Daily Papers

Long-term memory lets LLM agents personalize, stay consistent, and reuse what worked before. Parametric memories need training, consolidation can lose details for good, and keeping every record leaves a growing store to search. We present MIRIX-2.0, a multi-agent memory system designed to be practical, accurate, and efficient at once. It is the most accurate of the compared systems on four of five QA benchmarks. It reaches 91.4% on LoCoMo and 72.6% on LongMemEval-S, where it leads the strongest baseline by 14.3 points, and with AutoDream disabled it gains 31.0 and 22.0 points over HyperMem on single-hop and multi-hop document QA. As procedural memory, it yields the highest mean success among the compared memory methods on ALFWorld and WebShop and reaches 49.2% on MetaClaw-Bench, against 44.0% for MetaClaw's skill library. Six typed memory agents keep complete records as the system of record, and a provenance hypergraph indexes episodic and semantic records with n-ary frames that cite their rows. Retrieval runs under explicit budgets, so the evidence a question inspects does not grow with the history. AutoDream merges duplicate anchors outside the write path without rewriting any record, and it distills task sessions into skills. With AutoDream disabled, MIRIX-2.0 answers faster than HyperMem on all five timed benchmarks. It needs no fine-tuning, runs with closed and open models, and its code is public.

Provenance graphs are structured audit logs that describe the history of a system's execution. Recent studies have explored a variety of techniques to analyze provenance graphs for automated host intrusion detection, focusing particularly on advanced persistent threats. Sifting through their design documents, we identify four common dimensions that drive the development of provenance-based intrusion detection systems (PIDSes): scope (can PIDSes detect modern attacks that infiltrate across application boundaries?), attack agnosticity (can PIDSes detect novel attacks without a priori knowledge of attack characteristics?), timeliness (can PIDSes efficiently monitor host systems as they run?), and attack reconstruction (can PIDSes distill attack activity from large provenance graphs so that sysadmins can easily understand and quickly respond to system intrusion?). We present KAIROS, the first PIDS that simultaneously satisfies the desiderata in all four dimensions, whereas existing approaches sacrifice at least one and struggle to achieve comparable detection performance. Kairos leverages a novel graph neural network-based encoder-decoder architecture that learns the temporal evolution of a provenance graph's structural changes to quantify the degree of anomalousness for each system event. Then, based on this fine-grained information, Kairos reconstructs attack footprints, generating compact summary graphs that accurately describe malicious activity over a stream of system audit logs. Using state-of-the-art benchmark datasets, we demonstrate that Kairos outperforms previous approaches.

Hypergraphs are marked by complex topology, expressing higher-order interactions among multiple nodes with hyperedges, and better capturing the topology is essential for effective representation learning. Recent advances in generative self-supervised learning (SSL) suggest that hypergraph neural networks learned from generative self supervision have the potential to effectively encode the complex hypergraph topology. Designing a generative SSL strategy for hypergraphs, however, is not straightforward. Questions remain with regard to its generative SSL task, connection to downstream tasks, and empirical properties of learned representations. In light of the promises and challenges, we propose a novel generative SSL strategy for hypergraphs. We first formulate a generative SSL task on hypergraphs, hyperedge filling, and highlight its theoretical connection to node classification. Based on the generative SSL task, we propose a hypergraph SSL method, HypeBoy. HypeBoy learns effective general-purpose hypergraph representations, outperforming 16 baseline methods across 11 benchmark datasets.

Large language models (LLMs) have recently shown strong potential in modeling relational structures. However, existing approaches remain fundamentally graph-centric: they focus on processing pairwise graph structures into tokens that LLMs can understand. In contrast, many real-world relational patterns do not naturally conform to the pairwise-edge assumption, and are better modeled as high-order associations in hypergraphs. For hypergraph structures, existing methods often fail to preserve the native semantics that multiple objects are jointly connected by the same high-order relation, limiting their ability to exploit complex structures. To address this limitation, we put forth the "Hypergraph as Language" perspective and propose Hyper-Align, a hypergraph-native alignment framework for large language models. Hyper-Align compiles the query-object-centered hypergraph context into hypergraph tokens directly consumable by a base LLM. Specifically, we introduce Hypergraph Incidence Detail Template with Overview (HIDT-O), which serializes high-order association structures into a fixed-shape hybrid template combining local incidence details and overview-level summaries. We then design a Hypergraph Incidence Projector (HIP), which maps native high-order incidence structures into the LLM token space through explicit semantic-structural decoupling and bidirectional message passing between vertices and hyperedges. We further define a concrete Hypergraph-as-Language input protocol, which jointly feeds hypergraph tokens and textual prompts into a frozen base LLM, supporting both vertex-level and hyperedge-level tasks under a unified question-answering paradigm. To systematically evaluate different methods in hypergraph structural modeling, we introduce HyperAlign-Bench. Extensive experiments show that Hyper-Align significantly outperforms existing methods across in-domain and zero-shot evaluations.

