Weisfeiler Leman for Euclidean Equivariant Machine Learning
Faculty of Mathematics, Technion - Israel Institute of Technology（以色列理工学院数学学院）；Faculty of Computer Science, Technion - Israel Institute of Technology（以色列理工学院计算机科学学院）
The $k$-Weisfeiler-Leman ($k$-WL) graph isomorphism test hierarchy is a common method for assessing the expressive power of graph neural networks (GNNs). Recently, GNNs whose expressive power is equivalent to the $2$-WL test were proven to be universal on weighted graphs which encode $3\mathrm{D}$ point cloud data, yet this result is limited to invariant continuous functions on point clouds. In this paper, we extend this result in three ways: Firstly, we show that PPGN can simulate $2$-WL uniformly on all point clouds with low complexity. Secondly, we show that $2$-WL tests can be extended to point clouds which include both positions and velocities, a scenario often encountered in applications. Finally, we provide a general framework for proving equivariant universality and leverage it to prove that a simple modification of this invariant PPGN architecture can be used to obtain a universal equivariant architecture that can approximate all continuous equivariant functions uniformly. Building on our results, we develop our WeLNet architecture, which sets new state-of-the-art results on the N-Body dynamics task and the GEOM-QM9 molecular conformation generation task.
In recent years, graph neural networks (GNNs) have emerged as a promising tool for solving machine learning problems on graphs. Most GNNs are members of the family of message passing neural networks (MPNNs). There is a close connection between these models and the Weisfeiler-Leman (WL) test of isomorphism, an algorithm that can successfully test isomorphism for a broad class of graphs. Recently, much research has focused on measuring the expressive power of GNNs. For instance, it has been shown that standard MPNNs are at most as powerful as WL in terms of distinguishing non-isomorphic graphs. …
Weisfeiler and Leman Follow the Arrow of Time: Expressive Power of Message Passing in Temporal Event Graphs
Chair of Machine Learning for Complex Networks（复杂网络机器学习教授席）；Center for AI and Data Science (CAIDAS)（人工智能与数据科学中心（CAIDAS））；University of Würzburg（乌尔姆大学）；Karlsruhe Institute of Technology（卡尔斯鲁厄理工学院）；University of Karlsruhe（卡尔斯鲁厄大学）；Institute for Computer Science 1（计算机科学研究所1）；University of Bonn（波恩大学）
Technion – Israel Institute of Technology（以色列理工学院）
Graph isomorphism testing is usually approached via the comparison of graph invariants. Two popular alternatives that offer a good trade-off between expressive power and computational efficiency are combinatorial (i.e., obtained via the Weisfeiler-Leman (WL) test) and spectral invariants. While the exact power of the latter is still an open question, the former is regularly criticized for its limited power, when a standard configuration of uniform pre-coloring is used. This drawback hinders the applicability of Message Passing Graph Neural Networks (MPGNNs), whose expressive power is upper bou…
Graph Neural Networks (GNNs) are learning models aimed at processing graphs and signals on graphs. The most popular and successful GNNs are based on message passing schemes. Such schemes inherently have limited expressive power when it comes to distinguishing two non-isomorphic graphs. In this article, we rely on the theory of covering spaces to fully characterize the classes of graphs that GNNs cannot distinguish. We then generate arbitrarily many non-isomorphic graphs that cannot be distinguished by GNNs, leading to the GraphCovers dataset. We also show that the number of indistinguishable g…
Institute for Mathematical and Computational Engineering, PUC Chile（智利天主教大学数学与计算工程研究所）；IMFD Chile（智利数据基础研究所）；CENIA Chile（智利国家人工智能中心）；Mila Quebec AI Institute（魁北克人工智能研究所Mila）；McGill University（麦吉尔大学）；RWTH Aachen University（亚琛工业大学）；Universidad Adolfo Ibáñez（阿道夫·伊瓦涅斯大学）
Knowledge graphs, modeling multi-relational data, improve numerous applications such as question answering or graph logical reasoning. Many graph neural networks for such data emerged recently, often outperforming shallow architectures. However, the design of such multi-relational graph neural networks is ad-hoc, driven mainly by intuition and empirical insights. Up to now, their expressivity, their relation to each other, and their (practical) learning performance is poorly understood. Here, we initiate the study of deriving a more principled understanding of multi-relational graph neural net…
