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Proteins play a vital role in biological processes and are indispensable for living organisms. Accurate representation of proteins is crucial, especially in drug development. Recently, there has been a notable increase in interest in…

生物大分子 · 定量生物学 2026-05-28 Dan Kalifa , Uriel Singer , Kira Radinsky

Graph Neural Networks (GNNs) have become a powerful tool for modeling and analyzing data with graph structures. The wide adoption in numerous applications underscores the value of these models. However, the complexity of these methods often…

人工智能 · 计算机科学 2025-12-10 Tien Cuong Bui

Graph Neural Networks (GNNs) are neural models that leverage the dependency structure in graphical data via message passing among the graph nodes. GNNs have emerged as pivotal architectures in analyzing graph-structured data, and their…

机器学习 · 计算机科学 2024-03-19 Xu Zheng , Farhad Shirani , Tianchun Wang , Wei Cheng , Zhuomin Chen , Haifeng Chen , Hua Wei , Dongsheng Luo

Graph neural networks (GNNs) have recently achieved state-of-the-art performance in many graph-based applications. Despite the high expressive power, they typically need to perform an expensive recursive neighborhood expansion in multiple…

机器学习 · 计算机科学 2022-06-10 Wentao Zhang , Ziqi Yin , Zeang Sheng , Wen Ouyang , Xiaosen Li , Yangyu Tao , Zhi Yang , Bin Cui

With the rapid deployment of graph neural networks (GNNs) based techniques into a wide range of applications such as link prediction, node classification, and graph classification the explainability of GNNs has become an indispensable…

机器学习 · 计算机科学 2023-01-03 Yiqiao Li , Jianlong Zhou , Boyuan Zheng , Fang Chen

Graph Neural Networks (GNNs) are proficient in graph representation learning and achieve promising performance on versatile tasks such as node classification and link prediction. Usually, a comprehensive hyperparameter tuning is essential…

机器学习 · 计算机科学 2024-10-10 Lequan Lin , Dai Shi , Andi Han , Zhiyong Wang , Junbin Gao

Interpretability has emerged as a crucial aspect of building trust in machine learning systems, aimed at providing insights into the working of complex neural networks that are otherwise opaque to a user. There are a plethora of existing…

机器学习 · 统计学 2021-01-19 Rushil Anirudh , Jayaraman J. Thiagarajan , Rahul Sridhar , Peer-Timo Bremer

Graph neural network (GNN) pre-training methods have been proposed to enhance the power of GNNs. Specifically, a GNN is first pre-trained on a large-scale unlabeled graph and then fine-tuned on a separate small labeled graph for downstream…

机器学习 · 计算机科学 2022-09-16 Simiao Zuo , Haoming Jiang , Qingyu Yin , Xianfeng Tang , Bing Yin , Tuo Zhao

Graph neural networks (GNNs) have been widely used in graph-structured data computation, showing promising performance in various applications such as node classification, link prediction, and network recommendation. Existing works mainly…

机器学习 · 计算机科学 2023-02-07 Houyi Li , Zhihong Chen , Zhao Li , Qinkai Zheng , Peng Zhang , Shuigeng Zhou

Explaining machine learning models is an important and increasingly popular area of research interest. The Shapley value from game theory has been proposed as a prime approach to compute feature importance towards model predictions on…

机器学习 · 计算机科学 2023-01-02 Shichang Zhang , Yozen Liu , Neil Shah , Yizhou Sun

Finding the biomarkers associated with ASD is helpful for understanding the underlying roots of the disorder and can lead to earlier diagnosis and more targeted treatment. A promising approach to identify biomarkers is using Graph Neural…

机器学习 · 计算机科学 2019-07-15 Xiaoxiao Li , Nicha C. Dvornek , Yuan Zhou , Juntang Zhuang , Pamela Ventola , James S. Duncan

Graph Convolutional Neural Networks (GCNNs) are generalizations of CNNs to graph-structured data, in which convolution is guided by the graph topology. In many cases where graphs are unavailable, existing methods manually construct graphs…

机器学习 · 计算机科学 2019-09-17 Xiang Gao , Wei Hu , Zongming Guo

Distinguishing the automorphic equivalence of nodes in a graph plays an essential role in many scientific domains, e.g., computational biologist and social network analysis. However, existing graph neural networks (GNNs) fail to capture…

机器学习 · 计算机科学 2021-11-10 Fengli Xu , Quanming Yao , Pan Hui , Yong Li

Graph neural networks (GNNs) have shown advantages in graph-based analysis tasks. However, most existing methods have the homogeneity assumption and show poor performance on heterophilic graphs, where the linked nodes have dissimilar…

机器学习 · 计算机科学 2024-04-16 Tianhao Peng , Wenjun Wu , Haitao Yuan , Zhifeng Bao , Zhao Pengrui , Xin Yu , Xuetao Lin , Yu Liang , Yanjun Pu

Graph Neural Networks (GNNs) have achieved notable success in the analysis of non-Euclidean data across a wide range of domains. However, their applicability is constrained by the dependence on the observed graph structure. To solve this…

机器学习 · 计算机科学 2024-09-19 Ziyan Wang , Yaxuan He , Bin Liu

Enhancing the interpretability of graph neural networks (GNNs) is crucial to ensure their safe and fair deployment. Recent work has introduced self-explainable GNNs that generate explanations as part of training, improving both faithfulness…

机器学习 · 计算机科学 2025-08-18 Fanzhen Liu , Xiaoxiao Ma , Jian Yang , Alsharif Abuadbba , Kristen Moore , Surya Nepal , Cecile Paris , Quan Z. Sheng , Jia Wu

Similarity search is a fundamental task for exploiting information in various applications dealing with graph data, such as citation networks or knowledge graphs. While this task has been intensively approached from heuristics to graph…

机器学习 · 计算机科学 2026-05-12 Daniel Daza , Cuong Xuan Chu , Trung-Kien Tran , Daria Stepanova , Michael Cochez , Paul Groth

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) have shown remarkable effectiveness in capturing abundant information in graph-structured data. However, the black-box nature of GNNs hinders users from understanding and trusting the models, thus leading to…

机器学习 · 计算机科学 2022-07-25 Jiaxuan Xie , Yezi Liu , Yanning Shen

Graph Neural Networks (GNNs) have demonstrated remarkable efficacy in handling graph-structured data; however, they exhibit failures after deployment, which can cause severe consequences. Hence, conducting thorough testing before deployment…

软件工程 · 计算机科学 2025-12-23 Lichen Yang , Qiang Wang , Zhonghao Yang , Daojing He , Yu Li