graph neural network principle to learn mapping automatically, so one can compress a network to an arbitrary size, and also decompress it to the original node space with minimum information loss. Experiments and comparisons confirm that GEN can automatically find clusters and communities, and compress them as new nodes. Results also show that GEN achieves improved performance for numerous tasks, including graph classification and node clustering. 

   more » « less