Graph neural networks are designed to learn functions on graphs. Typically, the relevant target functions are invariant with respect to actions by permutations. Therefore the design of some graph neural network architectures has been inspired by graph-isomorphism algorithms. The classical Weisfeiler-Lehman algorithm (WL) -- a graph-isomorphism test based on color refinement -- became relevant to the study of graph neural networks. The WL test can be generalized to a hierarchy of higher-order tests, known as $k$-WL. This hierarchy has been used to characterize the expressive power of graph neural networks, and to inspire the design of graph neural network architectures. A few variants of the WL hierarchy appear in the literature. The goal of this short note is pedagogical and practical: We explain the differences between the WL and folklore-WL formulations, with pointers to existing discussions in the literature. We illuminate the differences between the formulations by visualizing an example.
Current GNN architectures use a vertex neighborhood aggregation scheme, which limits their discriminative power to that of the 1-dimensional Weisfeiler-Lehman (WL) graph isomorphism test. Here, we propose a novel graph convolution operator that is based on the 2-dimensional WL test. We formally show that the resulting 2-WL-GNN architecture is more discriminative than existing GNN approaches. This theoretical result is complemented by experimental studies using synthetic and real data. On multiple common graph classification benchmarks, we demonstrate that the proposed model is competitive with…
Preferred Networks, Inc.（Preferred Networks 公司）；The University of Tokyo（东京大学）
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…
Recent work shows that the expressive power of Graph Neural Networks (GNNs) in distinguishing non-isomorphic graphs is exactly the same as that of the Weisfeiler-Lehman (WL) graph test. In particular, they show that the WL test can be simulated by GNNs. However, those simulations involve neural networks for the 'combine' function of size polynomial or even exponential in the number of graph nodes $n$, as well as feature vectors of length linear in $n$. We present an improved simulation of the WL test on GNNs with \emph{exponentially} lower complexity. In particular, the neural network implemen…
Peking University（北京大学）；Purdue University（普渡大学）；Beijing Institute for General Artificial Intelligence（北京通用人工智能研究院）
Link prediction is one important application of graph neural networks (GNNs). Most existing GNNs for link prediction are based on one-dimensional Weisfeiler-Lehman (1-WL) test. 1-WL-GNNs first compute node representations by iteratively passing neighboring node features to the center, and then obtain link representations by aggregating the pairwise node representations. As pointed out by previous works, this two-step procedure results in low discriminating power, as 1-WL-GNNs by nature learn node-level representations instead of link-level. In this paper, we study a completely different approa…
Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所）；University of Chinese Academy of Sciences（中国科学院大学）
The expressive power of message passing GNNs is upper-bounded by Weisfeiler-Lehman (WL) test. To achieve high expressive GNNs beyond WL test, we propose a novel graph isomorphism test method, namely Twin-WL, which simultaneously passes node labels and node identities rather than only passes node label as WL. The identity-passing mechanism encodes complete structure information of rooted subgraph, and thus Twin-WL can offer extra power beyond WL at distinguishing graph structures. Based on Twin-WL, we implement two Twin-GNNs for graph classification via defining readout function over rooted sub…
University of California San Diego（加利福尼亚大学圣地亚哥分校）；Max Planck Institute for Mathematics in the Sciences（马克斯·普朗克数学科学研究所）；The Ohio State University（俄亥俄州立大学）；Halıcıoğlu Data Science Institute（哈利奇奥卢数据科学研究所）
The Weisfeiler-Lehman (WL) test is a classical procedure for graph isomorphism testing. The WL test has also been widely used both for designing graph kernels and for analyzing graph neural networks. In this paper, we propose the Weisfeiler-Lehman (WL) distance, a notion of distance between labeled measure Markov chains (LMMCs), of which labeled graphs are special cases. The WL distance is polynomial time computable and is also compatible with the WL test in the sense that the former is positive if and only if the WL test can distinguish the two involved graphs. The WL distance captures and co…
