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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.…

机器学习 · 计算机科学 2023-03-08 Mohammad Sadegh Akhondzadeh , Vijay Lingam , Aleksandar Bojchevski

The message-passing mechanism underlying Graph Neural Networks (GNNs) is not naturally suited for heterophilic datasets, where adjacent nodes often have different labels. Most solutions to this problem remain confined to the task of node…

机器学习 · 计算机科学 2025-06-30 Andrea Giuseppe Di Francesco , Francesco Caso , Maria Sofia Bucarelli , Fabrizio Silvestri

We investigate the explainability of graph neural networks (GNNs) as a step toward elucidating their working mechanisms. While most current methods focus on explaining graph nodes, edges, or features, we argue that, as the inherent…

机器学习 · 计算机科学 2024-01-02 Shurui Gui , Hao Yuan , Jie Wang , Qicheng Lao , Kang Li , Shuiwang Ji

Graph are a ubiquitous data representation, as they represent a flexible and compact representation. For instance, the 3D structure of RNA can be efficiently represented as $\textit{2.5D graphs}$, graphs whose nodes are nucleotides and…

机器学习 · 计算机科学 2021-09-21 Vincent Mallet , Carlos G. Oliver , William L. Hamilton

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…

机器学习 · 计算机科学 2022-02-01 Pál András Papp , Roger Wattenhofer

The growing use of deep learning necessitates efficient network design and deployment, making neural predictors vital for estimating attributes such as accuracy and latency. Recently, Graph Neural Networks (GNNs) and transformers have shown…

机器学习 · 计算机科学 2025-07-02 Ruihan Xu , Haokui Zhang , Yaowei Wang , Wei Zeng , Shiliang Zhang

Using Large Language Models (LLMs) to process graph-structured data is an active research area, yet current state-of-the-art approaches typically rely on multi-step pipelines with Graph Neural Network (GNN) encoders that compress rich…

机器学习 · 计算机科学 2026-05-12 Dario Vajda

Graph Neural Networks (GNNs) and their message passing framework that leverages both structural and feature information, have become a standard method for solving graph-based machine learning problems. However, these approaches still…

机器学习 · 计算机科学 2024-11-20 Simon Delarue , Thomas Bonald , Tiphaine Viard

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…

机器学习 · 计算机科学 2020-04-14 Stanisław Purgał

Theoretical studies on the representation power of GNNs have been centered around understanding the equivalence of GNNs, using WL-Tests for detecting graph isomorphism. In this paper, we argue that such equivalence ignores the accompanying…

机器学习 · 计算机科学 2024-08-26 P. Krishna Kumar a , Harish G. Ramaswamy

An important characteristic of temporal graphs is how the directed arrow of time influences their causal topology, i.e., which nodes can possibly influence each other causally via time-respecting paths. The resulting patterns are often…

机器学习 · 计算机科学 2026-05-19 Franziska Heeg , Jonas Sauer , Petra Mutzel , Ingo Scholtes

This paper studies asynchronous message passing (AMP), a new paradigm for applying neural network based learning to graphs. Existing graph neural networks use the synchronous distributed computing model and aggregate their neighbors in each…

机器学习 · 计算机科学 2022-05-25 Lukas Faber , Roger Wattenhofer

While graph neural networks (GNNs) have shown remarkable performance across diverse graph-related tasks, their high-dimensional hidden representations render them black boxes. In this work, we propose Graph Lingual Network (GLN), a GNN…

机器学习 · 计算机科学 2025-09-16 Sunwoo Kim , Soo Yong Lee , Jaemin Yoo , Kijung Shin

How to obtain informative representations of molecules is a crucial prerequisite in AI-driven drug design and discovery. Recent researches abstract molecules as graphs and employ Graph Neural Networks (GNNs) for molecular representation…

生物大分子 · 定量生物学 2020-10-30 Yu Rong , Yatao Bian , Tingyang Xu , Weiyang Xie , Ying Wei , Wenbing Huang , Junzhou Huang

Message passing plays a vital role in graph neural networks (GNNs) for effective feature learning. However, the over-reliance on input topology diminishes the efficacy of message passing and restricts the ability of GNNs. Despite efforts to…

机器学习 · 计算机科学 2024-12-03 Junshu Sun , Chenxue Yang , Xiangyang Ji , Qingming Huang , Shuhui Wang

GraphRAG conditions language models on subgraphs retrieved from knowledge graphs, encoded via message-passing GNNs. Because these encoders entangle node contributions through iterated neighborhood aggregation, there is no closed-form way to…

机器学习 · 计算机科学 2026-05-22 Yoav Kor Sade , Arvindh Arun , Rishi Puri , Steffen Staab , Maya Bechler-Speicher

Graph learning has become essential in various domains, including recommendation systems and social network analysis. Graph Neural Networks (GNNs) have emerged as promising techniques for encoding structural information and improving…

机器学习 · 计算机科学 2024-10-10 Lianghao Xia , Ben Kao , Chao Huang

Graph neural networks (GNNs) have gained significant attention in recent years for their ability to process data that may be represented as graphs. This has prompted several studies to explore their representational capability based on the…

机器学习 · 计算机科学 2025-10-15 Brian Godwin Lim , Galvin Brice Sy Lim , Renzo Roel Tan , Kazushi Ikeda

Graph Neural Networks (GNNs) have emerged as the predominant approach for learning over graph-structured data. However, most GNNs operate as black-box models and require post-hoc explanations, which may not suffice in high-stakes scenarios…

机器学习 · 计算机科学 2025-10-14 Maya Bechler-Speicher , Amir Globerson , Ran Gilad-Bachrach

Graph neural networks (GNNs) work remarkably well in semi-supervised node regression, yet a rigorous theory explaining when and why they succeed remains lacking. To address this gap, we study an aggregate-and-readout model that encompasses…

机器学习 · 统计学 2026-02-20 Juntong Chen , Claire Donnat , Olga Klopp , Johannes Schmidt-Hieber