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Message passing neural networks have become a method of choice for learning on graphs, in particular the prediction of chemical properties and the acceleration of molecular dynamics studies. While they readily scale to large training data…

Machine Learning · Computer Science 2021-06-08 Kristof T. Schütt , Oliver T. Unke , Michael Gastegger

Message passing (MP) is a computational technique used to find approximate solutions to a variety of problems defined on networks. MP approximations are generally accurate in locally tree-like networks but require corrections to maintain…

Physics and Society · Physics 2023-09-27 George T. Cantwell , Alec Kirkley , Filippo Radicchi

While Graph Neural Networks (GNNs) have achieved remarkable success, their design largely relies on empirical intuition rather than theoretical understanding. In this paper, we present a comprehensive analysis of GNN behavior through three…

Machine Learning · Computer Science 2025-02-04 Qin Jiang , Chengjia Wang , Michael Lones , Wei Pang

Message Passing Neural Networks (MPNNs) are instances of Graph Neural Networks that leverage the graph to send messages over the edges. This inductive bias leads to a phenomenon known as over-squashing, where a node feature is insensitive…

Machine Learning · Computer Science 2023-05-25 Francesco Di Giovanni , Lorenzo Giusti , Federico Barbero , Giulia Luise , Pietro Lio' , Michael Bronstein

Graph neural network have achieved impressive results in predicting molecular properties, but they do not directly account for local and hidden structures in the graph such as functional groups and molecular geometry. At each propagation…

Machine Learning · Computer Science 2020-02-25 Daniel Flam-Shepherd , Tony Wu , Pascal Friederich , Alan Aspuru-Guzik

The most prevalent class of neural networks operating on graphs are message passing neural networks (MPNNs), in which the representation of a node is updated iteratively by aggregating information in the 1-hop neighborhood. Since this…

Machine Learning · Computer Science 2023-10-25 Floor Eijkelboom , Erik Bekkers , Michael Bronstein , Francesco Di Giovanni

Machine learned interatomic potentials, particularly equivariant message-passing (MP) models, have demonstrated high fidelity in representing first-principles data, revolutionizing computational studies in materials science, biophysics, and…

Chemical Physics · Physics 2025-09-01 Yaolong Zhang , Hua Guo

Molecular representation learning (MRL) has long been crucial in the fields of drug discovery and materials science, and it has made significant progress due to the development of natural language processing (NLP) and graph neural networks…

Information Theory · Computer Science 2023-05-25 Chen Gong , Yvon Maday

Graph neural networks that leverage coordinates via directional message passing have recently set the state of the art on multiple molecular property prediction tasks. However, they rely on atom position information that is often…

Machine Learning · Computer Science 2022-04-06 Johannes Gasteiger , Chandan Yeshwanth , Stephan Günnemann

We introduce a new type of graphical model that we call a "memory factor network" (MFN). We show how to use MFNs to model the structure inherent in many types of data sets. We also introduce an associated message-passing style algorithm…

Artificial Intelligence · Computer Science 2016-01-19 Patrick Eschenfeldt , Dan Schmidt , Stark Draper , Jonathan Yedidia

Message passing-based graph neural networks (GNNs) have achieved great success in many real-world applications. For a sampled mini-batch of target nodes, the message passing process is divided into two parts: message passing between nodes…

Machine Learning · Computer Science 2025-02-28 Zhihao Shi , Jie Wang , Zhiwei Zhuang , Xize Liang , Bin Li , Feng Wu

Graph neural networks (GNNs) are known to be vulnerable to oversmoothing due to their implicit homophily assumption. We mitigate this problem with a novel scheme that regulates the aggregation of messages, modulating the type and extent of…

Machine Learning · Computer Science 2025-12-03 Haishan Wang , Arno Solin , Vikas Garg

Many real-world phenomena can be modeled as a graph, making them extremely valuable due to their ubiquitous presence. GNNs excel at capturing those relationships and patterns within these graphs, enabling effective learning and prediction…

Machine Learning · Computer Science 2023-11-28 Abhinav Raghuvanshi , Kushal Sokke Malleshappa

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) have gained significant attention as a powerful modeling and inference method, especially for homophilic graph-structured data. To empower GNNs in heterophilic graphs, where adjacent nodes exhibit dissimilar…

Machine Learning · Computer Science 2024-06-03 Langzhang Liang , Sunwoo Kim , Kijung Shin , Zenglin Xu , Shirui Pan , Yuan Qi

Message-passing graph neural networks (MPGNNs) dominate modern graph learning. Typical efforts enhance MPGNN's expressive power by enriching the adjacency-based aggregation. In contrast, we introduce an efficient aggregation over walk…

Machine Learning · Computer Science 2025-09-29 Marek Černý

In recent studies, neural message passing has proved to be an effective way to design graph neural networks (GNNs), which have achieved state-of-the-art performance in many graph-based tasks. However, current neural-message passing…

Machine Learning · Computer Science 2021-04-21 Wentao Zhang , Yu Shen , Zheyu Lin , Yang Li , Xiaosen Li , Wen Ouyang , Yangyu Tao , Zhi Yang , Bin Cui

Due to the massive number of devices in the M2M communication era, new challenges have been brought to the existing random-access (RA) mechanism, such as severe preamble collisions and resource block (RB) wastes. To address these problems,…

Information Theory · Computer Science 2019-10-09 Zhaoji Zhang , Ying Li , Lei Liu , Huimei Han

In recent years, the prediction of quantum mechanical observables with machine learning methods has become increasingly popular. Message-passing neural networks (MPNNs) solve this task by constructing atomic representations, from which the…

Complex Query Answering (CQA) over Knowledge Graphs (KGs) has attracted a lot of attention to potentially support many applications. Given that KGs are usually incomplete, neural models are proposed to answer the logical queries by…

Machine Learning · Computer Science 2023-08-29 Zihao Wang , Yangqiu Song , Ginny Y. Wong , Simon See