Weisfeiler-Leman at the margin: When more expressivity matters

The Weisfeiler-Leman algorithm ($1$-WL) is a well-studied heuristic for the graph isomorphism problem. Recently, the algorithm has played a prominent role in understanding the expressive power of message-passing graph neural networks (MPNNs) and being effective as a graph kernel. Despite its success, $1$-WL faces challenges in distinguishing non-isomorphic graphs, leading to the development of more expressive MPNN and kernel architectures. However, the relationship between enhanced expressivity and improved generalization performance remains unclear. Here, we show that an architecture's expressivity offers limited insights into its generalization performance when viewed through graph isomorphism. Moreover, we focus on augmenting $1$-WL and MPNNs with subgraph information and employ classical margin theory to investigate the conditions under which an architecture's increased expressivity aligns with improved generalization performance. In addition, we show that gradient flow pushes the MPNN's weights toward the maximum margin solution. Further, we introduce variations of expressive $1$-WL-based kernel and MPNN architectures with provable generalization properties. Our empirical study confirms the validity of our theoretical findings.

Future Directions in Foundations of Graph Machine Learning

Machine learning on graphs, especially using graph neural networks (GNNs), has seen a surge in interest due to the wide availability of graph data across a broad spectrum of disciplines, from life to social and engineering sciences. Despite their practical success, our theoretical understanding of the properties of GNNs remains highly incomplete. Recent theoretical advancements primarily focus on elucidating the coarse-grained expressive power of GNNs, predominantly employing combinatorial techniques. However, these studies do not perfectly align with practice, particularly in understanding the generalization behavior of GNNs when trained with stochastic first-order optimization techniques. In this position paper, we argue that the graph machine learning community needs to shift its attention to developing a more balanced theory of graph machine learning, focusing on a more thorough understanding of the interplay of expressive power, generalization, and optimization.

Towards Principled Graph Transformers

Graph learning architectures based on the k-dimensional Weisfeiler-Leman (k-WL) hierarchy offer a theoretically well-understood expressive power. However, such architectures often fail to deliver solid predictive performance on real-world tasks, limiting their practical impact. In contrast, global attention-based models such as graph transformers demonstrate strong performance in practice, but comparing their expressive power with the k-WL hierarchy remains challenging, particularly since these architectures rely on positional or structural encodings for their expressivity and predictive performance. To address this, we show that the recently proposed Edge Transformer, a global attention model operating on node pairs instead of nodes, has at least 3-WL expressive power. Empirically, we demonstrate that the Edge Transformer surpasses other theoretically aligned architectures regarding predictive performance while not relying on positional or structural encodings.

Towards Foundational Models for Molecular Learning on Large-Scale Multi-Task Datasets

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

Exploring the Power of Graph Neural Networks in Solving Linear Optimization Problems

Recently, machine learning, particularly message-passing graph neural networks (MPNNs), has gained traction in enhancing exact optimization algorithms. For example, MPNNs speed up solving mixed-integer optimization problems by imitating computational intensive heuristics like strong branching, which entails solving multiple linear optimization problems (LPs). Despite the empirical success, the reasons behind MPNNs' effectiveness in emulating linear optimization remain largely unclear. Here, we show that MPNNs can simulate standard interior-point methods for LPs, explaining their practical success. Furthermore, we highlight how MPNNs can serve as a lightweight proxy for solving LPs, adapting to a given problem instance distribution. Empirically, we show that MPNNs solve LP relaxations of standard combinatorial optimization problems close to optimality, often surpassing conventional solvers and competing approaches in solving time.

Probabilistically Rewired Message-Passing Neural Networks

Message-passing graph neural networks (MPNNs) emerged as powerful tools for processing graph-structured input. However, they operate on a fixed input graph structure, ignoring potential noise and missing information. Furthermore, their local aggregation mechanism can lead to problems such as over-squashing and limited expressive power in capturing relevant graph structures. Existing solutions to these challenges have primarily relied on heuristic methods, often disregarding the underlying data distribution. Hence, devising principled approaches for learning to infer graph structures relevant to the given prediction task remains an open challenge. In this work, leveraging recent progress in exact and differentiable $k$-subset sampling, we devise probabilistically rewired MPNNs (PR-MPNNs), which learn to add relevant edges while omitting less beneficial ones. For the first time, our theoretical analysis explores how PR-MPNNs enhance expressive power, and we identify precise conditions under which they outperform purely randomized approaches. Empirically, we demonstrate that our approach effectively mitigates issues like over-squashing and under-reaching. In addition, on established real-world datasets, our method exhibits competitive or superior predictive performance compared to traditional MPNN models and recent graph transformer architectures.

Fine-grained Expressivity of Graph Neural Networks

Numerous recent works have analyzed the expressive power of message-passing graph neural networks (MPNNs), primarily utilizing combinatorial techniques such as the $1$-dimensional Weisfeiler-Leman test ($1$-WL) for the graph isomorphism problem. However, the graph isomorphism objective is inherently binary, not giving insights into the degree of similarity between two given graphs. This work resolves this issue by considering continuous extensions of both $1$-WL and MPNNs to graphons. Concretely, we show that the continuous variant of $1$-WL delivers an accurate topological characterization of the expressive power of MPNNs on graphons, revealing which graphs these networks can distinguish and the level of difficulty in separating them. We identify the finest topology where MPNNs separate points and prove a universal approximation theorem. Consequently, we provide a theoretical framework for graph and graphon similarity combining various topological variants of classical characterizations of the $1$-WL. In particular, we characterize the expressive power of MPNNs in terms of the tree distance, which is a graph distance based on the concepts of fractional isomorphisms, and substructure counts via tree homomorphisms, showing that these concepts have the same expressive power as the $1$-WL and MPNNs on graphons. Empirically, we validate our theoretical findings by showing that randomly initialized MPNNs, without training, exhibit competitive performance compared to their trained counterparts. Moreover, we evaluate different MPNN architectures based on their ability to preserve graph distances, highlighting the significance of our continuous $1$-WL test in understanding MPNNs' expressivity.