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.

Xingyue Huang, Xueying Ding, Mingxuan Ju et al.

Softmax attention struggles with long contexts due to structural limitations: the strict sum-to-one constraint forces attention sinks on irrelevant tokens, and probability mass disperses as sequence lengths increase. We tackle these problems with Threshold Differential Attention (TDA), a sink-free attention mechanism that achieves ultra-sparsity and improved robustness at longer sequence lengths without the computational overhead of projection methods or the performance degradation caused by noise accumulation of standard rectified attention. TDA applies row-wise extreme-value thresholding with a length-dependent gate, retaining only exceedances. Inspired by the differential transformer, TDA also subtracts an inhibitory view to enhance expressivity. Theoretically, we prove that TDA controls the expected number of spurious survivors per row to $O(1)$ and that consensus spurious matches across independent views vanish as context grows. Empirically, TDA produces $>99\%$ exact zeros and eliminates attention sinks while maintaining competitive performance on standard and long-context benchmarks.

Krzysztof Olejniczak, Radoslav Dimitrov, Xingyue Huang et al.

Formal theorem provers based on large language models (LLMs) are highly sensitive to superficial variations in problem representation: semantically equivalent statements can exhibit drastically different proof success rates, revealing a failure to respect structural symmetries inherent in formal mathematics. This raises a central question: what are the right symmetries for formal theorem proving? We introduce rewriting categories, a category-theoretic framework capturing the compositional, generally non-invertible transformations induced by proof tactics, and use it to formalize two symmetry notions: proof equivariance, governing how proof distributions transform under rewrites, and success invariance (i.e., invariance of success probability), requiring equivalent statements to be solved with the same probability. We observe that state-based next-tactic provers naturally satisfy proof equivariance by operating on proof states. In contrast, state-of-the-art LLM-based provers satisfy neither property, exhibiting large performance variation across equivalent formulations. To mitigate this, we propose test-time methods that aggregate over equivalent rewritings of the input, showing theoretically that they recover success invariance in the sampling limit, and empirically, that they improve robustness and performance under fixed inference budgets. Our results highlight symmetry as a key missing inductive bias in LLM-based theorem proving and suggest test-time computation as a practical route to approximate it.

Xingyue Huang, Rishabh, Gregor Franke et al.

Recent advances in Large Language Models (LLMs) have shown that their reasoning capabilities can be significantly improved through Reinforcement Learning with Verifiable Reward (RLVR), particularly in domains like mathematics and programming, where ground-truth correctness can be automatically evaluated. However, extending this success to other reasoning-intensive domains remains challenging due to the scarcity of high-quality, verifiable datasets and the high cost of human supervision. In this work, we introduce the Loong Project: an open-source framework for scalable synthetic data generation and verification across a diverse range of reasoning-intensive domains. The framework consists of two key components: (1) LoongBench, a curated seed dataset containing 8,729 human-vetted examples across 12 domains (e.g., Advanced Mathematics, Chemistry, Logic), each paired with executable code and rich metadata; and (2) LoongEnv, a modular synthetic data generation environment that supports multiple prompting strategies to produce new question-answer-code triples. Together, these components form an agent-environment loop that enables reinforcement learning, where an LLM-based agent is rewarded for generating Chain-of-Thought (CoT) solutions that align with code-executed answers. Empirically, we benchmark LoongBench on a broad suite of both open-source and proprietary LLMs to evaluate domain coverage and reveal performance bottlenecks. In addition, we conduct a comprehensive analysis of synthetic data generated by LoongEnv, examining correctness, difficulty, and diversity. Code and documentation are available at https://github.com/camel-ai/loong.

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, Louis Tichelman, Jinwoo Kim et al.

Relational learning is a challenging problem that has motivated a wide range of approaches, including graph-based models (e.g., graph neural networks, graph transformers), tabular methods (e.g., tabular foundation models), and sequence-based approaches (e.g., large language models), each with its own advantages and limitations. We propose RelAgent, an LLM-based autonomous data scientist for relational learning, which operates in two phases. In the search phase, an LLM agent uses database, validation, and evaluation workspace tools to construct SQL feature programs and select a predictive model. In the inference phase, the resulting program is executed without further LLM calls. The final predictor consists of SQL queries and a classical model, enabling fast, deterministic, and intrinsically interpretable predictions: features are human-readable queries, and predictions depend only on the resulting query-defined feature map, enabling scalable deployment using standard database systems.

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.

Jinwoo Kim, Xingyue Huang, Krzysztof Olejniczak et al.

We study the problem of zero-shot link prediction on knowledge graphs (KGs), which requires models to generalize over novel entities and novel relations. Knowledge graph foundation models (KGFMs) address this task by enforcing equivariance over both nodes and relations, learning from structural properties of nodes and relations, which are then transferable to novel graphs with similar structural properties. However, the conventional notion of deterministic equivariance imposes inherent limits on the expressive power of KGFMs, preventing them from distinguishing structurally similar but semantically distinct relations. To overcome this limitation, we introduce probabilistic node-relation equivariance, which preserves equivariance in distribution while incorporating a principled randomization to break symmetries during inference. Building on this principle, we present Flock, a KGFM that iteratively samples random walks, encodes them into sequences via a recording protocol, embeds them with a sequence model, and aggregates representations of nodes and relations via learned pooling. Crucially, Flock respects probabilistic node-relation equivariance and is a universal approximator for isomorphism-invariant link-level functions over KGs. Empirically, Flock perfectly solves our new diagnostic dataset Petals where current KGFMs fail, and achieves state-of-the-art performances on entity- and relation prediction tasks on 54 KGs from diverse domains.

Xiangxiang Zhang, Jingxuan Wei, Donghong Zhong et al.

Existing Vision-Language Models often struggle with complex, multi-question reasoning tasks where partial correctness is crucial for effective learning. Traditional reward mechanisms, which provide a single binary score for an entire response, are too coarse to guide models through intricate problems with multiple sub-parts. To address this, we introduce StructVRM, a method that aligns multimodal reasoning with Structured and Verifiable Reward Models. At its core is a model-based verifier trained to provide fine-grained, sub-question-level feedback, assessing semantic and mathematical equivalence rather than relying on rigid string matching. This allows for nuanced, partial credit scoring in previously intractable problem formats. Extensive experiments demonstrate the effectiveness of StructVRM. Our trained model, Seed-StructVRM, achieves state-of-the-art performance on six out of twelve public multimodal benchmarks and our newly curated, high-difficulty STEM-Bench. The success of StructVRM validates that training with structured, verifiable rewards is a highly effective approach for advancing the capabilities of multimodal models in complex, real-world reasoning domains.

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.

Xueying Ding, Xingyue Huang, Mingxuan Ju et al.

Large language models produce powerful text embeddings, but their causal attention mechanism restricts the flow of information from later to earlier tokens, degrading representation quality. While recent methods attempt to solve this by prepending a single summary token, they over-compress information, hence harming performance on long documents. We propose Hierarchical Token Prepending (HTP), a method that resolves two critical bottlenecks. To mitigate attention-level compression, HTP partitions the input into blocks and prepends block-level summary tokens to subsequent blocks, creating multiple pathways for backward information flow. To address readout-level over-squashing, we replace last-token pooling with mean-pooling, a choice supported by theoretical analysis. HTP achieves consistent performance gains across 11 retrieval datasets and 30 general embedding benchmarks, especially in long-context settings. As a simple, architecture-agnostic method, HTP enhances both zero-shot and finetuned models, offering a scalable route to superior long-document embeddings.

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.