POSTECH（浦项科技大学）；Center for Geometry and Physics, Institute for Basic Science (IBS)（基础科学研究院几何与物理中心）；Korea Advanced Institute of Science and Technology (KAIST)（韩国科学技术院）
University of Cambridge（剑桥大学）；Imperial College London（伦敦帝国理工学院）；Twitter（推特）；UCLA（加州大学洛杉矶分校）；MPI-MIS（马克斯·普朗克智能系统研究所）；SJTU（上海交通大学）；UNSW（新南威尔士大学）
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 can be severely constrained by the rigid combinatorial structure of Simplicial Complexes (SCs). In this work, we extend recent the…
HWL-HIN: A Hypergraph-Level Hypergraph Isomorphism Network as Powerful as the Hypergraph Weisfeiler-Lehman Test with Application to Higher-Order Network Robustness
University of Cambridge（剑桥大学）；Twitter（推特）；Imperial College London（帝国理工学院）；University of New South Wales（新南威尔士大学）；Max Planck Institute for Mathematics in the Sciences（马克斯·普朗克数学科学研究所）；Shanghai Jiao Tong University（上海交通大学）；University of California, Los Angeles（加州大学洛杉矶分校）
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 no…
Recently, subgraph GNNs have emerged as an important direction for developing expressive graph neural networks (GNNs). While numerous architectures have been proposed, so far there is still a limited understanding of how various design paradigms differ in terms of expressive power, nor is it clear what design principle achieves maximal expressiveness with minimal architectural complexity. To address these fundamental questions, this paper conducts a systematic study of general node-based subgraph GNNs through the lens of Subgraph Weisfeiler-Lehman Tests (SWL). Our central result is to build a …
Center for Machine Learning, Sankt Augustin（机器学习中心，圣奥古斯丁）
The majority of popular graph kernels is based on the concept of Haussler's $\mathcal{R}$-convolution kernel and defines graph similarities in terms of mutual substructures. In this work, we enrich these similarity measures by considering graph filtrations: Using meaningful orders on the set of edges, which allow to construct a sequence of nested graphs, we can consider a graph at multiple granularities. For one thing, this provides access to features on different levels of resolution. Furthermore, rather than to simply compare frequencies of features in graphs, it allows for their comparison …
Attacking Graph Neural Networks with Bit Flips: Weisfeiler and Lehman Go Indifferent
University of Vienna（维也纳大学）；Doctoral School Computer Science, Faculty of Computer Science, University of Vienna（维也纳大学计算机学院计算机科学博士学院）；Christian Doppler Laboratory for Assurance and Transparency in Software Protection, Faculty of Computer Science, University of Vienna（维也纳大学计算机学院克里斯蒂安·多普勒软件保护保障与透明度实验室）；Research Network Data Science, Faculty of Computer Science, University of Vienna（维也纳大学计算机学院数据科学研究网络）
该研究提出首个专门针对图神经网络的Injectivity Bit Flip Attack，通过攻击量化消息传递神经网络的邻域聚合函数削弱其结构区分能力，仅翻转少量比特就能让高表达力的图同构网络输出随机结果，破坏力优于迁移自CNN的位翻转攻击。
In recent years, Graph Neural Network (GNN) has bloomly progressed for its power in processing graph-based data. Most GNNs follow a message passing scheme, and their expressive power is mathematically limited by the discriminative ability of the Weisfeiler-Lehman (WL) test. Following Tinhofer's research on compact graphs, we propose a variation of the message passing scheme, called the Weisfeiler-Lehman-Tinhofer GNN (WLT-GNN), that theoretically breaks through the limitation of the WL test. In addition, we conduct comparative experiments and ablation studies on several well-known datasets. The…
Most state-of-the-art graph kernels only take local graph properties into account, i.e., the kernel is computed with regard to properties of the neighborhood of vertices or other small substructures. On the other hand, kernels that do take global graph propertiesinto account may not scale well to large graph databases. Here we propose to start exploring the space between local and global graph kernels, striking the balance between both worlds. Specifically, we introduce a novel graph kernel based on the $k$-dimensional Weisfeiler-Lehman algorithm. Unfortunately, the $k$-dimensional Weisfeiler-…
Kernels for structured data are commonly obtained by decomposing objects into their parts and adding up the similarities between all pairs of parts measured by a base kernel. Assignment kernels are based on an optimal bijection between the parts and have proven to be an effective alternative to the established convolution kernels. We explore how the base kernel can be learned as part of the classification problem. We build on the theory of valid assignment kernels derived from hierarchies defined on the parts. We show that the weights of this hierarchy can be optimized via multiple kernel lear…
