Related papers: Walk Message Passing Neural Networks and Second-Or…

We present many-body Message Passing Neural Network (MPNN) framework that models higher-order node interactions ($\ge 2$ nodes). We model higher-order terms as tree-shaped motifs, comprising a central node with its neighborhood, and apply…

Graph Neural Networks (GNNs) have become the standard approach for learning and reasoning over relational data, leveraging the message-passing mechanism that iteratively propagates node embeddings through graph structures. While GNNs have…

Graph Neural Networks (GNNs) are a broad class of connectionist models for graph processing. Recent studies have shown that GNNs can approximate any function on graphs, modulo the equivalence relation on graphs defined by the…

Accurate RNA secondary structure prediction is vital for understanding cellular regulation and disease mechanisms. Deep learning (DL) methods have surpassed traditional algorithms by predicting complex features like pseudoknots and…

Graph Neural Networks (GNNs) have become important machine learning tools for graph analysis, and its explainability is crucial for safety, fairness, and robustness. Layer-wise relevance propagation for GNNs (GNN-LRP) evaluates the…

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…

In this article we present new results about the expressivity of Graph Neural Networks (GNNs). We prove that for any GNN with piecewise polynomial activations, whose architecture size does not grow with the graph input sizes, there exists a…

We investigate the distance function learned by message passing neural networks (MPNNs) in specific tasks, aiming to capture the functional distance between prediction targets that MPNNs implicitly learn. This contrasts with previous work,…

Graph neural networks (GNNs) have limited expressive power, failing to represent many graph classes correctly. While more expressive graph representation learning (GRL) alternatives can distinguish some of these classes, they are…

We perform the first adversarial robustness study into Graph Neural Networks (GNNs) that are provably more powerful than traditional Message Passing Neural Networks (MPNNs). In particular, we use adversarial robustness as a tool to uncover…

Combinatorial complexes have unified set-based (e.g., graphs, hypergraphs) and part-whole (e.g., simplicial, cellular complexes) structures into a common topological framework. Existing topological neural networks and Weisfeiler-Lehman…

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…

Graph neural networks (GNNs) have drawn increasing attention in recent years and achieved remarkable performance in many graph-based tasks, especially in semi-supervised learning on graphs. However, most existing GNNs are based on the…

Message-passing graph neural networks (MPGNNs) are commonly compared with the Weisfeiler-Lehman (WL) color-refinement procedure, but this comparison does not quantify the resource parameters a network needs to realize color refinement with…

Message passing neural networks (MPNNs) operate on graphs by exchanging information between neigbouring nodes. MPNNs have been successfully applied to various node-, edge-, and graph-level tasks in areas like molecular science, computer…

The $k$-dimensional Weisfeiler-Leman algorithm ($k$-WL) is a fruitful approach to the Graph Isomorphism problem. 2-WL corresponds to the original algorithm suggested by Weisfeiler and Leman over 50 years ago. 1-WL is the classical color…

Neural architectures that learn potential energy surfaces from molecular data have undergone fast improvement in recent years. A key driver of this success is the Message Passing Neural Network (MPNN) paradigm. Its favorable scaling with…

Graph Neural Networks (GNNs) suffer from over-smoothing in deep architectures and expressiveness bounded by the 1-Weisfeiler-Leman (1-WL) test. We adapt Manifold-Constrained Hyper-Connections (\mhc)~\citep{xie2025mhc}, recently proposed for…

In pioneering work from 2019, Barcel\'o and coauthors identified logics that precisely match the expressive power of constant iteration-depth graph neural networks (GNNs) relative to properties definable in first-order logic. In this…

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…