Evaluating graph neural networks for link prediction: Current pitfalls and new benchmarking

J Li, H Shomer, H Mao, S Zeng, Y Ma… - Advances in …, 2024 - proceedings.neurips.cc
Link prediction attempts to predict whether an unseen edge exists based on only a portion of
the graph. A flurry of methods has been created in recent years that attempt to make use of …

Revisiting link prediction: A data perspective

H Mao, J Li, H Shomer, B Li, W Fan, Y Ma… - arXiv preprint arXiv …, 2023 - arxiv.org
Link prediction, a fundamental task on graphs, has proven indispensable in various
applications, eg, friend recommendation, protein analysis, and drug interaction prediction …

Artificial Intelligence for Complex Network: Potential, Methodology and Application

J Ding, C Liu, Y Zheng, Y Zhang, Z Yu, R Li… - arXiv preprint arXiv …, 2024 - arxiv.org
Complex networks pervade various real-world systems, from the natural environment to
human societies. The essence of these networks is in their ability to transition and evolve …

Graph foundation models

H Mao, Z Chen, W Tang, J Zhao, Y Ma, T Zhao… - arXiv preprint arXiv …, 2024 - arxiv.org
Graph Foundation Model (GFM) is a new trending research topic in the graph domain,
aiming to develop a graph model capable of generalizing across different graphs and tasks …

A topological perspective on demystifying gnn-based link prediction performance

Y Wang, T Zhao, Y Zhao, Y Liu, X Cheng… - arXiv preprint arXiv …, 2023 - arxiv.org
Graph Neural Networks (GNNs) have shown great promise in learning node embeddings for
link prediction (LP). While numerous studies aim to improve the overall LP performance of …

Universal link predictor by In-context Learning

K Dong, H Mao, Z Guo, NV Chawla - arXiv preprint arXiv:2402.07738, 2024 - arxiv.org
Link prediction is a crucial task in graph machine learning, where the goal is to infer missing
or future links within a graph. Traditional approaches leverage heuristic methods based on …

[HTML][HTML] A variational expectation-maximization framework for balanced multi-scale learning of protein and drug interactions

J Rao, J Xie, Q Yuan, D Liu, Z Wang, Y Lu… - Nature …, 2024 - nature.com
Protein functions are characterized by interactions with proteins, drugs, and other
biomolecules. Understanding these interactions is essential for deciphering the molecular …

Pitfalls in link prediction with graph neural networks: Understanding the impact of target-link inclusion & better practices

J Zhu, Y Zhou, VN Ioannidis, S Qian, W Ai… - Proceedings of the 17th …, 2024 - dl.acm.org
While Graph Neural Networks (GNNs) are remarkably successful in a variety of high-impact
applications, we demonstrate that, in link prediction, the common practices of including the …

Structure-aware Semantic Node Identifiers for Learning on Graphs

Y Luo, Q Liu, L Shi, XM Wu - arXiv preprint arXiv:2405.16435, 2024 - arxiv.org
We present a novel graph tokenization framework that generates structure-aware, semantic
node identifiers (IDs) in the form of a short sequence of discrete codes, serving as symbolic …

Edge contrastive learning for link prediction

L Liu, Q Xie, W Wen, J Zhu, M Peng - Information Processing & …, 2024 - Elsevier
Link prediction is a critical task within the realm of graph machine learning. While recent
advancements mainly emphasize node representation learning, the rich information …