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Register a new userWeisfeiler-Lehman Embedding for Molecular Graph Neural Networks
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A graph neural network (GNN) is a good choice for predicting the chemical properties of molecules. Compared with other deep networks, however, the current performance of a GNN is limited owing to the curse of depth. Inspired by long-established feature engineering in the field of chemistry, we expanded an atom representation using Weisfeiler-Lehman (WL) embedding, which is designed to capture local atomic patterns dominating the chemical properties of a molecule. In terms of representability, we show WL embedding can replace the first two layers of ReLU GNN -- a normal embedding and a hidden GNN layer -- with a smaller weight norm. We then demonstrate that WL embedding consistently improves the empirical performance over multiple GNN architectures and several molecular graph datasets.
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Graph Neural Networks (GNNs) are limited in their expressive power, struggle with long-range interactions and lack a principled way to model higher-order structures. These problems can be attributed to the strong coupling between the computational graph and the input graph structure. The recently proposed Message Passing Simplicial Networks naturally decouple these elements by performing message passing on the clique complex of the graph. Nevertheless, these models are severely constrained by the rigid combinatorial structure of Simplicial Complexes (SCs). In this work, we extend recent theoretical results on SCs to regular Cell Complexes, topological objects that flexibly subsume SCs and graphs. We show that this generalisation provides a powerful set of graph ``lifting transformations, each leading to a unique hierarchical message passing procedure. The resulting methods, which we collectively call CW Networks (CWNs), are strictly more powerful than the WL test and, in certain cases, not less powerful than the 3-WL test. In particular, we demonstrate the effectiveness of one such scheme, based on rings, when applied to molecular graph problems. The proposed architecture benefits from provably larger expressivity than commonly used GNNs, principled modelling of higher-order signals and from compressing the distances between nodes. We demonstrate that our model achieves state-of-the-art results on a variety of molecular datasets.
The pairwise interaction paradigm of graph machine learning has predominantly governed the modelling of relational systems. However, graphs alone cannot capture the multi-level interactions present in many complex systems and the expressive power of such schemes was proven to be limited. To overcome these limitations, we propose Message Passing Simplicial Networks (MPSNs), a class of models that perform message passing on simplicial complexes (SCs). To theoretically analyse the expressivity of our model we introduce a Simplicial Weisfeiler-Lehman (SWL) colouring procedure for distinguishing non-isomorphic SCs. We relate the power of SWL to the problem of distinguishing non-isomorphic graphs and show that SWL and MPSNs are strictly more powerful than the WL test and not less powerful than the 3-WL test. We deepen the analysis by comparing our model with traditional graph neural networks (GNNs) with ReLU activations in terms of the number of linear regions of the functions they can represent. We empirically support our theoretical claims by showing that MPSNs can distinguish challenging strongly regular graphs for which GNNs fail and, when equipped with orientation equivariant layers, they can improve classification accuracy in oriented SCs compared to a GNN baseline.
The graph Laplacian regularization term is usually used in semi-supervised representation learning to provide graph structure information for a model $f(X)$. However, with the recent popularity of graph neural networks (GNNs), directly encoding graph structure $A$ into a model, i.e., $f(A, X)$, has become the more common approach. While we show that graph Laplacian regularization brings little-to-no benefit to existing GNNs, and propose a simple but non-trivial variant of graph Laplacian regularization, called Propagation-regularization (P-reg), to boost the performance of existing GNN models. We provide formal analyses to show that P-reg not only infuses extra information (that is not captured by the traditional graph Laplacian regularization) into GNNs, but also has the capacity equivalent to an infinite-depth graph convolutional network. We demonstrate that P-reg can effectively boost the performance of existing GNN models on both node-level and graph-level tasks across many different datasets.
Data augmentation has been widely used to improve generalizability of machine learning models. However, comparatively little work studies data augmentation for graphs. This is largely due to the complex, non-Euclidean structure of graphs, which limits possible manipulation operations. Augmentation operations commonly used in vision and language have no analogs for graphs. Our work studies graph data augmentation for graph neural networks (GNNs) in the context of improving semi-supervised node-classification. We discuss practical and theoretical motivations, considerations and strategies for graph data augmentation. Our work shows that neural edge predictors can effectively encode class-homophilic structure to promote intra-class edges and demote inter-class edges in given graph structure, and our main contribution introduces the GAug graph data augmentation framework, which leverages these insights to improve performance in GNN-based node classification via edge prediction. Extensive experiments on multiple benchmarks show that augmentation via GAug improves performance across GNN architectures and datasets.
Graph representation learning has achieved great success in many areas, including e-commerce, chemistry, biology, etc. However, the fundamental problem of choosing the appropriate dimension of node embedding for a given graph still remains unsolved. The commonly used strategies for Node Embedding Dimension Selection (NEDS) based on grid search or empirical knowledge suffer from heavy computation and poor model performance. In this paper, we revisit NEDS from the perspective of minimum entropy principle. Subsequently, we propose a novel Minimum Graph Entropy (MinGE) algorithm for NEDS with graph data. To be specific, MinGE considers both feature entropy and structure entropy on graphs, which are carefully designed according to the characteristics of the rich information in them. The feature entropy, which assumes the embeddings of adjacent nodes to be more similar, connects node features and link topology on graphs. The structure entropy takes the normalized degree as basic unit to further measure the higher-order structure of graphs. Based on them, we design MinGE to directly calculate the ideal node embedding dimension for any graph. Finally, comprehensive experiments with popular Graph Neural Networks (GNNs) on benchmark datasets demonstrate the effectiveness and generalizability of our proposed MinGE.
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