A comprehensive survey on deep graph representation learning

W Ju, Z Fang, Y Gu, Z Liu, Q Long, Z Qiao, Y Qin… - Neural Networks, 2024 - Elsevier
Graph representation learning aims to effectively encode high-dimensional sparse graph-
structured data into low-dimensional dense vectors, which is a fundamental task that has …

Towards graph foundation models: A survey and beyond

J Liu, C Yang, Z Lu, J Chen, Y Li, M Zhang… - arxiv preprint arxiv …, 2023 - arxiv.org
Foundation models have emerged as critical components in a variety of artificial intelligence
applications, and showcase significant success in natural language processing and several …

Gpt4rec: Graph prompt tuning for streaming recommendation

P Zhang, Y Yan, X Zhang, L Kang, C Li… - Proceedings of the 47th …, 2024 - dl.acm.org
In the realm of personalized recommender systems, the challenge of adapting to evolving
user preferences and the continuous influx of new users and items is paramount …

How do large language models understand genes and cells

C Fang, Y Wang, Y Song, Q Long, W Lu… - ACM Transactions on …, 2024 - dl.acm.org
Researching genes and their interactions is crucial for deciphering the fundamental laws of
cellular activity, advancing disease treatment, drug discovery, and more. Large language …

GFT: Graph Foundation Model with Transferable Tree Vocabulary

Z Wang, Z Zhang, NV Chawla, C Zhang… - arxiv preprint arxiv …, 2024 - arxiv.org
Inspired by the success of foundation models in applications such as ChatGPT, as graph
data has been ubiquitous, one can envision the far-reaching impacts that can be brought by …

A Survey on Learning from Graphs with Heterophily: Recent Advances and Future Directions

C Gong, Y Cheng, J Yu, C Xu, C Shan, S Luo… - arxiv preprint arxiv …, 2024 - arxiv.org
Graphs are structured data that models complex relations between real-world entities.
Heterophilic graphs, where linked nodes are prone to be with different labels or dissimilar …

Refining computational inference of gene regulatory networks: integrating knockout data within a multi-task framework

W Cui, Q Long, M **ao, X Wang, G Feng… - Briefings in …, 2024 - academic.oup.com
Constructing accurate gene regulatory network s (GRNs), which reflect the dynamic
governing process between genes, is critical to understanding the diverse cellular process …

MOAT: Graph prompting for 3D molecular graphs

Q Long, Y Yan, W Cui, W Ju, Z Zhu, Y Zhou… - Proceedings of the 33rd …, 2024 - dl.acm.org
Molecular property prediction stands as a cornerstone task in AI-driven drug design and
discovery, wherein the atoms within a molecule serve as nodes, collectively forming a graph …

PIXEL: Prompt-based Zero-shot Hashing via Visual and Textual Semantic Alignment

Z Dong, Q Long, Y Zhou, P Wang, Z Zhu… - Proceedings of the 33rd …, 2024 - dl.acm.org
Zero-Shot Hashing (ZSH) has aroused significant attention due to its efficiency and
generalizability in multi-modal retrieval scenarios, which aims to encode semantic …

DAGPrompT: Pushing the Limits of Graph Prompting with a Distribution-aware Graph Prompt Tuning Approach

Q Chen, L Wang, B Zheng, G Song - arxiv preprint arxiv:2501.15142, 2025 - arxiv.org
The pre-train then fine-tune approach has advanced GNNs by enabling general knowledge
capture without task-specific labels. However, an objective gap between pre-training and …