We propose a Graph Neural Network with greater expressive power than commonly used GNNs - not constrained to only differentiate between graphs that Weisfeiler-Lehman test recognizes to be non-isomorphic. We use a graph attention network with expanding attention window that aggregates information from nodes exponentially far away. We also use partially random initial embeddings, allowing differentiation between nodes that would otherwise look the same. This could cause problem with a traditional dropout mechanism, therefore we use a "head dropout", randomly ignoring some attention heads rather …
Current neural architecture search (NAS) strategies focus only on finding a single, good, architecture. They offer little insight into why a specific network is performing well, or how we should modify the architecture if we want further improvements. We propose a Bayesian optimisation (BO) approach for NAS that combines the Weisfeiler-Lehman graph kernel with a Gaussian process surrogate. Our method optimises the architecture in a highly data-efficient manner: it is capable of capturing the topological structures of the architectures and is scalable to large graphs, thus making the high-dimen…
IBM Research（IBM研究院）；EPFL（洛桑联邦理工学院）；ETH（苏黎世联邦理工学院）
The ability of a graph neural network (GNN) to leverage both the graph topology and graph labels is fundamental to building discriminative node and graph embeddings. Building on previous work, we theoretically show that edGNN, our model for directed labeled graphs, is as powerful as the Weisfeiler-Lehman algorithm for graph isomorphism. Our experiments support our theoretical findings, confirming that graph neural networks can be used effectively for inference problems on directed graphs with both node and edge labels. Code available at https://github.com/guillaumejaume/edGNN.
Computer Science and Artificial Intelligence Lab, MIT（麻省理工学院计算机科学与人工智能实验室）；Department of Chemical Engineering, MIT（麻省理工学院化学工程系）
The prediction of organic reaction outcomes is a fundamental problem in computational chemistry. Since a reaction may involve hundreds of atoms, fully exploring the space of possible transformations is intractable. The current solution utilizes reaction templates to limit the space, but it suffers from coverage and efficiency issues. In this paper, we propose a template-free approach to efficiently explore the space of product molecules by first pinpointing the reaction center -- the set of nodes and edges where graph edits occur. Since only a small number of atoms contribute to reaction cente…
ETH Zurich（苏黎世联邦理工学院）；SIB Swiss Institute of Bioinformatics（SIB瑞士生物信息学研究所）
Most graph kernels are an instance of the class of $\mathcal{R}$-Convolution kernels, which measure the similarity of objects by comparing their substructures. Despite their empirical success, most graph kernels use a naive aggregation of the final set of substructures, usually a sum or average, thereby potentially discarding valuable information about the distribution of individual components. Furthermore, only a limited instance of these approaches can be extended to continuously attributed graphs. We propose a novel method that relies on the Wasserstein distance between the node feature vec…
Graph neural networks have been widely used on modeling graph data, achieving impressive results on node classification and link prediction tasks. Yet, obtaining an accurate representation for a graph further requires a pooling function that maps a set of node representations into a compact form. A simple sum or average over all node representations considers all node features equally without consideration of their task relevance, and any structural dependencies among them. Recently proposed hierarchical graph pooling methods, on the other hand, may yield the same representation for two differ…
This work generalizes graph neural networks (GNNs) beyond those based on the Weisfeiler-Lehman (WL) algorithm, graph Laplacians, and diffusions. Our approach, denoted Relational Pooling (RP), draws from the theory of finite partial exchangeability to provide a framework with maximal representation power for graphs. RP can work with existing graph representation models and, somewhat counterintuitively, can make them even more powerful than the original WL isomorphism test. Additionally, RP allows architectures like Recurrent Neural Networks and Convolutional Neural Networks to be used in a theo…
ETH Zurich（苏黎世联邦理工学院）；SIB Swiss Institute of Bioinformatics（瑞士生物信息学研究所）；KU Leuven（鲁汶大学）；Helmholtz Munich（亥姆霍兹慕尼黑中心）；Technical University of Munich（慕尼黑工业大学）