Host-based threats such as Program Attack, Malware Implantation, and Advanced Persistent Threats (APT), are commonly adopted by modern attackers. Recent studies propose leveraging the rich contextual information in data provenance to detect threats in a host. Data provenance is a directed acyclic graph constructed from system audit data. Nodes in a provenance graph represent system entities (e.g., processes and files) and edges represent system calls in the direction of information flow. However, previous studies, which extract features of the whole provenance graph, are not sensitive to the small number of threat-related entities and thus result in low performance when hunting stealthy threats. We present threaTrace, an anomaly-based detector that detects host-based threats at system entity level without prior knowledge of attack patterns. We tailor GraphSAGE, an inductive graph neural network, to learn every benign entity's role in a provenance graph. threaTrace is a real-time system, which is scalable of monitoring a long-term running host and capable of detecting host-based intrusion in their early phase. We evaluate threaTrace on three public datasets. The results show that threaTrace outperforms three state-of-the-art host intrusion detection systems.

We present ProvenanceWidgets, a Javascript library of UI control elements such as radio buttons, checkboxes, and dropdowns to track and dynamically overlay a user's analytic provenance. These in situ overlays not only save screen space but also minimize the amount of time and effort needed to access the same information from elsewhere in the UI. In this paper, we discuss how we design modular UI control elements to track how often and how recently a user interacts with them and design visual overlays showing an aggregated summary as well as a detailed temporal history. We demonstrate the capability of ProvenanceWidgets by recreating three prior widget libraries: (1) Scented Widgets, (2) Phosphor objects, and (3) Dynamic Query Widgets. We also evaluated its expressiveness and conducted case studies with visualization developers to evaluate its effectiveness. We find that ProvenanceWidgets enables developers to implement custom provenance-tracking applications effectively. ProvenanceWidgets is available as open-source software at https://github.com/ProvenanceWidgets to help application developers build custom provenance-based systems.

Analytic provenance can be visually encoded to help users track their ongoing analysis trajectories, recall past interactions, and inform new analytic directions. Despite its significance, provenance is often hardwired into analytics systems, affording limited user control and opportunities for self-reflection. We thus propose modeling provenance as an attribute that is available to users during analysis. We demonstrate this concept by modeling two provenance attributes that track the recency and frequency of user interactions with data. We integrate these attributes into a visual data analysis system prototype, ProvenanceLens, wherein users can visualize their interaction recency and frequency by mapping them to encoding channels (e.g., color, size) or applying data transformations (e.g., filter, sort). Using ProvenanceLens as a design probe, we conduct an exploratory study with sixteen users to investigate how these provenance-tracking affordances are utilized for both decision-making and self-reflection. We find that users can accurately and confidently answer questions about their analysis, and we show that mismatches between the user's mental model and the provenance encodings can be surprising, thereby prompting useful self-reflection. We also report on the user strategies surrounding these affordances, and reflect on their intuitiveness and effectiveness in representing provenance.

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.

