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.
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.
arXiv:2605. 15511v2 Announce Type: replace Abstract: Graph Neural Networks (GNNs) have become the dominant framework for inductive graph-level learning.
arXiv:2609.39673v1 Announce Type: new Abstract: Can a pretrained graph model replace training and tuning a separate predictor for each dataset? Answering this requires evaluating prediction quality a...
arXiv:2606. 00328v1 Announce Type: new Abstract: Large language models (LLMs) are increasingly used for knowledge base question answering (KBQA), where answering requires selecting entities from a question-specific knowledge-graph subgraph.
The paper introduces PromptGFM, a Graph Foundation Model designed for text‑attributed graphs (TAGs). It integrates Large Language Models (LLMs) and Graph Neural Networks (GNNs) through a Graph Understanding Module that prompts LLMs to emulate GNN workflows, and a Graph Inference Module that creates a language‑based graph vocabulary for better alignment and scalability. Experiments show PromptGFM outperforms existing methods and transfers effectively across various graphs and tasks.
arXiv:2607. 17272v1 Announce Type: new Abstract: Node representation learning has advanced rapidly, yet most existing methods rely on per-dataset training and hyperparameter tuning.
arXiv:2609.37604v1 Announce Type: new Abstract: Graph foundation models need a discrete token representation, but casting a graph as a generatable token sequence faces a structural obstacle: edges sp...
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%.
arXiv:2608. 12391v1 Announce Type: cross Abstract: Graph reasoning provides a promising testbed for evaluating the reasoning ability of large language models (LLMs), as graph instances can be programmatically generated, structurally controlled, and naturally scaled to long-input settings.
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.
arXiv:2602. 11641v2 Announce Type: replace Abstract: Text-attributed graphs (TAGs) associate nodes with textual attributes and graph structure, enabling GNNs to jointly model semantic and structural information.
arXiv:2607. 20477v1 Announce Type: new Abstract: {\em Text-Attributed Graphs} (TAGs) have emerged as an expressive data model for integrating graph topology with rich textual semantics.
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...