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With the growing adoption of AI-based systems across everyday life, the need to understand their decision-making mechanisms is correspondingly increasing. The level at which we can trust the statistical inferences made from AI-based…

Machine Learning · Statistics 2024-04-15 Adam Spannaus , Heidi A. Hanson , Lynne Penberthy , Georgia Tourassi

The ability of message-passing neural networks (MPNNs) to fit complex functions over graphs is limited as most graph convolutions amplify the same signal across all feature channels, a phenomenon known as rank collapse, and over-smoothing…

Machine Learning · Computer Science 2024-12-10 Andreas Roth , Franka Bause , Nils M. Kriege , Thomas Liebig

Graph Neural Networks are highly effective at learning from relational data, leveraging node and edge features while maintaining the symmetries inherent to graph structures. However, many real-world systems, such as social or biological…

Machine Learning · Computer Science 2025-08-18 Michael Banf , Dominik Filipiak , Max Schattauer , Liliya Imasheva

Topology-imbalance is a graph-specific imbalance problem caused by the uneven topology positions of labeled nodes, which significantly damages the performance of GNNs. What topology-imbalance means and how to measure its impact on graph…

Machine Learning · Computer Science 2022-08-18 Qingyun Sun , Jianxin Li , Haonan Yuan , Xingcheng Fu , Hao Peng , Cheng Ji , Qian Li , Philip S. Yu

Graph Neural Networks (GNNs) have become a prominent approach to machine learning with graphs and have been increasingly applied in a multitude of domains. Nevertheless, since most existing GNN models are based on flat message-passing…

Machine Learning · Computer Science 2022-10-27 Zhiqiang Zhong , Cheng-Te Li , Jun Pang

Graph neural networks operate on graph-structured data via exchanging messages along edges. One limitation of this message passing paradigm is the over-squashing problem. Over-squashing occurs when messages from a node's expanded receptive…

Machine Learning · Computer Science 2023-11-15 Thomas Christie , Yu He

Question answering over knowledge graphs (KGQA) has evolved from simple single-fact questions to complex questions that require graph traversal and aggregation. We propose a novel approach for complex KGQA that uses unsupervised message…

Computation and Language · Computer Science 2019-08-20 Svitlana Vakulenko , Javier David Fernandez Garcia , Axel Polleres , Maarten de Rijke , Michael Cochez

Dynamic graphs serve as a generic abstraction and description of the evolutionary behaviors of various complex systems (e.g., social networks and communication networks). Temporal link prediction (TLP) is a classic yet challenging inference…

Social and Information Networks · Computer Science 2023-06-30 Meng Qin , Dit-Yan Yeung

The goal of this paper is to establish the fundamental tools to analyze signals defined over a topological space, i.e. a set of points along with a set of neighborhood relations. This setup does not require the definition of a metric and…

Signal Processing · Electrical Eng. & Systems 2020-10-28 Sergio Barbarossa , Stefania Sardellitti

Graph Neural Networks (GNNs) have demonstrated remarkable success in learning from graph-structured data. However, they face significant limitations in expressive power, struggling with long-range interactions and lacking a principled…

Machine Learning · Computer Science 2023-06-07 Lorenzo Giusti , Teodora Reu , Francesco Ceccarelli , Cristian Bodnar , Pietro Liò

Graph Neural Networks (GNNs) excel at learning from pairwise interactions but often overlook multi-way and hierarchical relationships. Topological Deep Learning (TDL) addresses this limitation by leveraging combinatorial topological spaces.…

Graph Neural Networks (GNNs) have become essential in high-stakes domains such as drug discovery, yet their black-box nature remains a significant barrier to trustworthiness. While self-explainable GNNs attempt to bridge this gap, they…

Machine Learning · Computer Science 2026-02-25 Chuqin Geng , Li Zhang , Haolin Ye , Ziyu Zhao , Yuhe Jiang , Tara Saba , Xinyu Wang , Xujie Si

Recent work in Topological Deep Learning (TDL) seeks to generalize graph learning's preeminent $message \ passing$ paradigm to more complex relational structures: simplicial complexes, cell complexes, hypergraphs, and combinations thereof.…

Machine Learning · Computer Science 2025-09-30 Jacob Hume , Pietro Liò

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…

Machine Learning · Computer Science 2022-02-01 Cristian Bodnar , Fabrizio Frasca , Nina Otter , Yu Guang Wang , Pietro Liò , Guido Montúfar , Michael Bronstein

Graph machine learning has led to a significant increase in the capabilities of models that learn on arbitrary graph-structured data and has been applied to molecules, social networks, recommendation systems, and transportation, among other…

Machine Learning · Computer Science 2025-06-23 Vijay Prakash Dwivedi , Charilaos Kanatsoulis , Shenyang Huang , Jure Leskovec

Knowledge graph completion aims to predict missing relations between entities in a knowledge graph. In this work, we propose a relational message passing method for knowledge graph completion. Different from existing embedding-based…

Machine Learning · Computer Science 2021-05-31 Hongwei Wang , Hongyu Ren , Jure Leskovec

Knowledge is a network of interconnected concepts. Yet, precisely how the topological structure of knowledge constrains its acquisition remains unknown, hampering the development of learning enhancement strategies. Here we study the…

Computation and Language · Computer Science 2021-03-17 Nicolas H. Christianson , Ann Sizemore Blevins , Danielle S. Bassett

Message passing neural networks have shown a lot of success on graph-structured data. However, there are many instances where message passing can lead to over-smoothing or fail when neighboring nodes belong to different classes. In this…

Hypergraph representations are both more efficient and better suited to describe data characterized by relations between two or more objects. In this work, we present a new graph neural network based on message passing capable of processing…

Machine Learning · Computer Science 2022-09-19 Sajjad Heydari , Lorenzo Livi

Complex systems are difficult to study not only because they are nonlinear, multiscale, and often nonstationary, but because their scientifically relevant organization is often invisible at the level of individual components, pairwise…

Physics and Society · Physics 2026-03-30 Mark M. Bailey