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Predicting molecular properties with data-driven methods has drawn much attention in recent years. Particularly, Graph Neural Networks (GNNs) have demonstrated remarkable success in various molecular generation and prediction tasks. In…

Quantitative Methods · Quantitative Biology 2021-10-19 Zaixi Zhang , Qi Liu , Hao Wang , Chengqiang Lu , Chee-Kong Lee

In recent years, deep learning on graphs has achieved remarkable success in various domains. However, the reliance on annotated graph data remains a significant bottleneck due to its prohibitive cost and time-intensive nature. To address…

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…

Machine Learning · Computer Science 2024-11-20 Simon Delarue , Thomas Bonald , Tiphaine Viard

Graph Neural Networks (GNNs) have become powerful tools for learning from graph-structured data, finding applications across diverse domains. However, as graph sizes and connectivity increase, standard GNN training methods face significant…

Machine Learning · Computer Science 2025-12-01 Eshed Gal , Moshe Eliasof , Carola-Bibiane Schönlieb , Ivan I. Kyrchei , Eldad Haber , Eran Treister

Graph learning methods have recently been receiving increasing interest as means to infer structure in datasets. Most of the recent approaches focus on different relationships between a graph and data sample distributions, mostly in…

Machine Learning · Computer Science 2020-03-23 Hermina Petric Maretic , Pascal Frossard

Graph Self-Supervised Learning (GSSL) provides a robust pathway for acquiring embeddings without expert labelling, a capability that carries profound implications for molecular graphs due to the staggering number of potential molecules and…

Machine Learning · Computer Science 2023-10-19 Hanchen Wang , Jean Kaddour , Shengchao Liu , Jian Tang , Joan Lasenby , Qi Liu

In recent years, there has been a growing interest in mapping data from different domains to graph structures. Among others, neural network models such as the multi-layer perceptron (MLP) can be modeled as graphs. In fact, MLPs can be…

Machine Learning · Statistics 2024-02-06 Giannis Nikolentzos , Siyun Wang , Johannes Lutzeyer , Michalis Vazirgiannis

Graph neural networks (GNNs) demonstrate great performance in compound property and activity prediction due to their capability to efficiently learn complex molecular graph structures. However, two main limitations persist including…

Biomolecules · Quantitative Biology 2023-10-10 Apakorn Kengkanna , Masahito Ohue

Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics systems, learning molecular fingerprints, predicting protein interface, and classifying diseases demand a model…

Machine Learning · Computer Science 2021-10-07 Jie Zhou , Ganqu Cui , Shengding Hu , Zhengyan Zhang , Cheng Yang , Zhiyuan Liu , Lifeng Wang , Changcheng Li , Maosong Sun

Supply chain network data is a valuable asset for businesses wishing to understand their ethical profile, security of supply, and efficiency. Possession of a dataset alone however is not a sufficient enabler of actionable decisions due to…

Machine Learning · Computer Science 2021-07-23 Ajmal Aziz , Edward Elson Kosasih , Ryan-Rhys Griffiths , Alexandra Brintrup

Research in Graph Signal Processing (GSP) aims to develop tools for processing data defined on irregular graph domains. In this paper we first provide an overview of core ideas in GSP and their connection to conventional digital signal…

Signal Processing · Electrical Eng. & Systems 2018-03-28 Antonio Ortega , Pascal Frossard , Jelena Kovačević , José M. F. Moura , Pierre Vandergheynst

Integrating large language models (LLMs) with knowledge graphs derived from domain-specific data represents an important advancement towards more powerful and factual reasoning. As these models grow more capable, it is crucial to enable…

Artificial Intelligence · Computer Science 2024-04-19 Stefan Dernbach , Khushbu Agarwal , Alejandro Zuniga , Michael Henry , Sutanay Choudhury

Graph neural networks have developed by leaps and bounds in recent years due to the restriction of traditional convolutional filters on non-Euclidean structured data. Spectral graph theory mainly studies fundamental graph properties using…

Spectral Theory · Mathematics 2023-09-08 Xinye Chen

The demand for data privacy has led to the development of frameworks like Federated Graph Learning (FGL), which facilitate decentralized model training. However, a significant operational challenge in such systems is adhering to the right…

Machine Learning · Computer Science 2025-08-05 Yuming Ai , Xunkai Li , Jiaqi Chao , Bowen Fan , Zhengyu Wu , Yinlin Zhu , Rong-Hua Li , Guoren Wang

Graph Neural Networks (GNNs) are de facto solutions to structural data learning. However, it is susceptible to low-quality and unreliable structure, which has been a norm rather than an exception in real-world graphs. Existing graph…

Machine Learning · Computer Science 2023-03-20 Dongcheng Zou , Hao Peng , Xiang Huang , Renyu Yang , Jianxin Li , Jia Wu , Chunyang Liu , Philip S. Yu

Standard deep learning architectures used for classification generate label predictions with a projection head and softmax activation function. Although successful, these methods fail to leverage the relational information between samples…

Machine Learning · Computer Science 2025-12-10 Jason Brown , Bohan Chen , Harris Hardiman-Mostow , Jeff Calder , Andrea L. Bertozzi

Graph representation learning (GRL) has emerged as a powerful technique for solving graph analytics tasks. It can effectively convert discrete graph data into a low-dimensional space where the graph structural information and graph…

Social and Information Networks · Computer Science 2023-09-21 Chunyu Miao , Chenxuan Xie , Jiajun Zhou , Shanqing Yu , Lina Chen , Qi Xuan

Graph-based methods have been demonstrated as one of the most effective approaches for semi-supervised learning, as they can exploit the connectivity patterns between labeled and unlabeled data samples to improve learning performance.…

Machine Learning · Computer Science 2019-07-01 Qimai Li , Xiao-Ming Wu , Han Liu , Xiaotong Zhang , Zhichao Guan

Network-topology inference from (vertex) signal observations is a prominent problem across data-science and engineering disciplines. Most existing schemes assume that observations from all nodes are available, but in many practical…

Methodology · Statistics 2021-11-11 Andrei Buciulea , Samuel Rey , Antonio G. Marques

Federated Graph Learning (FGL) combines the privacy-preserving capabilities of federated learning (FL) with the strong graph modeling capability of Graph Neural Networks (GNNs). Current research addresses subgraph-FL from the structural…

Machine Learning · Computer Science 2025-08-19 Zihan Tan , Suyuan Huang , Guancheng Wan , Wenke Huang , He Li , Mang Ye