Xingyue Huang

Xingyue Huang, Miguel Romero Orth, İsmail İlkan Ceylan et al.

Graph neural networks are prominent models for representation learning over graph-structured data. While the capabilities and limitations of these models are well-understood for simple graphs, our understanding remains incomplete in the context of knowledge graphs. Our goal is to provide a systematic understanding of the landscape of graph neural networks for knowledge graphs pertaining to the prominent task of link prediction. Our analysis entails a unifying perspective on seemingly unrelated models and unlocks a series of other models. The expressive power of various models is characterized via a corresponding relational Weisfeiler-Leman algorithm. This analysis is extended to provide a precise logical characterization of the class of functions captured by a class of graph neural networks. The theoretical findings presented in this paper explain the benefits of some widely employed practical design choices, which are validated empirically.

Ben Finkelshtein, Xingyue Huang, Michael Bronstein et al.

Graph neural networks are popular architectures for graph machine learning, based on iterative computation of node representations of an input graph through a series of invariant transformations. A large class of graph neural networks follow a standard message-passing paradigm: at every layer, each node state is updated based on an aggregate of messages from its neighborhood. In this work, we propose a novel framework for training graph neural networks, where every node is viewed as a player that can choose to either 'listen', 'broadcast', 'listen and broadcast', or to 'isolate'. The standard message propagation scheme can then be viewed as a special case of this framework where every node 'listens and broadcasts' to all neighbors. Our approach offers a more flexible and dynamic message-passing paradigm, where each node can determine its own strategy based on their state, effectively exploring the graph topology while learning. We provide a theoretical analysis of the new message-passing scheme which is further supported by an extensive empirical analysis on a synthetic dataset and on real-world datasets.

Krzysztof Olejniczak, Xingyue Huang, Mikhail Galkin et al.

Motivated by the incompleteness of modern knowledge graphs, a new setup for query answering has emerged, where the goal is to predict answers that do not necessarily appear in the knowledge graph, but are present in its completion. In this paper, we formally introduce and study two query answering problems, namely, query answer classification and query answer retrieval. To solve these problems, we propose AnyCQ, a model that can classify answers to any conjunctive query on any knowledge graph. At the core of our framework lies a graph neural network trained using a reinforcement learning objective to answer Boolean queries. Trained only on simple, small instances, AnyCQ generalizes to large queries of arbitrary structure, reliably classifying and retrieving answers to queries that existing approaches fail to handle. This is empirically validated through our newly proposed, challenging benchmarks. Finally, we empirically show that AnyCQ can effectively transfer to completely novel knowledge graphs when equipped with an appropriate link prediction model, highlighting its potential for querying incomplete data.

Xingyue Huang, Xianglong Hu, Zifeng Ding et al.

Large language models (LLMs) often struggle with mathematical problems that require exact computation or multi-step algebraic reasoning. Tool-integrated reasoning (TIR) offers a promising solution by leveraging external tools such as code interpreters to ensure correctness, but it introduces inference-time dependencies that hinder scalability and deployment. In this work, we propose a new paradigm for distilling tool knowledge into LLMs purely through natural language. We first construct a Solver Agent that solves math problems by interleaving planning, symbolic tool calls, and reflective reasoning. Then, using a back-translation pipeline powered by multiple LLM-based agents, we convert interleaved TIR traces into natural language reasoning traces. A Translator Agent generates explanations for individual tool calls, while a Rephrase Agent merges them into a fluent and globally coherent narrative. Empirically, we show that fine-tuning a small open-source model on these synthesized traces enables it to internalize both tool knowledge and structured reasoning patterns, yielding gains on competition-level math benchmarks without requiring tool access at inference.

Xingyue Huang, Pablo Barceló, Michael M. Bronstein et al. · deepmind

Knowledge Graph Foundation Models (KGFMs) are at the frontier for deep learning on knowledge graphs (KGs), as they can generalize to completely novel knowledge graphs with different relational vocabularies. Despite their empirical success, our theoretical understanding of KGFMs remains very limited. In this paper, we conduct a rigorous study of the expressive power of KGFMs. Specifically, we show that the expressive power of KGFMs directly depends on the motifs that are used to learn the relation representations. We then observe that the most typical motifs used in the existing literature are binary, as the representations are learned based on how pairs of relations interact, which limits the model's expressiveness. As part of our study, we design more expressive KGFMs using richer motifs, which necessitate learning relation representations based on, e.g., how triples of relations interact with each other. Finally, we empirically validate our theoretical findings, showing that the use of richer motifs results in better performance on a wide range of datasets drawn from different domains.

Xingyue Huang, Miguel Romero Orth, Pablo Barceló et al.

