Graph neural networks (GNNs) are composed of layers consisting of graph convolutions and pointwise nonlinearities. Due to their invariance and stability properties, GNNs are provably successful at learning representations from data supported on moderate-scale graphs. However, they are difficult to learn on large-scale graphs. In this paper, we study the problem of training GNNs on graphs of moderate size and transferring them to large-scale graphs. We use graph limits called graphons to define limit objects for graph filters and GNNs -- graphon filters and graphon neural networks (WNNs) -- which we interpret as generative models for graph filters and GNNs. We then show that graphon filters and WNNs can be approximated by graph filters and GNNs sampled from them on weighted and stochastic graphs. Because the error of these approximations can be upper bounded, by a triangle inequality argument we can further bound the error of transferring a graph filter or a GNN across graphs. Our results show that (i) the transference error decreases with the graph size, and (ii) that graph filters have a transferability-discriminability tradeoff that in GNNs is alleviated by the scattering behavior of the nonlinearity. These findings are demonstrated empirically in a movie recommendation problem and in a decentralized control task.
Message passing graph neural networks (GNNs) are known to have their expressiveness upper-bounded by 1-dimensional Weisfeiler-Lehman (1-WL) algorithm. To achieve more powerful GNNs, existing attempts either require ad hoc features, or involve operations that incur high time and space complexities. In this work, we propose a general and provably powerful GNN framework that preserves the scalability of message passing scheme. In particular, we first propose to empower 1-WL for graph isomorphism test by considering edges among neighbors, giving rise to NC-1-WL. The expressiveness of NC-1-WL is shown to be strictly above 1-WL but below 3-WL theoretically. Further, we propose the NC-GNN framework as a differentiable neural version of NC-1-WL. Our simple implementation of NC-GNN is provably as powerful as NC-1-WL. Experiments demonstrate that our NC-GNN achieves remarkable performance on various benchmarks.
Causality can be described in terms of a structural causal model (SCM) that carries information on the variables of interest and their mechanistic relations. For most processes of interest the underlying SCM will only be partially observable, thus causal inference tries to leverage any exposed information. Graph neural networks (GNN) as universal approximators on structured input pose a viable candidate for causal learning, suggesting a tighter integration with SCM. To this effect we present a theoretical analysis from first principles that establishes a novel connection between GNN and SCM while providing an extended view on general neural-causal models. We then establish a new model class for GNN-based causal inference that is necessary and sufficient for causal effect identification. Our empirical illustration on simulations and standard benchmarks validate our theoretical proofs.
Residual networks (ResNets) have displayed impressive results in pattern recognition and, recently, have garnered considerable theoretical interest due to a perceived link with neural ordinary differential equations (neural ODEs). This link relies on the convergence of network weights to a smooth function as the number of layers increases. We investigate the properties of weights trained by stochastic gradient descent and their scaling with network depth through detailed numerical experiments. We observe the existence of scaling regimes markedly different from those assumed in neural ODE literature. Depending on certain features of the network architecture, such as the smoothness of the activation function, one may obtain an alternative ODE limit, a stochastic differential equation or neither of these. These findings cast doubts on the validity of the neural ODE model as an adequate asymptotic description of deep ResNets and point to an alternative class of differential equations as a better description of the deep network limit.
Graph Neural Networks (GNNs) have proven to be useful for many different practical applications. However, many existing GNN models have implicitly assumed homophily among the nodes connected in the graph, and therefore have largely overlooked the important setting of heterophily, where most connected nodes are from different classes. In this work, we propose a novel framework called CPGNN that generalizes GNNs for graphs with either homophily or heterophily. The proposed framework incorporates an interpretable compatibility matrix for modeling the heterophily or homophily level in the graph, which can be learned in an end-to-end fashion, enabling it to go beyond the assumption of strong homophily. Theoretically, we show that replacing the compatibility matrix in our framework with the identity (which represents pure homophily) reduces to GCN. Our extensive experiments demonstrate the effectiveness of our approach in more realistic and challenging experimental settings with significantly less training data compared to previous works: CPGNN variants achieve state-of-the-art results in heterophily settings with or without contextual node features, while maintaining comparable performance in homophily settings.
In order to overcome the expressive limitations of graph neural networks (GNNs), we propose the first method that exploits vector flows over graphs to develop globally consistent directional and asymmetric aggregation functions. We show that our directional graph networks (DGNs) generalize convolutional neural networks (CNNs) when applied on a grid. Whereas recent theoretical works focus on understanding local neighbourhoods, local structures and local isomorphism with no global information flow, our novel theoretical framework allows directional convolutional kernels in any graph. First, by defining a vector field in the graph, we develop a method of applying directional derivatives and smoothing by projecting node-specific messages into the field. Then we propose the use of the Laplacian eigenvectors as such vector field, and we show that the method generalizes CNNs on an n-dimensional grid, and is provably more discriminative than standard GNNs regarding the Weisfeiler-Lehman 1-WL test. Finally, we bring the power of CNN data augmentation to graphs by providing a means of doing reflection, rotation and distortion on the underlying directional field. We evaluate our method on different standard benchmarks and see a relative error reduction of 8\% on the CIFAR10 graph dataset and 11% to 32% on the molecular ZINC dataset. An important outcome of this work is that it enables to translate any physical or biological problems with intrinsic directional axes into a graph network formalism with an embedded directional field.
