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Machine learning, and representation learning in particular, has the potential to facilitate drug discovery by screening a large chemical space in silico. A successful approach for representing molecules is to treat them as a graph and…

Chemical Physics · Physics 2023-10-06 Ronen Taub , Yonatan Savir

Graph neural networks (GNNs) build on the success of deep learning models by extending them for use in graph spaces. Transfer learning has proven extremely successful for traditional deep learning problems: resulting in faster training and…

Machine Learning · Computer Science 2022-02-03 Nishai Kooverjee , Steven James , Terence van Zyl

We consider a setting where multiple entities inter-act with each other over time and the time-varying statuses of the entities are represented as multiple correlated time series. For example, speed sensors are deployed in different…

Machine Learning · Computer Science 2021-03-23 Razvan-Gabriel Cirstea , Chenjuan Guo , Bin Yang

Numerous subgraph-enhanced graph neural networks (GNNs) have emerged recently, provably boosting the expressive power of standard (message-passing) GNNs. However, there is a limited understanding of how these approaches relate to each other…

Machine Learning · Computer Science 2022-10-18 Chendi Qian , Gaurav Rattan , Floris Geerts , Christopher Morris , Mathias Niepert

Node embeddings have become an ubiquitous technique for representing graph data in a low dimensional space. Graph autoencoders, as one of the widely adapted deep models, have been proposed to learn graph embeddings in an unsupervised way by…

Machine Learning · Computer Science 2019-08-13 Vaibhav , Po-Yao Huang , Robert Frederking

Variants of Graph Neural Networks (GNNs) for representation learning have been proposed recently and achieved fruitful results in various fields. Among them, Graph Attention Network (GAT) first employs a self-attention strategy to learn…

Machine Learning · Computer Science 2021-07-28 Heng Chang , Yu Rong , Tingyang Xu , Wenbing Huang , Somayeh Sojoudi , Junzhou Huang , Wenwu Zhu

Graph neural networks (GNN) has been successfully applied to operate on the graph-structured data. Given a specific scenario, rich human expertise and tremendous laborious trials are usually required to identify a suitable GNN architecture.…

Machine Learning · Computer Science 2019-09-11 Kaixiong Zhou , Qingquan Song , Xiao Huang , Xia Hu

Graph neural networks (GNNs) are a class of powerful machine learning tools that model node relations for making predictions of nodes or links. GNN developers rely on quantitative metrics of the predictions to evaluate a GNN, but similar to…

Machine Learning · Computer Science 2025-07-08 Zipeng Liu , Yang Wang , Jürgen Bernard , Tamara Munzner

Learning community structures in graphs has broad applications across scientific domains. While graph neural networks (GNNs) have been successful in encoding graph structures, existing GNN-based methods for community detection are limited…

Machine Learning · Statistics 2024-08-05 Yueqi Wang , Yoonho Lee , Pallab Basu , Juho Lee , Yee Whye Teh , Liam Paninski , Ari Pakman

A fundamental computation for statistical inference and accurate decision-making is to compute the marginal probabilities or most probable states of task-relevant variables. Probabilistic graphical models can efficiently represent the…

Machine Learning · Computer Science 2019-06-28 KiJung Yoon , Renjie Liao , Yuwen Xiong , Lisa Zhang , Ethan Fetaya , Raquel Urtasun , Richard Zemel , Xaq Pitkow

Graph Neural Networks (GNNs) typically scale with the number of graph edges, making them well suited for sparse graphs but less efficient on dense graphs, such as point clouds or molecular interactions. A common remedy is to sparsify the…

Machine Learning · Computer Science 2025-12-03 Shiyu Chen , Ningyuan Huang , Soledad Villar

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

Approximate Nearest Neighbor Search (ANNS) in high-dimensional spaces finds extensive applications in databases, information retrieval, recommender systems, etc. While graph-based methods have emerged as the leading solution for ANNS due to…

Databases · Computer Science 2025-06-23 Jiancheng Ruan , Tingyang Chen , Renchi Yang , Xiangyu Ke , Yunjun Gao

Graph neural networks (GNNs) are important tools for transductive learning tasks, such as node classification in graphs, due to their expressive power in capturing complex interdependency between nodes. To enable graph neural network…

Machine Learning · Computer Science 2022-05-17 Man Wu , Shirui Pan , Lan Du , Xingquan Zhu

Node classification in attributed graphs is an important task in multiple practical settings, but it can often be difficult or expensive to obtain labels. Active learning can improve the achieved classification performance for a given…

Machine Learning · Computer Science 2020-07-13 Florence Regol , Soumyasundar Pal , Yingxue Zhang , Mark Coates

Graph Neural Networks (GNNs) have demonstrated impressive performance across diverse graph-based tasks by leveraging message passing to capture complex node relationships. However, on large-scale real-world graphs, GNNs face two major…

Machine Learning · Computer Science 2026-03-10 Xiang Li , Jianpeng Qi , Haobing Liu , Yuan Cao , Guoqing Chao , Zhongying Zhao , Junyu Dong , Xinwang Liu , Yanwei Yu

Knowledge Graphs (KGs) have shown great success in recommendation. This is attributed to the rich attribute information contained in KG to improve item and user representations as side information. However, existing knowledge-aware methods…

Information Retrieval · Computer Science 2021-12-20 Zepeng Huai , Jianhua Tao , Feihu Che , Guohua Yang , Dawei Zhang

In light of the recent success of Graph Neural Networks (GNNs) and their ability to perform inference on complex data structures, many studies apply GNNs to the task of text classification. In most previous methods, a heterogeneous graph,…

Machine Learning · Computer Science 2024-10-29 Yassine Abbahaddou , Johannes F. Lutzeyer , Michalis Vazirgiannis

Since their introduction, graph attention networks achieved outstanding results in graph representation learning tasks. However, these networks consider only pairwise relationships among nodes and then they are not able to fully exploit…

Machine Learning · Computer Science 2022-09-20 Lorenzo Giusti , Claudio Battiloro , Lucia Testa , Paolo Di Lorenzo , Stefania Sardellitti , Sergio Barbarossa

Graph Convolutional Networks (GCNs) are a popular method from graph representation learning that have proved effective for tasks like node classification tasks. Although typical GCN models focus on classifying nodes within a static graph,…

Machine Learning · Computer Science 2021-10-13 Yucai Fan , Yuhang Yao , Carlee Joe-Wong
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