Daily Papers

Embedding-based methods for reasoning in knowledge hypergraphs learn a representation for each entity and relation. Current methods do not capture the procedural rules underlying the relations in the graph. We propose a simple embedding-based model called ReAlE that performs link prediction in knowledge hypergraphs (generalized knowledge graphs) and can represent high-level abstractions in terms of relational algebra operations. We show theoretically that ReAlE is fully expressive and provide proofs and empirical evidence that it can represent a large subset of the primitive relational algebra operations, namely renaming, projection, set union, selection, and set difference. We also verify experimentally that ReAlE outperforms state-of-the-art models in knowledge hypergraph completion, and in representing each of these primitive relational algebra operations. For the latter experiment, we generate a synthetic knowledge hypergraph, for which we design an algorithm based on the Erdos-R'enyi model for generating random graphs.

Standard Retrieval-Augmented Generation (RAG) relies on chunk-based retrieval, whereas GraphRAG advances this approach by graph-based knowledge representation. However, existing graph-based RAG approaches are constrained by binary relations, as each edge in an ordinary graph connects only two entities, limiting their ability to represent the n-ary relations (n >= 2) in real-world knowledge. In this work, we propose HyperGraphRAG, a novel hypergraph-based RAG method that represents n-ary relational facts via hyperedges, and consists of knowledge hypergraph construction, retrieval, and generation. Experiments across medicine, agriculture, computer science, and law demonstrate that HyperGraphRAG outperforms both standard RAG and previous graph-based RAG methods in answer accuracy, retrieval efficiency, and generation quality.

Retrieval-Augmented Generation (RAG) mitigates hallucination in LLMs by incorporating external knowledge, but relies on chunk-based retrieval that lacks structural semantics. GraphRAG methods improve RAG by modeling knowledge as entity-relation graphs, but still face challenges in high construction cost, fixed one-time retrieval, and reliance on long-context reasoning and prompt design. To address these challenges, we propose Graph-R1, an agentic GraphRAG framework via end-to-end reinforcement learning (RL). It introduces lightweight knowledge hypergraph construction, models retrieval as a multi-turn agent-environment interaction, and optimizes the agent process via an end-to-end reward mechanism. Experiments on standard RAG datasets show that Graph-R1 outperforms traditional GraphRAG and RL-enhanced RAG methods in reasoning accuracy, retrieval efficiency, and generation quality.

Scientific inquiry requires systems-level reasoning that integrates heterogeneous experimental data, cross-domain knowledge, and mechanistic evidence into coherent explanations. While Large Language Models (LLMs) offer inferential capabilities, they often depend on retrieval-augmented contexts that lack structural depth. Traditional Knowledge Graphs (KGs) attempt to bridge this gap, yet their pairwise constraints fail to capture the irreducible higher-order interactions that govern emergent physical behavior. To address this, we introduce a methodology for constructing hypergraph-based knowledge representations that faithfully encode multi-entity relationships. Applied to a corpus of ~1,100 manuscripts on biocomposite scaffolds, our framework constructs a global hypergraph of 161,172 nodes and 320,201 hyperedges, revealing a scale-free topology (power law exponent ~1.23) organized around highly connected conceptual hubs. This representation prevents the combinatorial explosion typical of pairwise expansions and explicitly preserves the co-occurrence context of scientific formulations. We further demonstrate that equipping agentic systems with hypergraph traversal tools, specifically using node-intersection constraints, enables them to bridge semantically distant concepts. By exploiting these higher-order pathways, the system successfully generates grounded mechanistic hypotheses for novel composite materials, such as linking cerium oxide to PCL scaffolds via chitosan intermediates. This work establishes a "teacherless" agentic reasoning system where hypergraph topology acts as a verifiable guardrail, accelerating scientific discovery by uncovering relationships obscured by traditional graph methods.

Node importance estimation (NIE) in heterogeneous knowledge graphs is a critical yet challenging task, essential for applications such as recommendation, knowledge reasoning, and question answering. Existing methods often rely on pairwise connections, neglecting high-order dependencies among multiple entities and relations, and they treat structural and semantic signals independently, hindering effective cross-modal integration. To address these challenges, we propose MetaHGNIE, a meta-path induced hypergraph contrastive learning framework for disentangling and aligning structural and semantic information. MetaHGNIE constructs a higher-order knowledge graph via meta-path sequences, where typed hyperedges capture multi-entity relational contexts. Structural dependencies are aggregated with local attention, while semantic representations are encoded through a hypergraph transformer equipped with sparse chunking to reduce redundancy. Finally, a multimodal fusion module integrates structural and semantic embeddings under contrastive learning with auxiliary supervision, ensuring robust cross-modal alignment. Extensive experiments on benchmark NIE datasets demonstrate that MetaHGNIE consistently outperforms state-of-the-art baselines. These results highlight the effectiveness of explicitly modeling higher-order interactions and cross-modal alignment in heterogeneous knowledge graphs. Our code is available at https://github.com/SEU-WENJIA/DualHNIE

