Graph-Dependent Pooling (GDPool) introduces a dynamic approach to hierarchical graph pooling, allowing each graph to determine its own pooling granularity rather than relying on fixed cluster numbers or ratios. The method employs self-attention to select graph-specific anchors and uses soft node assignment to build coarser graphs, addressing optimization conflicts identified through gradient alignment analysis. Experiments on metal‑organic framework and molecular graph datasets demonstrate that GDPool outperforms existing methods in predictive accuracy, modularity, and exhibits stable behavior across various hyperparameters.
By Bohan Yoon, Hyejin Jang
arXiv:2607. 03097v1 Announce Type: new Abstract: Heterogeneous Graph Neural Networks (HGNNs) have exhibited remarkable efficacy in modeling complex systems with multiple types of nodes and relations, yet their training on large-scale heterogeneous graphs remains computationally prohibitive.
By Fuyan Ou, Yulin Hu, Ye Yuan
arXiv:2606. 19374v1 Announce Type: cross Abstract: Graph-based representations are widely used in protein modeling, yet many existing approaches rely primarily on sequence adjacency or geometric proximity, which only partially reflect the principles governing protein folding.
By Mohamed Mouhajir, Limei Wang, El Houcine Bergou, Hajar El Hammouti, Lamiae Azizi, Dongqi Fu
arXiv:2605. 15511v2 Announce Type: replace Abstract: Graph Neural Networks (GNNs) have become the dominant framework for inductive graph-level learning.
By Louisa Cornelis, Johan Mathe, Louis Van Langendonck, Guillermo Bern\'ardez, Nina Miolane
arXiv:2510. 04567v3 Announce Type: replace-cross Abstract: Graph Neural Networks (GNNs) are powerful tools for processing relational data but often struggle to generalize to unseen graphs, giving rise to the development of Graph Foundational Models (GFMs).
By Weishuo Ma, Yanbo Wang, Xiyuan Wang, Lei Zou, Muhan Zhang
arXiv:2606. 29773v1 Announce Type: new Abstract: Graphs are widely used to model relational systems, with applications in domains such as social networks, finance, and biomedicine.
By Haoxin Sun, Yiqing Lin, Yajun Huang, Chenhui Dong, Mingjun Li, Zhongzhi Zhang
The paper introduces Topology-Preserving Adaptive Graph Pooling (TPAGP), a method that partitions graphs into granular balls by combining node features and topology to create multi-granularity representations. TPAGP captures both global and local structural patterns, unlike prior pooling methods that coarsen graphs by removing or clustering nodes. Experiments show TPAGP outperforms existing pooling techniques on benchmark datasets, reducing information loss from fixed-granularity strategies.
By Sen Zhao, Gaojie Xu, Shuyin Xia, Yifan Guan, Yi Liu, Yi Wang, Wei Wang
arXiv:2609.37057v1 Announce Type: new
Abstract: Achieving strong performance with graph neural networks (GNNs) typically requires training and hyperparameter tuning for each dataset, incurring repeat...
By Dooho Lee, Jinmo Lee, Minho Jeong, Kijung Shin, Jaemin Yoo
arXiv:2606. 05116v1 Announce Type: new Abstract: We introduce the Graph Set Transformer (GST), a neural network architecture for learning on sets of graphs, designed for tasks in which per-element predictions depend on set-wide context as well as local structure.
By Jose E. Escrig Molina, Baoquan Chen, Daniel Probst
arXiv:2606. 08491v1 Announce Type: new Abstract: Relational deep learning (RDL) converts relational databases (RDBs) into heterogeneous graphs, but graphs derived directly from database schemas are often not well suited for how graph neural networks (GNNs) perform relational reasoning.
By Yao Cheng, Siqiang Luo
arXiv:2602.23566v4 Announce Type: replace-cross
Abstract: We study generative modeling of graphs with recurring subgraph motifs. We propose Flowette, a continuous flow matching framework that employs...
By Asiri Wijesinghe, Sevvandi Kandanaarachchi, Daniel M. Steinberg, Cheng Soon Ong
arXiv:2608. 02128v1 Announce Type: new Abstract: Training Graph Neural Networks on large graphs is challenged by the memory cost of storing all node representations across layers.
By Antonin Joly, Nicolas Keriven, Aline Roumy