Multi-hop question answering in retrieval-augmented gener?ation (RAG) often benefits from retrieving beyond the few candidates that will finally be read: narrow retrieval can miss an indispensable hop, while expanded retrieval introduces topical distractors. This challenge is not tied to a particu?lar knowledge-base format. Candidate pools may come from standalone retrievers, standard RAG backends, or graph-based retrieval pipelines. What is needed is a query-aware selection layer that can use relational structure to filter candidates be?fore generation. PAGE-RAG addresses this setting by using a graph as a temporary selection structure, rather than assum?ing a graph-structured knowledge base. It builds a query-local graph over retrieved candidates, records why candidates are connected, and treats each connection as a support hypothe?sis rather than support itself. We identify the resulting failure mode as a connectivity-support gap: connected candidates do not necessarily support the answer. We propose PAGE-RAG, a Provenance-Aware Graph Evidence promotion method that scores candidate paths with relevance, source-tracing meta?data, specificity, hubness, noise, and coherence signals, and applies minimal sufficient selection to promote supporting facts into a compact reader context. PAGE-RAG can serve as a complete retrieval-to-reading pipeline, and the same promo?tion stage can be inserted after existing retrieval or RAG sys?tems without replacing their upstream retrieval logic. Across three multi-hop QA benchmarks under the same final bud?get, PAGE-RAG improves support F1 and answer F1 by 10.4 and 3.3 points on a weighted average over a strong retriever. As a plug-in, PAGE-RAG further improves all reported RAG backends, including reasoning-oriented, compression-based, graph-based, and document/chunk-level systems.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

Due to the advantages of hypergraphs in modeling high-order relationships in complex systems, they have been applied to higher-order clustering, hypergraph neural networks and computer vision. These applications rely heavily on access to high-quality, large-scale real-world hypergraph data. Yet, compared to traditional pairwise graphs, real hypergraph datasets remain scarce in both scale and diversity. This shortage significantly limits the development and evaluation of advanced hypergraph learning algorithms. Therefore, how to quickly generate large-scale hypergraphs that conform to the characteristics of real networks is a crucial task that has not received sufficient attention. Motivated by recent advances in large language models (LLMs), particularly their capabilities in semantic reasoning, structured generation, and simulating human behavior, we investigate whether LLMs can facilitate hypergraph generation from a fundamentally new perspective. We introduce HyperLLM, a novel LLM-driven hypergraph generator that simulates the formation and evolution of hypergraphs through a multi-agent collaboration. The framework integrates prompts and structural feedback mechanisms to ensure that the generated hypergraphs reflect key real-world patterns. Extensive experiments across diverse datasets demonstrate that HyperLLM achieves superior fidelity to structural and temporal hypergraph patterns, while requiring minimal statistical priors. Our findings suggest that LLM-based frameworks offer a promising new direction for hypergraph modeling.

Cyber-physical-social systems (CPSSs) have emerged in many applications over recent decades, requiring increased attention to security concerns. The rise of sophisticated threats like Advanced Persistent Threats (APTs) makes ensuring security in CPSSs particularly challenging. Provenance graph analysis has proven effective for tracing and detecting anomalies within systems, but the sheer size and complexity of these graphs hinder the efficiency of existing methods, especially those relying on graph neural networks (GNNs). To address these challenges, we present GraphDART, a modular framework designed to distill provenance graphs into compact yet informative representations, enabling scalable and effective anomaly detection. GraphDART can take advantage of diverse graph distillation techniques, including classic and modern graph distillation methods, to condense large provenance graphs while preserving essential structural and contextual information. This approach significantly reduces computational overhead, allowing GNNs to learn from distilled graphs efficiently and enhance detection performance. Extensive evaluations on benchmark datasets demonstrate the robustness of GraphDART in detecting malicious activities across cyber-physical-social systems. By optimizing computational efficiency, GraphDART provides a scalable and practical solution to safeguard interconnected environments against APTs.

Automated clinical diagnosis remains a core challenge in medical AI, which usually requires models to integrate multi-modal data and reason across complex, case-specific contexts. Although recent methods have advanced medical report generation (MRG) and visual question answering (VQA) with medical vision-language models (VLMs), these methods, however, predominantly operate under a sample-isolated inference paradigm, as such processing cases independently without access to longitudinal electronic health records (EHRs) or structurally related patient examples. This paradigm limits reasoning to image-derived information alone, which ignores external complementary medical evidence for potentially more accurate diagnosis. To overcome this limitation, we propose HyperWalker, a Deep Diagnosis framework that reformulates clinical reasoning via dynamic hypergraphs and test-time training. First, we construct a dynamic hypergraph, termed iBrochure, to model the structural heterogeneity of EHR data and implicit high-order associations among multimodal clinical information. Within this hypergraph, a reinforcement learning agent, Walker, navigates to and identifies optimal diagnostic paths. To ensure comprehensive coverage of diverse clinical characteristics in test samples, we incorporate a linger mechanism, a multi-hop orthogonal retrieval strategy that iteratively selects clinically complementary neighborhood cases reflecting distinct clinical attributes. Experiments on MRG with MIMIC and medical VQA on EHRXQA demonstrate that HyperWalker achieves state-of-the-art performance. Code is available at: https://github.com/Bean-Young/HyperWalker