Hypergraph Neural Networks (HGNNs) have recently attracted much attention and exhibited satisfactory performance due to their superiority in high-order correlation modeling. However, it is noticed that the high-order modeling capability of hypergraph also brings increased computation complexity, which hinders its practical industrial deployment. In practice, we find that one key barrier to the efficient deployment of HGNNs is the high-order structural dependencies during inference. In this paper, we propose to bridge the gap between the HGNNs and inference-efficient Multi-Layer Perceptron (MLPs) to eliminate the hypergraph dependency of HGNNs and thus reduce computational complexity as well as improve inference speed. Specifically, we introduce LightHGNN and LightHGNN^+ for fast inference with low complexity. LightHGNN directly distills the knowledge from teacher HGNNs to student MLPs via soft labels, and LightHGNN^+ further explicitly injects reliable high-order correlations into the student MLPs to achieve topology-aware distillation and resistance to over-smoothing. Experiments on eight hypergraph datasets demonstrate that even without hypergraph dependency, the proposed LightHGNNs can still achieve competitive or even better performance than HGNNs and outperform vanilla MLPs by 16.3 on average. Extensive experiments on three graph datasets further show the average best performance of our LightHGNNs compared with all other methods. Experiments on synthetic hypergraphs with 5.5w vertices indicate LightHGNNs can run 100times faster than HGNNs, showcasing their ability for latency-sensitive deployments.

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph representations have recently yielded new drug repurposing hypotheses. In this study, we present a novel, disease-specific hypergraph representation learning technique to derive contextual embeddings of biological pathways of various lengths but that all start at any given drug and all end at the disease of interest. Further, we extend this method to multi-disease hypergraphs. To determine the repurposing potential of each of the 1,522 drugs, we derive drug-specific distributions of cosine similarity values and ultimately consider the median for ranking. Cosine similarity values are computed between (1) all biological pathways starting at the considered drug and ending at the disease of interest and (2) all biological pathways starting at drugs currently prescribed against that disease and ending at the disease of interest. We illustrate our approach with Alzheimer's disease (AD) and two of its risk factors: hypertension (HTN) and type 2 diabetes (T2D). We compare each drug's rank across four hypergraph settings (single- or multi-disease): AD only, AD + HTN, AD + T2D, and AD + HTN + T2D. Notably, our framework led to the identification of two promising drugs whose repurposing potential was significantly higher in hypergraphs combining two diseases: dapagliflozin (antidiabetic; moved up, from top 32% to top 7%, across all considered drugs) and debrisoquine (antihypertensive; moved up, from top 76% to top 23%). Our approach serves as a hypothesis generation tool, to be paired with a validation pipeline relying on laboratory experiments and semi-automated parsing of the biomedical literature.

We propose a many-sorted modal logic for reasoning about knowledge in multi-agent systems. Our logic introduces a clear distinction between participating agents and the environment. This allows to express local properties of agents and global properties of worlds in a uniform way, as well as to talk about the presence or absence of agents in a world. The logic subsumes the standard epistemic logic and is a conservative extension of it. The semantics is given in chromatic hypergraphs, a generalization of chromatic simplicial complexes, which were recently used to model knowledge in distributed systems. We show that the logic is sound and complete with respect to the intended semantics. We also show a further connection of chromatic hypergraphs with neighborhood frames.

Multi-step retrieval-augmented generation (RAG) has become a widely adopted strategy for enhancing large language models (LLMs) on tasks that demand global comprehension and intensive reasoning. Many RAG systems incorporate a working memory module to consolidate retrieved information. However, existing memory designs function primarily as passive storage that accumulates isolated facts for the purpose of condensing the lengthy inputs and generating new sub-queries through deduction. This static nature overlooks the crucial high-order correlations among primitive facts, the compositions of which can often provide stronger guidance for subsequent steps. Therefore, their representational strength and impact on multi-step reasoning and knowledge evolution are limited, resulting in fragmented reasoning and weak global sense-making capacity in extended contexts. We introduce HGMem, a hypergraph-based memory mechanism that extends the concept of memory beyond simple storage into a dynamic, expressive structure for complex reasoning and global understanding. In our approach, memory is represented as a hypergraph whose hyperedges correspond to distinct memory units, enabling the progressive formation of higher-order interactions within memory. This mechanism connects facts and thoughts around the focal problem, evolving into an integrated and situated knowledge structure that provides strong propositions for deeper reasoning in subsequent steps. We evaluate HGMem on several challenging datasets designed for global sense-making. Extensive experiments and in-depth analyses show that our method consistently improves multi-step RAG and substantially outperforms strong baseline systems across diverse tasks.