Graph neural networks (GNNs) are a powerful architecture for tackling graph learning tasks, yet have been shown to be oblivious to eminent substructures such as cycles. We present TOGL, a novel layer that incorporates global topological information of a graph using persistent homology. TOGL can be easily integrated into any type of GNN and is strictly more expressive (in terms the Weisfeiler--Lehman graph isomorphism test) than message-passing GNNs. Augmenting GNNs with TOGL leads to improved predictive performance for graph and node classification tasks, both on synthetic data sets, which can…
Tsinghua University（清华大学）；Johns Hopkins University（约翰斯·霍普金斯大学）；Microsoft Research Asia（微软亚洲研究院）
The invariance to permutations of the adjacency matrix, i.e., graph isomorphism, is an overarching requirement for Graph Neural Networks (GNNs). Conventionally, this prerequisite can be satisfied by the invariant operations over node permutations when aggregating messages. However, such an invariant manner may ignore the relationships among neighboring nodes, thereby hindering the expressivity of GNNs. In this work, we devise an efficient permutation-sensitive aggregation mechanism via permutation groups, capturing pairwise correlations between neighboring nodes. We prove that our approach is …
CNRS（法国国家科学研究中心）；GIPSA-lab（GIPSA实验室）；NYU Center for Data Science（纽约大学数据科学中心）；IMB, Université de Bourgogne（勃艮第大学IMB研究所）
We study the approximation power of Graph Neural Networks (GNNs) on latent position random graphs. In the large graph limit, GNNs are known to converge to certain "continuous" models known as c-GNNs, which directly enables a study of their approximation power on random graph models. In the absence of input node features however, just as GNNs are limited by the Weisfeiler-Lehman isomorphism test, c-GNNs will be severely limited on simple random graph models. For instance, they will fail to distinguish the communities of a well-separated Stochastic Block Model (SBM) with constant degree function…
Operational Research Center（运筹学研究中心）；Massachusetts Institute of Technology（麻省理工学院）；Institute for Applied Computational Science（应用计算科学研究所）；Harvard University（哈佛大学）；Harvard School of Engineering and Applied Sciences（哈佛工程与应用科学学院）
Graph neural networks (GNNs) are a powerful tool to learn representations on graphs by iteratively aggregating features from node neighbourhoods. Many variant models have been proposed, but there is limited understanding on both how to compare different architectures and how to construct GNNs systematically. Here, we propose a hierarchy of GNNs based on their aggregation regions. We derive theoretical results about the discriminative power and feature representation capabilities of each class. Then, we show how this framework can be utilized to systematically construct arbitrarily powerful GNN…
CISPA Helmholtz Center for Information Security（CISPA亥姆霍兹信息安全中心）
Today we have a good theoretical understanding of the representational power of Graph Neural Networks (GNNs). For example, their limitations have been characterized in relation to a hierarchy of Weisfeiler-Lehman (WL) isomorphism tests. However, we do not know what is encoded in the learned representations. This is our main question. We answer it using a probing framework to quantify the amount of meaningful information captured in graph representations. Our findings on molecular datasets show the potential of probing for understanding the inductive biases of graph-based models. We compare dif…
Graph Neural Networks (GNNs) are an effective framework for representation learning of graphs. GNNs follow a neighborhood aggregation scheme, where the representation vector of a node is computed by recursively aggregating and transforming representation 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 f…
The message-passing scheme is the core of graph representation learning. While most existing message-passing graph neural networks (MPNNs) are permutation-invariant in graph-level representation learning and permutation-equivariant in node- and edge-level representation learning, their expressive power is commonly limited by the 1-Weisfeiler-Lehman (1-WL) graph isomorphism test. Recently proposed expressive graph neural networks (GNNs) with specially designed complex message-passing mechanisms are not practical. To bridge the gap, we propose a plug-in Equivariant Distance ENcoding (EDEN) for M…
University of Antwerp（安特卫普大学）；Max Planck Institute for Software Sciences（马克斯·普朗克软件科学研究所）
