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In this work, we benchmark a variety of single- and multi-task graph neural network (GNN) models against lower-bar and higher-bar traditional machine learning approaches employing human engineered molecular features. We consider four GNN…

Quantitative Methods · Quantitative Biology 2022-02-28 Fabio Broccatelli , Richard Trager , Michael Reutlinger , George Karypis , Mufei Li

Boolean satisfiability (SAT) problem, the first problem proven to be NP-complete, has become a fundamental challenge in computational complexity, with widespread applications in optimization and verification across many domains. Despite…

Logic in Computer Science · Computer Science 2026-04-01 Curie Kim , Carsten Portner , Mingju Liu , Steve Dai , Haoxing Ren , Brucek Khailany , Alvaro Velasquez , Ismail Alkhouri , Cunxi Yu

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

Code search aims to retrieve accurate code snippets based on a natural language query to improve software productivity and quality. With the massive amount of available programs such as (on GitHub or Stack Overflow), identifying and…

Software Engineering · Computer Science 2023-02-14 Shangqing Liu , Xiaofei Xie , Jingkai Siow , Lei Ma , Guozhu Meng , Yang Liu

Recent studies have shown that graph neural networks (GNNs) exhibit strong biases towards the node degree: they usually perform satisfactorily on high-degree nodes with rich neighbor information but struggle with low-degree nodes. Existing…

Machine Learning · Computer Science 2023-10-03 Mingxuan Ju , Tong Zhao , Wenhao Yu , Neil Shah , Yanfang Ye

Graph Neural Networks (GNNs) have emerged as the de facto standard for representation learning on graphs, owing to their ability to effectively integrate graph topology and node attributes. However, the inherent suboptimal nature of node…

Machine Learning · Computer Science 2023-12-27 Zhiyao Zhou , Sheng Zhou , Bochao Mao , Xuanyi Zhou , Jiawei Chen , Qiaoyu Tan , Daochen Zha , Yan Feng , Chun Chen , Can Wang

We propose a novel benchmarking methodology for graph neural networks (GNNs) based on the graph alignment problem, a combinatorial optimization task that generalizes graph isomorphism by aligning two unlabeled graphs to maximize overlapping…

Machine Learning · Computer Science 2025-05-20 Adrien Lagesse , Marc Lelarge

Graph-structured data exhibits universality and widespread applicability across diverse domains, such as social network analysis, biochemistry, financial fraud detection, and network security. Significant strides have been made in…

Machine Learning · Computer Science 2025-11-06 Wei Ju , Siyu Yi , Yifan Wang , Zhiping Xiao , Zhengyang Mao , Hourun Li , Yiyang Gu , Yifang Qin , Nan Yin , Senzhang Wang , Xinwang Liu , Philip S. Yu , Ming Zhang

Graph neural networks (GNNs) have brought revolutionary advancements to the field of link prediction (LP), providing powerful tools for mining potential relationships in graphs. However, existing methods face challenges when dealing with…

Machine Learning · Computer Science 2025-12-30 Huashen Lu , Wensheng Gan , Guoting Chen , Zhichao Huang , Philip S. Yu

In recent years, owing to the outstanding performance in graph representation learning, graph neural network (GNN) techniques have gained considerable interests in many real-world scenarios, such as recommender systems and social networks.…

Machine Learning · Computer Science 2021-12-09 Weibin Li , Mingkai He , Zhengjie Huang , Xianming Wang , Shikun Feng , Weiyue Su , Yu Sun

Graph Neural Networks (GNNs) have been extensively used for mining graph-structured data with impressive performance. However, because these traditional GNNs do not distinguish among various downstream tasks, embeddings embedded by them are…

Machine Learning · Computer Science 2024-09-20 Jianpeng Chen , Yujing Wang , Ming Zeng , Zongyi Xiang , Bitan Hou , Yunhai Tong , Ole J. Mengshoel , Yazhou Ren

The remarkable achievements of machine learning techniques in analyzing discrete structures have drawn significant attention towards their integration into combinatorial optimization algorithms. Typically, these methodologies improve…

Artificial Intelligence · Computer Science 2024-02-07 Abdelrahman Hosny , Sherief Reda

Graph Neural Networks (GNNs) have achieved great success on a node classification task. Despite the broad interest in developing and evaluating GNNs, they have been assessed with limited benchmark datasets. As a result, the existing…

Machine Learning · Computer Science 2022-12-29 Seiji Maekawa , Koki Noda , Yuya Sasaki , Makoto Onizuka

Semi-supervised node classification in graphs is a fundamental problem in graph mining, and the recently proposed graph neural networks (GNNs) have achieved unparalleled results on this task. Due to their massive success, GNNs have…

Machine Learning · Computer Science 2019-06-19 Oleksandr Shchur , Maximilian Mumme , Aleksandar Bojchevski , Stephan Günnemann

Graph Neural Networks (GNNs) have achieved remarkable success in various graph-based learning tasks. While their performance is often attributed to the powerful neighborhood aggregation mechanism, recent studies suggest that other…

Machine Learning · Computer Science 2024-12-11 Yushun Dong , Patrick Soga , Yinhan He , Song Wang , Jundong Li

Graph neural networks (GNNs) are emerging for machine learning research on graph-structured data. GNNs achieve state-of-the-art performance on many tasks, but they face scalability challenges when it comes to real-world applications that…

Machine Learning · Computer Science 2026-04-02 Shichang Zhang , Atefeh Sohrabizadeh , Cheng Wan , Zijie Huang , Ziniu Hu , Yewen Wang , Yingyan , Lin , Jason Cong , Yizhou Sun

Graph Convolutional Networks (GCNs) are powerful models for learning representations of attributed graphs. To scale GCNs to large graphs, state-of-the-art methods use various layer sampling techniques to alleviate the "neighbor explosion"…

Machine Learning · Computer Science 2020-02-18 Hanqing Zeng , Hongkuan Zhou , Ajitesh Srivastava , Rajgopal Kannan , Viktor Prasanna

Boolean satisfiability (SAT) is a fundamental NP-complete problem with many applications, including automated planning and scheduling. To solve large instances, SAT solvers have to rely on heuristics, e.g., choosing a branching variable in…

Artificial Intelligence · Computer Science 2023-07-19 Mikhail Shirokikh , Ilya Shenbin , Anton Alekseev , Sergey Nikolenko

Graph Neural Networks (GNNs) are exemplary deep models designed for graph data. Message passing mechanism enables GNNs to effectively capture graph topology and push the performance boundaries across various graph tasks. However, the trend…

Neural and Evolutionary Computing · Computer Science 2025-09-29 Huizhe Zhang , Jintang Li , Yuchang Zhu , Liang Chen , Li Kuang

The Boolean SATisfiability problem (SAT) is of central importance in computer science. Although SAT is known to be NP-complete, progress on the engineering side, especially that of Conflict-Driven Clause Learning (CDCL) and Local Search SAT…

Logic in Computer Science · Computer Science 2020-02-25 Anastasios Kyrillidis , Anshumali Shrivastava , Moshe Y. Vardi , Zhiwei Zhang