Retrieval-Augmented Generation (RAG) enhances the response quality and domain-specific performance of large language models (LLMs) by incorporating external knowledge to combat hallucinations. In recent research, graph structures have been integrated into RAG to enhance the capture of semantic relations between entities. However, it primarily focuses on low-order pairwise entity relations, limiting the high-order associations among multiple entities. Hypergraph-enhanced approaches address this limitation by modeling multi-entity interactions via hyperedges, but they are typically constrained to inter-chunk entity-level representations, overlooking the global thematic organization and alignment across chunks. Drawing inspiration from the top-down cognitive process of human reasoning, we propose a theme-aligned dual-hypergraph RAG framework (Cog-RAG) that uses a theme hypergraph to capture inter-chunk thematic structure and an entity hypergraph to model high-order semantic relations. Furthermore, we design a cognitive-inspired two-stage retrieval strategy that first activates query-relevant thematic content from the theme hypergraph, and then guides fine-grained recall and diffusion in the entity hypergraph, achieving semantic alignment and consistent generation from global themes to local details. Our extensive experiments demonstrate that Cog-RAG significantly outperforms existing state-of-the-art baseline approaches.

Large language models (LLMs) have transformed various sectors, including education, finance, and medicine, by enhancing content generation and decision-making processes. However, their integration into the medical field is cautious due to hallucinations, instances where generated content deviates from factual accuracy, potentially leading to adverse outcomes. To address this, we introduce Hyper-RAG, a hypergraph-driven Retrieval-Augmented Generation method that comprehensively captures both pairwise and beyond-pairwise correlations in domain-specific knowledge, thereby mitigating hallucinations. Experiments on the NeurologyCrop dataset with six prominent LLMs demonstrated that Hyper-RAG improves accuracy by an average of 12.3% over direct LLM use and outperforms Graph RAG and Light RAG by 6.3% and 6.0%, respectively. Additionally, Hyper-RAG maintained stable performance with increasing query complexity, unlike existing methods which declined. Further validation across nine diverse datasets showed a 35.5% performance improvement over Light RAG using a selection-based assessment. The lightweight variant, Hyper-RAG-Lite, achieved twice the retrieval speed and a 3.3% performance boost compared with Light RAG. These results confirm Hyper-RAG's effectiveness in enhancing LLM reliability and reducing hallucinations, making it a robust solution for high-stakes applications like medical diagnostics.

This paper presents OG-RAG, an Ontology-Grounded Retrieval Augmented Generation method designed to enhance LLM-generated responses by anchoring retrieval processes in domain-specific ontologies. While LLMs are widely used for tasks like question answering and search, they struggle to adapt to specialized knowledge, such as industrial workflows or knowledge work, without expensive fine-tuning or sub-optimal retrieval methods. Existing retrieval-augmented models, such as RAG, offer improvements but fail to account for structured domain knowledge, leading to suboptimal context generation. Ontologies, which conceptually organize domain knowledge by defining entities and their interrelationships, offer a structured representation to address this gap. OG-RAG constructs a hypergraph representation of domain documents, where each hyperedge encapsulates clusters of factual knowledge grounded using domain-specific ontology. An optimization algorithm then retrieves the minimal set of hyperedges that constructs a precise, conceptually grounded context for the LLM. This method enables efficient retrieval while preserving the complex relationships between entities. OG-RAG applies to domains where fact-based reasoning is essential, particularly in tasks that require workflows or decision-making steps to follow predefined rules and procedures. These include industrial workflows in healthcare, legal, and agricultural sectors, as well as knowledge-driven tasks such as news journalism, investigative research, consulting and more. Our evaluations demonstrate that OG-RAG increases the recall of accurate facts by 55% and improves response correctness by 40% across four different LLMs. Additionally, OG-RAG enables 30% faster attribution of responses to context and boosts fact-based reasoning accuracy by 27% compared to baseline methods.