Pre-training with Graph Transformers

ALINC: Active Learning for Inductive Node Classification via Graph Sampling

arXiv:2606. 04647v1 Announce Type: new Abstract: Active learning (AL) for node classification typically focuses on selecting the most informative nodes for annotation within one or a few large graphs (e.

OgBench: A Framework for Evaluating Graph Neural Networks on Omics Data

arXiv:2605. 15511v2 Announce Type: replace Abstract: Graph Neural Networks (GNNs) have become the dominant framework for inductive graph-level learning.

Graph Classification with Transformers

Graph-dependent pooling: adaptive granularity in hierarchical graph neural networks

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.

Handling Feature Heterogeneity with Learnable Graph Patches

arXiv:2606. 17667v1 Announce Type: cross Abstract: In recent years, the rapid development of foundation models and graph pre-training technologies has spurred increasing interest in constructing a universal pre-trained graph model or Graph Foundation Model (GFM).

Benchmarking graph-based models for in-silico toxicity prediction in drug discovery

arXiv:2609.37555v1 Announce Type: new Abstract: Drug discovery is a costly and high-risk process, where toxicity-related failures remain a major cause of attrition in both preclinical and clinical st...