TU Dortmund University（多特蒙德工业大学）；RWTH Aachen University（亚琛工业大学）；McGill University（麦吉尔大学）；MILA（MILA（蒙特利尔学习算法研究所））
In recent years, graph neural networks (GNNs) have emerged as a powerful neural architecture to learn vector representations of nodes and graphs in a supervised, end-to-end fashion. Up to now, GNNs have only been evaluated empirically -- showing promising results. The following work investigates GNNs from a theoretical point of view and relates them to the $1$-dimensional Weisfeiler-Leman graph isomorphism heuristic ($1$-WL). We show that GNNs have the same expressiveness as the $1$-WL in terms of distinguishing non-isomorphic (sub-)graphs. Hence, both algorithms also have the same shortcoming…
Scalable Message-Passing Quantum Graph Neural Networks in the Weisfeiler-Leman Hierarchy
LIP6, CNRS, Sorbonne Université, Paris, France（巴黎大学LIP6研究所、法国国家科学研究中心、索邦大学）；QC Ware, Palo Alto, USA and Paris, France（QC Ware公司，美国帕洛阿尔托及法国巴黎）；School of Informatics, University of Edinburgh, Edinburgh, UK（爱丁堡大学信息学院，英国爱丁堡）；Fujitsu Research of Europe Ltd., United Kingdom（日本富士通欧洲研究有限公司，英国）；Terra Quantum GmbH, Germany（德国Terra Quantum GmbH公司）；Quantum Research Center, Technology Innovation Institute, Abu Dhabi, UAE（阿布扎赫尔技术创新研究所量子研究中心，阿联酋）
Random walk kernels have been introduced in seminal work on graph learning and were later largely superseded by kernels based on the Weisfeiler-Leman test for graph isomorphism. We give a unified view on both classes of graph kernels. We study walk-based node refinement methods and formally relate them to several widely-used techniques, including Morgan's algorithm for molecule canonization and the Weisfeiler-Leman test. We define corresponding walk-based kernels on nodes that allow fine-grained parameterized neighborhood comparison, reach Weisfeiler-Leman expressiveness, and are computed usin…
Graph neural networks (GNNs) are deep learning architectures for machine learning problems on graphs. It has recently been shown that the expressiveness of GNNs can be characterised precisely by the combinatorial Weisfeiler-Leman algorithms and by finite variable counting logics. The correspondence has even led to new, higher-order GNNs corresponding to the WL algorithm in higher dimensions. The purpose of this paper is to explain these descriptive characterisations of GNNs.
Polytechnique Montréal（蒙特利尔理工学院）；TU Dortmund University（多特蒙德工业大学）；University of Vienna（维也纳大学）
In recent years, algorithms and neural architectures based on the Weisfeiler-Leman algorithm, a well-known heuristic for the graph isomorphism problem, emerged as a powerful tool for (supervised) machine learning with graphs and relational data. Here, we give a comprehensive overview of the algorithm's use in a machine learning setting. We discuss the theoretical background, show how to use it for supervised graph- and node classification, discuss recent extensions, and its connection to neural architectures. Moreover, we give an overview of current applications and future directions to stimul…
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…
The classical Weisfeiler-Leman algorithm aka color refinement is fundamental for graph learning with kernels and neural networks. Originally developed for graph isomorphism testing, the algorithm iteratively refines vertex colors. On many datasets, the stable coloring is reached after a few iterations and the optimal number of iterations for machine learning tasks is typically even lower. This suggests that the colors diverge too fast, defining a similarity that is too coarse. We generalize the concept of color refinement and propose a framework for gradual neighborhood refinement, which allow…
