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Graph-based Neural Networks (GNNs) are recent models created for learning representations of nodes (and graphs), which have achieved promising results when detecting patterns that occur in large-scale data relating different entities. Among…

Machine Learning · Computer Science 2021-08-20 Ronald D. R. Pereira , Fabrício Murai

Graphs are fundamental data structures which concisely capture the relational structure in many important real-world domains, such as knowledge graphs, physical and social interactions, language, and chemistry. Here we introduce a powerful…

Machine Learning · Computer Science 2018-03-12 Yujia Li , Oriol Vinyals , Chris Dyer , Razvan Pascanu , Peter Battaglia

Uncovering rationales behind predictions of graph neural networks (GNNs) has received increasing attention over recent years. Instance-level GNN explanation aims to discover critical input elements, like nodes or edges, that the target GNN…

Machine Learning · Computer Science 2023-09-06 Tianxiang Zhao , Dongsheng Luo , Xiang Zhang , Suhang Wang

This paper addresses the challenging problem of retrieval and matching of graph structured objects, and makes two key contributions. First, we demonstrate how Graph Neural Networks (GNN), which have emerged as an effective model for various…

Machine Learning · Computer Science 2019-05-14 Yujia Li , Chenjie Gu , Thomas Dullien , Oriol Vinyals , Pushmeet Kohli

Biomarker discovery from high-throughput transcriptomic data is crucial for advancing precision medicine. However, existing methods often neglect gene-gene regulatory relationships and lack stability across datasets, leading to conflation…

Quantitative Methods · Quantitative Biology 2025-11-18 Chaowang Lan , Jingxin Wu , Yulong Yuan , Chuxun Liu , Huangyi Kang , Caihua Liu

Modeling causal relationships in graph representation learning remains a fundamental challenge. Existing approaches often draw on theories and methods from causal inference to identify causal subgraphs or mitigate confounders. However, due…

Machine Learning · Computer Science 2026-04-13 Hang Gao , Kunyu Li , Huang Hong , Baoquan Cui , Fengge Wu

Graph neural networks (GNNs) have achieved extraordinary enhancements in various areas including the fields medical imaging and network neuroscience where they displayed a high accuracy in diagnosing challenging neurological disorders such…

Machine Learning · Computer Science 2022-09-14 Mehmet Yigit Balik , Arwa Rekik , Islem Rekik

Graph Neural Networks (GNNs) have recently emerged as a robust framework for graph-structured data. They have been applied to many problems such as knowledge graph analysis, social networks recommendation, and even Covid19 detection and…

Software Engineering · Computer Science 2022-01-04 Thanh-Dat Nguyen , Thanh Le-Cong , ThanhVu H. Nguyen , Xuan-Bach D. Le , Quyet-Thang Huynh

In clinical artificial intelligence (AI), graph representation learning, mainly through graph neural networks (GNNs), stands out for its capability to capture intricate relationships within structured clinical datasets. With diverse data --…

Machine Learning · Computer Science 2023-12-13 Ruth Johnson , Michelle M. Li , Ayush Noori , Owen Queen , Marinka Zitnik

Most Graph Neural Networks (GNNs) predict the labels of unseen graphs by learning the correlation between the input graphs and labels. However, by presenting a graph classification investigation on the training graphs with severe bias,…

Machine Learning · Computer Science 2022-09-29 Shaohua Fan , Xiao Wang , Yanhu Mo , Chuan Shi , Jian Tang

Real data collected from different applications that have additional topological structures and connection information are amenable to be represented as a weighted graph. Considering the node labeling problem, Graph Neural Networks (GNNs)…

Social and Information Networks · Computer Science 2020-02-06 Xiaoxiao Li , Joao Saude

Graph Neural Networks (GNNs) have achieved impressive performance in graph-related tasks. However, they suffer from poor generalization on out-of-distribution (OOD) data, as they tend to learn spurious correlations. Such correlations…

Machine Learning · Statistics 2026-03-26 Bowen Lu , Liangqiang Yang , Teng Li

Graph neural networks (GNNs) have emerged as a powerful tool for effectively mining and learning from graph-structured data, with applications spanning numerous domains. However, most research focuses on static graphs, neglecting the…

Machine Learning · Computer Science 2024-04-30 Yanping Zheng , Lu Yi , Zhewei Wei

Causal opacity denotes the difficulty in understanding the "hidden" causal structure underlying the decisions of deep neural network (DNN) models. This leads to the inability to rely on and verify state-of-the-art DNN-based systems,…

Neural-symbolic computing has now become the subject of interest of both academic and industry research laboratories. Graph Neural Networks (GNN) have been widely used in relational and symbolic domains, with widespread application of GNNs…

Artificial Intelligence · Computer Science 2021-06-15 Luis C. Lamb , Artur Garcez , Marco Gori , Marcelo Prates , Pedro Avelar , Moshe Vardi

Graph neural networks (GNN) have shown outstanding applications in many fields where data is fundamentally represented as graphs (e.g., chemistry, biology, recommendation systems). In this vein, communication networks comprise many…

Developing models that can learn to reason is a notoriously challenging problem. We focus on reasoning in relational domains, where the use of Graph Neural Networks (GNNs) seems like a natural choice. However, previous work has shown that…

Artificial Intelligence · Computer Science 2025-03-03 Irtaza Khalid , Steven Schockaert

We present Causal Generative Neural Networks (CGNNs) to learn functional causal models from observational data. CGNNs leverage conditional independencies and distributional asymmetries to discover bivariate and multivariate causal…

Graph neural networks (GNN) represent an emerging line of deep learning models that operate on graph structures. It is becoming more and more popular due to its high accuracy achieved in many graph-related tasks. However, GNN is not as well…

Hardware Architecture · Computer Science 2021-12-28 Zhihui Zhang , Jingwen Leng , Lingxiao Ma , Youshan Miao , Chao Li , Minyi Guo

Graph Neural Networks (GNNs) are able to achieve high classification accuracy on many important real world datasets, but provide no rigorous notion of predictive uncertainty. Quantifying the confidence of GNN models is difficult due to the…

Machine Learning · Statistics 2024-01-10 Jase Clarkson