The paper presents a comparative analysis of six state‑of‑the‑art counterfactual explainers for graph neural networks, focusing on methods that can both add and remove edges to alter model predictions. It evaluates these explainers across diverse real‑world and synthetic datasets, covering binary and multi‑class graph and node classification tasks, using a range of quantitative and qualitative metrics. The study highlights the trade‑offs between explanation size, coverage, and quality, aiming to pinpoint each method’s strengths and weaknesses to inform future research.
By Maria Myrto Villia, Filippos Gouidis, Theodore Patkos, Panos Trahanias
arXiv:2608. 11431v1 Announce Type: new Abstract: Graph learning presupposes a graph, and tables and relational databases do not come with one.
By Tamara Cucumides, Floris Geerts
HyGRAIL is a framework for discovering scientific hypotheses in incomplete knowledge graphs by combining a graph neural network (GNN) triage with large language model (LLM) review. The GNN scores candidate hypotheses and routes only ambiguous cases to the LLM, which receives structured evidence from the graph converted into natural language. Experiments on MatKG show HyGRAIL achieves the highest F1 score, improves over baselines, and cuts LLM calls by over 54%.
By Yihang Sun, Zhihan Zhu, Zhiyuan Jiang, Jingyi Ge, Zixuan Li, Jiaxuan You
The paper introduces a method that transforms knowledge graph facts into a fixed vocabulary representation, where each fact becomes a node linked to its subject, object, and relation type via six meta-relations. Using this representation, standard GNNs (e.g., GAT, GINE, GraphSAGE, R-GCN) trained on a single small graph can achieve zero‑shot link prediction on 40 inductive benchmarks, matching the performance of specialized foundation models like ULTRA. The approach also generalizes to relational databases, enabling foreign‑key prediction without cell values or schema text, and the authors provide code, checkpoints, and evaluation tools for all benchmarks.
By Camille Pradel
Euston is an 8‑B parameter mathematical claim‑verification model that resists producing false derivations when presented with corrupted theorems. It was trained on 3,026 matched true/corrupted statement pairs generated by GraphSynth, a probabilistic factor‑graph generator, and fine‑tuned from DeepSeek‑R1‑8B using GRPO. On a balanced held‑out split, Euston’s balanced accuracy rose from 29.50 % to 63.75 %, and its discrimination gap improved from –0.5 % to +27.5 %, while maintaining comparable general mathematical ability and reducing response length and truncation rates.
By Zehua Cheng, Wei Dai, Jiahao Sun
Scientific knowledge graphs organize entities and relations extracted from scientific literature, but they remain inherently incomplete. Missing typed links in such graphs can therefore represent plau...
The paper investigates a failure mode in Graph-JEPA, a joint‑embedding predictive model trained on a large scientific‑reasoning graph. Despite achieving high linear‑probe accuracy and effective rank, the learned representation contains almost no usable instance information, as shown by retrieval metrics. The authors diagnose the issue to variance allocation in the objective, propose a repair that restores near‑perfect information recovery, and demonstrate that the problem persists even after repair, highlighting limitations in the evaluation metrics used.
By Gollam Rabby, S\"oren Auer
arXiv:2606. 11562v1 Announce Type: new Abstract: Graph analysis underlies many applications whose answers cannot be looked up in a single record or retrieved along a path: laundering rings, drug repurposing, user preference, and scientific theme are all inferred from a node together with its neighbourhood.
By Zhuoyi Peng, Jingzhou Jiang, Hanlin Gu, Lixin Fan, Yi Yang
arXiv:2607. 27905v1 Announce Type: new Abstract: Counterfactual explanations (CFEs) enhance the interpretability of black-box models by generating alternative instances with adjusted feature values that achieve a contrastive outcome.
By Muhammad Adil Saleem, Syed Ali Raza, Mary-Anne Williams
arXiv:2606. 14476v1 Announce Type: new Abstract: A growing line of work equips large language model (LLM) agents with graph neural networks (GNNs) as callable tools, assuming the agent exercises judgment over when and how much to rely on such a tool.
By Zhongyuan Wang, Pratyusha Vemuri
arXiv:2608. 12083v1 Announce Type: cross Abstract: Graph Neural Networks (GNNs) achieve strong predictive performance on graph-structured data across domains such as chemistry, biology, and network analysis, yet they provide no intrinsic explanation of their predictions.
By David Bechtoldt, Sidney Bender
arXiv:2608. 18242v1 Announce Type: new Abstract: We introduce ClosureBench, a constructive benchmark for compositional graph-relational reasoning with programmatically verified ground truth.
By Stefano Goria (AIM Research Lab)