Large Language Models (LLMs) and other foundation models are increasingly used as the core of AI agents. In agentic workflows, these agents plan tasks, interact with humans and peers, and influence scientific outcomes across federated and heterogeneous environments. However, agents can hallucinate or reason incorrectly, propagating errors when one agent's output becomes another's input. Thus, assuring that agents' actions are transparent, traceable, reproducible, and reliable is critical to assess hallucination risks and mitigate their workflow impacts. While provenance techniques have long supported these principles, existing methods fail to capture and relate agent-centric metadata such as prompts, responses, and decisions with the broader workflow context and downstream outcomes. In this paper, we introduce PROV-AGENT, a provenance model that extends W3C PROV and leverages the Model Context Protocol (MCP) and data observability to integrate agent interactions into end-to-end workflow provenance. Our contributions include: (1) a provenance model tailored for agentic workflows, (2) a near real-time, open-source system for capturing agentic provenance, and (3) a cross-facility evaluation spanning edge, cloud, and HPC environments, demonstrating support for critical provenance queries and agent reliability analysis.

Looped Transformers have shown exceptional neural algorithmic reasoning capability in simulating traditional graph algorithms, but their application to more complex structures like hypergraphs remains underexplored. Hypergraphs generalize graphs by modeling higher-order relationships among multiple entities, enabling richer representations but introducing significant computational challenges. In this work, we extend the Loop Transformer architecture's neural algorithmic reasoning capability to simulate hypergraph algorithms, addressing the gap between neural networks and combinatorial optimization over hypergraphs. Specifically, we propose a novel degradation mechanism for reducing hypergraphs to graph representations, enabling the simulation of graph-based algorithms, such as Dijkstra's shortest path. Furthermore, we introduce a hyperedge-aware encoding scheme to simulate hypergraph-specific algorithms, exemplified by Helly's algorithm. We establish theoretical guarantees for these simulations, demonstrating the feasibility of processing high-dimensional and combinatorial data using Loop Transformers. This work highlights the potential of Transformers as general-purpose algorithmic solvers for structured data.

In this work, we propose HypergraphFormer, a novel and efficient approach to floor plan generation based on learning hypergraph representations with a large language model (LLM). The model is trained via supervised fine-tuning to generate a hypergraph-based textual representation that encodes spatial relationships and connectivity information within floor plans. We train and evaluate our approach on the RPLAN dataset, and further demonstrate its generalizability on a separate out-of-distribution dataset, which we release in this paper. Our method outperforms state-of-the-art techniques based on rasterized or vectorized representations across a diverse set of metrics. We also show improved data efficiency, particularly under distribution shift. The hypergraph formulation enables the generation of floor plans for arbitrary, irregular, user-specified boundaries by decoupling apartment footprints from their functional and geometric subdivisions. Furthermore, we show that the proposed methodology offers a high degree of editability, making it particularly well suited to design-oriented workflows supported by LLMs.

Hypergraphs are a powerful abstraction for representing higher-order interactions between entities of interest. To exploit these relationships in making downstream predictions, a variety of hypergraph neural network architectures have recently been proposed, in large part building upon precursors from the more traditional graph neural network (GNN) literature. Somewhat differently, in this paper we begin by presenting an expressive family of parameterized, hypergraph-regularized energy functions. We then demonstrate how minimizers of these energies effectively serve as node embeddings that, when paired with a parameterized classifier, can be trained end-to-end via a supervised bilevel optimization process. Later, we draw parallels between the implicit architecture of the predictive models emerging from the proposed bilevel hypergraph optimization, and existing GNN architectures in common use. Empirically, we demonstrate state-of-the-art results on various hypergraph node classification benchmarks. Code is available at https://github.com/yxzwang/PhenomNN.