We study and compare different Graph Neural Network extensions that increase the expressive power of GNNs beyond the Weisfeiler-Leman test. We focus on (i) GNNs based on higher order WL methods, (ii) GNNs that preprocess small substructures in the graph, (iii) GNNs that preprocess the graph up to a small radius, and (iv) GNNs that slightly perturb the graph to compute an embedding. We begin by presenting a simple improvement for this last extension that strictly increases the expressive power of this GNN variant. Then, as our main result, we compare the expressiveness of these extensions to ea…
The expressive power of message passing neural networks (MPNNs) is known to match the expressive power of the 1-dimensional Weisfeiler-Leman graph (1-WL) isomorphism test. To boost the expressive power of MPNNs, a number of graph neural network architectures have recently been proposed based on higher-dimensional Weisfeiler-Leman tests. In this paper we consider the two-dimensional (2-WL) test and introduce a new type of MPNNs, referred to as $\ell$-walk MPNNs, which aggregate features along walks of length $\ell$ between vertices. We show that $2$-walk MPNNs match 2-WL in expressive power. Mo…
UiT the Arctic University of Norway（挪威北极大学）；Sapienza University of Rome（罗马第一大学）；NORCE Norwegian Research Centre（挪威NORCE研究中心）
Recently, subgraphs-enhanced Graph Neural Networks (SGNNs) have been introduced to enhance the expressive power of Graph Neural Networks (GNNs), which was proved to be not higher than the 1-dimensional Weisfeiler-Leman isomorphism test. The new paradigm suggests using subgraphs extracted from the input graph to improve the model's expressiveness, but the additional complexity exacerbates an already challenging problem in GNNs: explaining their predictions. In this work, we adapt PGExplainer, one of the most recent explainers for GNNs, to SGNNs. The proposed explainer accounts for the contribut…
Weisfeiler and Leman go Machine Learning: The Story so far
RWTH Aachen University（亚琛工业大学）；Meta AI Research（Meta人工智能研究院）；Weizmann Institute of Science（魏茨曼科学研究所）；NVIDIA Research（英伟达研究院）；Helmholtz Zentrum München（慕尼黑亥姆霍兹中心）；Technical University of Munich（慕尼黑工业大学）；University of Vienna（维也纳大学）；ETH Zürich（苏黎世联邦理工学院）；Swiss Institute of Bioinformatics（瑞士生物信息学研究所）；Max Planck Institute of Biochemistry（马克斯·普朗克生物化学研究所）
Message passing neural networks (MPNNs) learn the representation of graph-structured data based on graph original information, including node features and graph structures, and have shown astonishing improvement in node classification tasks. However, the expressive power of MPNNs is upper bounded by the first-order Weisfeiler-Leman test and its accuracy still has room for improvement. This work studies how to improve MPNNs' expressiveness and generalizability by fully exploiting graph original information both theoretically and empirically. It further proposes a new GNN model called INGNN (INf…
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…
This work formalizes the associational task of predicting node attribute evolution in temporal graphs from the perspective of learning equivariant representations. We show that node representations in temporal graphs can be cast into two distinct frameworks: (a) The most popular approach, which we denote as time-and-graph, where equivariant graph (e.g., GNN) and sequence (e.g., RNN) representations are intertwined to represent the temporal evolution of node attributes in the graph; and (b) an approach that we denote as time-then-graph, where the sequences describing the node and edge dynamics …
Iterative Graph Neural Network Enhancement via Frequent Subgraph Mining of Explanations
University of Illinois at Chicago（伊利诺伊大学芝加哥分校）；University of Bonn（波恩大学）；Fraunhofer IAIS（弗劳恩霍夫智能分析与信息系统研究所）；Lamarr Institute for Machine Learning and Artificial Intelligence（拉马尔机器学习与人工智能研究所）；HUN-REN-SZTE Research Group on AI（HUN-REN-塞格德大学人工智能研究组）
PUC Chile（智利天主教大学）；IMFD Chile（智利数据基础研究所）；University of Antwerp（安特卫普大学）
Various recent proposals increase the distinguishing power of Graph Neural Networks GNNs by propagating features between $k$-tuples of vertices. The distinguishing power of these "higher-order'' GNNs is known to be bounded by the $k$-dimensional Weisfeiler-Leman (WL) test, yet their $\mathcal O(n^k)$ memory requirements limit their applicability. Other proposals infuse GNNs with local higher-order graph structural information from the start, hereby inheriting the desirable $\mathcal O(n)$ memory requirement from GNNs at the cost of a one-time, possibly non-linear, preprocessing step. We propos…