In this paper we cast neural networks defined on graphs as message-passing neural networks (MPNNs) in order to study the distinguishing power of different classes of such models. We are interested in whether certain architectures are able to tell vertices apart based on the feature labels given as input with the graph. We consider two variants of MPNNS: anonymous MPNNs whose message functions depend only on the labels of vertices involved; and degree-aware MPNNs in which message functions can additionally use information regarding the degree of vertices. The former class covers a popular forma…
Identifying similar network structures is key to capture graph isomorphisms and learn representations that exploit structural information encoded in graph data. This work shows that ego-networks can produce a structural encoding scheme for arbitrary graphs with greater expressivity than the Weisfeiler-Lehman (1-WL) test. We introduce IGEL, a preprocessing step to produce features that augment node representations by encoding ego-networks into sparse vectors that enrich Message Passing (MP) Graph Neural Networks (GNNs) beyond 1-WL expressivity. We describe formally the relation between IGEL and…
This paper advocates incorporating a Low-Rank Global Attention (LRGA) module, a computation and memory efficient variant of the dot-product attention (Vaswani et al., 2017), to Graph Neural Networks (GNNs) for improving their generalization power. To theoretically quantify the generalization properties granted by adding the LRGA module to GNNs, we focus on a specific family of expressive GNNs and show that augmenting it with LRGA provides algorithmic alignment to a powerful graph isomorphism test, namely the 2-Folklore Weisfeiler-Lehman (2-FWL) algorithm. In more detail we: (i) consider the re…
We focus on graph classification using a graph neural network (GNN) model that precomputes the node features using a bank of neighborhood aggregation graph operators arranged in parallel. These GNN models have a natural advantage of reduced training and inference time due to the precomputations but are also fundamentally different from popular GNN variants that update node features through a sequential neighborhood aggregation procedure during training. We provide theoretical conditions under which a generic GNN model with parallel neighborhood aggregations (PA-GNNs, in short) are provably as …
The success of kernel methods has initiated the design of novel positive semidefinite functions, in particular for structured data. A leading design paradigm for this is the convolution kernel, which decomposes structured objects into their parts and sums over all pairs of parts. Assignment kernels, in contrast, are obtained from an optimal bijection between parts, which can provide a more valid notion of similarity. In general however, optimal assignments yield indefinite functions, which complicates their use in kernel methods. We characterize a class of base kernels used to compare parts th…
Recently, the Weisfeiler-Lehman (WL) graph isomorphism test was used to measure the expressive power of graph neural networks (GNN). It was shown that the popular message passing GNN cannot distinguish between graphs that are indistinguishable by the 1-WL test (Morris et al. 2018; Xu et al. 2019). Unfortunately, many simple instances of graphs are indistinguishable by the 1-WL test. In search for more expressive graph learning models we build upon the recent k-order invariant and equivariant graph neural networks (Maron et al. 2019a,b) and present two results: First, we show that such k-order …
Applying machine learning to molecules is challenging because of their natural representation as graphs rather than vectors.Several architectures have been recently proposed for deep learning from molecular graphs, but they suffer from informationbottlenecks because they only pass information from a graph node to its direct neighbors. Here, we introduce a more expressiveroute-based multi-attention mechanism that incorporates features from routes between node pairs. We call the resulting methodGraph Informer. A single network layer can therefore attend to nodes several steps away. We show empir…
Arizona State University（亚利桑那州立大学）；HRL Laboratories, LLC（HRL实验室有限责任公司）
Graph data widely exist in many high-impact applications. Inspired by the success of deep learning in grid-structured data, graph neural network models have been proposed to learn powerful node-level or graph-level representation. However, most of the existing graph neural networks suffer from the following limitations: (1) there is limited analysis regarding the graph convolution properties, such as seed-oriented, degree-aware and order-free; (2) the node's degree-specific graph structure is not explicitly expressed in graph convolution for distinguishing structure-aware node neighborhoods; (…