Graph Neural Networks (GNN) is an emerging field for learning on non-Euclidean data. Recently, there has been increased interest in designing GNN that scales to large graphs. Most existing methods use "graph sampling" or "layer-wise sampling" techniques to reduce training time. However, these methods still suffer from degrading performance and scalability problems when applying to graphs with billions of edges. This paper presents GBP, a scalable GNN that utilizes a localized bidirectional propagation process from both the feature vectors and the training/testing nodes. Theoretical analysis shows that GBP is the first method that achieves sub-linear time complexity for both the precomputation and the training phases. An extensive empirical study demonstrates that GBP achieves state-of-the-art performance with significantly less training/testing time. Most notably, GBP can deliver superior performance on a graph with over 60 million nodes and 1.8 billion edges in less than half an hour on a single machine.
Graph Neural Networks (GNNs) are information processing architectures for signals supported on graphs. They are presented here as generalizations of convolutional neural networks (CNNs) in which individual layers contain banks of graph convolutional filters instead of banks of classical convolutional filters. Otherwise, GNNs operate as CNNs. Filters are composed with pointwise nonlinearities and stacked in layers. It is shown that GNN architectures exhibit equivariance to permutation and stability to graph deformations. These properties provide a measure of explanation respecting the good performance of GNNs that can be observed empirically. It is also shown that if graphs converge to a limit object, a graphon, GNNs converge to a corresponding limit object, a graphon neural network. This convergence justifies the transferability of GNNs across networks with different number of nodes.
Deep learning methods for graphs achieve remarkable performance on many node-level and graph-level prediction tasks. However, despite the proliferation of the methods and their success, prevailing Graph Neural Networks (GNNs) neglect subgraphs, rendering subgraph prediction tasks challenging to tackle in many impactful applications. Further, subgraph prediction tasks present several unique challenges, because subgraphs can have non-trivial internal topology, but also carry a notion of position and external connectivity information relative to the underlying graph in which they exist. Here, we introduce SUB-GNN, a subgraph neural network to learn disentangled subgraph representations. In particular, we propose a novel subgraph routing mechanism that propagates neural messages between the subgraph's components and randomly sampled anchor patches from the underlying graph, yielding highly accurate subgraph representations. SUB-GNN specifies three channels, each designed to capture a distinct aspect of subgraph structure, and we provide empirical evidence that the channels encode their intended properties. We design a series of new synthetic and real-world subgraph datasets. Empirical results for subgraph classification on eight datasets show that SUB-GNN achieves considerable performance gains, outperforming strong baseline methods, including node-level and graph-level GNNs, by 12.4% over the strongest baseline. SUB-GNN performs exceptionally well on challenging biomedical datasets when subgraphs have complex topology and even comprise multiple disconnected components.
Graph convolution networks (GCN) are increasingly popular in many applications, yet remain notoriously hard to train over large graph datasets. They need to compute node representations recursively from their neighbors. Current GCN training algorithms suffer from either high computational costs that grow exponentially with the number of layers, or high memory usage for loading the entire graph and node embeddings. In this paper, we propose a novel efficient layer-wise training framework for GCN (L-GCN), that disentangles feature aggregation and feature transformation during training, hence greatly reducing time and memory complexities. We present theoretical analysis for L-GCN under the graph isomorphism framework, that L-GCN leads to as powerful GCNs as the more costly conventional training algorithm does, under mild conditions. We further propose L^2-GCN, which learns a controller for each layer that can automatically adjust the training epochs per layer in L-GCN. Experiments show that L-GCN is faster than state-of-the-arts by at least an order of magnitude, with a consistent of memory usage not dependent on dataset size, while maintaining comparable prediction performance. With the learned controller, L^2-GCN can further cut the training time in half. Our codes are available at //github.com/Shen-Lab/L2-GCN.
Graph Neural Networks (GNNs) for representation learning of graphs broadly follow a neighborhood aggregation framework, where the representation vector of a node is computed by recursively aggregating and transforming feature vectors of its neighboring nodes. Many GNN variants have been proposed and have achieved state-of-the-art results on both node and graph classification tasks. However, despite GNNs revolutionizing graph representation learning, there is limited understanding of their representational properties and limitations. Here, we present a theoretical framework for analyzing the expressive power of GNNs in capturing different graph structures. Our results characterize the discriminative power of popular GNN variants, such as Graph Convolutional Networks and GraphSAGE, and show that they cannot learn to distinguish certain simple graph structures. We then develop a simple architecture that is provably the most expressive among the class of GNNs and is as powerful as the Weisfeiler-Lehman graph isomorphism test. We empirically validate our theoretical findings on a number of graph classification benchmarks, and demonstrate that our model achieves state-of-the-art performance.