École Polytechnique（巴黎综合理工学院）；Athens University of Economics and Business（雅典经济与商业大学）
Graph neural networks (GNNs) have emerged recently as a powerful architecture for learning node and graph representations. Standard GNNs have the same expressive power as the Weisfeiler-Leman test of graph isomorphism in terms of distinguishing non-isomorphic graphs. However, it was recently shown that this test cannot identify fundamental graph properties such as connectivity and triangle freeness. We show that GNNs also suffer from the same limitation. To address this limitation, we propose a more expressive architecture, k-hop GNNs, which updates a node's representation by aggregating infor…
Graph Neural Networks (GNNs) are widely used for graph representation learning in many application domains. The expressiveness of vanilla GNNs is upper-bounded by 1-dimensional Weisfeiler-Leman (1-WL) test as they operate on rooted subtrees through iterative message passing. In this paper, we empower GNNs by injecting neighbor-connectivity information extracted from a new type of substructure. We first investigate different kinds of connectivities existing in a local neighborhood and identify a substructure called union subgraph, which is able to capture the complete picture of the 1-hop neigh…
Expressivity and Generalization: Fragment-Biases for Molecular GNNs
School of Computation, Information & Technology, Technical University of Munich（慕尼黑工业大学计算、信息与技术学院）；Munich Data Science Institute（慕尼黑数据科学研究所）；Helmholtz Center for Computational Health（亥姆霍兹计算健康中心）
University of Antwerp（安特卫普大学）；Pontificia Universidad Católica de Chile（智利天主教大学）；IMFD（智利数学与计算机科学研究所）
Characterizing the separation power of graph neural networks (GNNs) provides an understanding of their limitations for graph learning tasks. Results regarding separation power are, however, usually geared at specific GNN architectures, and tools for understanding arbitrary GNN architectures are generally lacking. We provide an elegant way to easily obtain bounds on the separation power of GNNs in terms of the Weisfeiler-Leman (WL) tests, which have become the yardstick to measure the separation power of GNNs. The crux is to view GNNs as expressions in a procedural tensor language describing th…
The expressive power of graph neural network formalisms is commonly measured by their ability to distinguish graphs. For many formalisms, the k-dimensional Weisfeiler-Leman (k-WL) graph isomorphism test is used as a yardstick. In this paper we consider the expressive power of kth-order invariant (linear) graph networks (k-IGNs). It is known that k-IGNs are expressive enough to simulate k-WL. This means that for any two graphs that can be distinguished by k-WL, one can find a k-IGN which also distinguishes those graphs. The question remains whether k-IGNs can distinguish more graphs than k-WL. …
Message passing neural networks (MPNNs) have become a dominant flavor of graph neural networks (GNNs) in recent years. Yet, MPNNs come with notable limitations; namely, they are at most as powerful as the 1-dimensional Weisfeiler-Leman (1-WL) test in distinguishing graphs in a graph isomorphism testing frame-work. To this end, researchers have drawn inspiration from the k-WL hierarchy to develop more expressive GNNs. However, current k-WL-equivalent GNNs are not practical for even small values of k, as k-WL becomes combinatorially more complex as k grows. At the same time, several works have f…
Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University（上海交通大学图像处理与模式识别研究所）
Hypergraph, an expressive structure with flexibility to model the higher-order correlations among entities, has recently attracted increasing attention from various research domains. Despite the success of Graph Neural Networks (GNNs) for graph representation learning, how to adapt the powerful GNN-variants directly into hypergraphs remains a challenging problem. In this paper, we propose UniGNN, a unified framework for interpreting the message passing process in graph and hypergraph neural networks, which can generalize general GNN models into hypergraphs. In this framework, meticulously-desi…