Link prediction with knowledge graphs has been thoroughly studied in graph machine learning, leading to a rich landscape of graph neural network architectures with successful applications. Nonetheless, it remains challenging to transfer the success of these architectures to relational hypergraphs, where the task of link prediction is over $k$-ary relations, which is substantially harder than link prediction with knowledge graphs. In this paper, we propose a framework for link prediction with relational hypergraphs, unlocking applications of graph neural networks to fully relational structures. Theoretically, we conduct a thorough analysis of the expressive power of the resulting model architectures via corresponding relational Weisfeiler-Leman algorithms and also via logical expressiveness. Empirically, we validate the power of the proposed model architectures on various relational hypergraph benchmarks. The resulting model architectures substantially outperform every baseline for inductive link prediction, and lead to state-of-the-art results for transductive link prediction.

Adrian Hayler, Xingyue Huang, İsmail İlkan Ceylan et al.

Graph foundation models (GFMs) have recently emerged as a promising paradigm for achieving broad generalization across various graph data. However, existing GFMs are often trained on datasets that may not fully reflect real-world graphs, limiting their generalization performance. In contrast, tabular foundation models (TFMs) not only excel at classical tabular prediction tasks but have also shown strong applicability in other domains such as time series forecasting, natural language processing, and computer vision. Motivated by this, we take an alternative view to the standard perspective of GFMs and reformulate node classification as a tabular problem. In this reformulation, each node is represented as a row with feature, structure, and label information as columns, enabling TFMs to directly perform zero-shot node classification via in-context learning. In this work, we introduce TAG, a tabular approach for graph learning that first converts a graph into a table via feature and structural encoders, applies multiple TFMs to diversely subsampled tables, and then aggregates their outputs through ensemble selection. Experiments on 28 real-world datasets demonstrate that TAG consistently improves upon task-specific GNNs and state-of-the-art GFMs, highlighting the potential of the tabular reformulation for scalable and generalizable graph learning.

Xingyue Huang, Mikhail Galkin, Michael M. Bronstein et al.

Inductive link prediction with knowledge hypergraphs is the task of predicting missing hyperedges involving completely novel entities (i.e., nodes unseen during training). Existing methods for inductive link prediction with knowledge hypergraphs assume a fixed relational vocabulary and, as a result, cannot generalize to knowledge hypergraphs with novel relation types (i.e., relations unseen during training). Inspired by knowledge graph foundation models, we propose HYPER as a foundation model for link prediction, which can generalize to any knowledge hypergraph, including novel entities and novel relations. Importantly, HYPER can learn and transfer across different relation types of varying arities, by encoding the entities of each hyperedge along with their respective positions in the hyperedge. To evaluate HYPER, we construct 16 new inductive datasets from existing knowledge hypergraphs, covering a diverse range of relation types of varying arities. Empirically, HYPER consistently outperforms all existing methods in both node-only and node-and-relation inductive settings, showing strong generalization to unseen, higher-arity relational structures.

Zifeng Ding, Shenyang Huang, Zeyu Cao et al. · cambridge

Forecasting future links is a central task in temporal graph (TG) reasoning, requiring models to leverage historical interactions to predict upcoming ones. Traditional neural approaches, such as temporal graph neural networks, achieve strong performance but lack explainability and cannot be applied to unseen graphs without retraining. Recent studies have begun to explore using large language models (LLMs) for graph reasoning, but most of them are constrained to static graphs or small synthetic TGs and lack the evaluation of the quality of reasoning traces generated by LLMs. In this work, we present Reasoning-Enhanced Learning for Temporal Graphs (ReaL-TG), a reinforcement learning framework that fine-tunes LLMs to perform explainable link forecasting on real-world TGs. ReaL-TG uses outcome-based reward to encourage models to self-explore reasoning strategies from graph structure and to produce explanations that directly justify their predictions. To enable evaluation on LLM-generated reasoning traces, we propose a new evaluation protocol combining ranking metrics with an LLM-as-a-Judge system that assesses both the quality of reasoning and the impact of hallucinations. Experiments with ReaL-TG-4B, obtained by fine-tuning Qwen3-4B under our framework, show that it outperforms much larger frontier LLMs, including GPT-5 mini, on ranking metrics, while producing high-quality explanations confirmed by both the LLM judge and human evaluation.

Fan Yang, Xingyue Huang

Line graph transformation has been widely studied in graph theory, where each node in a line graph corresponds to an edge in the original graph. This has inspired a series of graph neural networks (GNNs) applied to transformed line graphs, which have proven effective in various graph representation learning tasks. However, there is limited theoretical study on how line graph transformation affects the expressivity of GNN models. In this study, we focus on two types of graphs known to be challenging to the Weisfeiler-Leman (WL) tests: Cai-Fürer-Immerman (CFI) graphs and strongly regular graphs, and show that applying line graph transformation helps exclude these challenging graph properties, thus potentially assist WL tests in distinguishing these graphs. We empirically validate our findings by conducting a series of experiments that compare the accuracy and efficiency of graph isomorphism tests and GNNs on both line-transformed and original graphs across these graph structure types.