In the field of representation learning on knowledge graphs (KGs), a hyper-relational fact consists of a main triple and several auxiliary attribute-value descriptions, which is considered more comprehensive and specific than a triple-based fact. However, currently available hyper-relational KG embedding methods in a single view are limited in application because they weaken the hierarchical structure that represents the affiliation between entities. To overcome this limitation, we propose a dual-view hyper-relational KG structure (DH-KG) that contains a hyper-relational instance view for entities and a hyper-relational ontology view for concepts that are abstracted hierarchically from the entities. This paper defines link prediction and entity typing tasks on DH-KG for the first time and constructs two DH-KG datasets, JW44K-6K, extracted from Wikidata, and HTDM based on medical data. Furthermore, we propose DHGE, a DH-KG embedding model based on GRAN encoders, HGNNs, and joint learning. DHGE outperforms baseline models on DH-KG, according to experimental results. Finally, we provide an example of how this technology can be used to treat hypertension. Our model and new datasets are publicly available.

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.

Hypergraphs offer a powerful framework for modeling higher-order interactions that traditional pairwise graphs cannot fully capture. However, practical constraints often lead to their simplification into projected graphs, resulting in substantial information loss and ambiguity in representing higher-order relationships. In this work, we propose MARIOH, a supervised approach for reconstructing the original hypergraph from its projected graph by leveraging edge multiplicity. To overcome the difficulties posed by the large search space, MARIOH integrates several key ideas: (a) identifying provable size-2 hyperedges, which reduces the candidate search space, (b) predicting the likelihood of candidates being hyperedges by utilizing both structural and multiplicity-related features, and (c) not only targeting promising hyperedge candidates but also examining less confident ones to explore alternative possibilities. Together, these ideas enable MARIOH to efficiently and effectively explore the search space. In our experiments using 10 real-world datasets, MARIOH achieves up to 74.51% higher reconstruction accuracy compared to state-of-the-art methods.

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.

Semantic-ID mappings are reusable interfaces between item tokenizers and generative recommenders, yet released mappings rarely state whether they are coherent, what structure they expose, how generated paths resolve, or what must be revalidated after a refresh. SIDScope is a source-traced diagnostic resource for these decisions. It normalizes item-to-code artifacts, verifies provenance and joins, profiles mapping structure, compares paired revisions, and accounts for path-to-item outcomes in generated traces. Across nine source-traced tokenizer exports from seven families on Amazon and Yelp data - eight executable routes plus one auditable snapshot - SIDScope reveals that interface health is multi-signal rather than scalar. Its central finding is mechanism-conditional: prefix alignment strongly tracks held-out candidate exposure when retrieval consumes SID prefixes, then weakens as scoring becomes prefix-independent. Trained trace accounting exposes a second hidden gap: a valid target path can survive without uniquely retrieving the target item by 1.2-3.0 percentage points. A refresh case establishes a third: repairing the mapping does not by itself restore an inherited generator; model reuse requires a separate handoff check. The package provides frozen evidence summaries, conformance reports, trace labels, table builders, and CPU-only verifiers. It supports decisions about artifact readiness, interface risks, and revalidation before model reuse.

Graph Retrieval-Augmented Generation (GraphRAG) has emerged as a promising paradigm that organizes external knowledge into structured graphs of entities and relations, enabling large language models (LLMs) to perform complex reasoning beyond text-chunk retrieval. Recent advances have integrated reinforcement learning (RL) into agentic GraphRAG approaches, enabling iterative interactions with knowledge graphs during training. However, existing RL-based methods suffer from two key limitations: (1) they primarily depend on semantic similarity for retrieval, often overlooking the underlying graph topology, and (2) they rely on sparse, outcome-level rewards that fail to capture the quality of intermediate retrieval steps and their dependencies. To address these limitations, we propose HyperGraphPro, a progress-aware agentic framework for graph-based retrieval and multi-step reasoning. HyperGraphPro introduces a structure-aware hypergraph retrieval mechanism that jointly considers semantic relevance and graph connectivity, promoting coherent traversal along multi-hop reasoning paths. Furthermore, we design a progress-based stepwise policy optimization that provides dense learning signals by modulating advantages according to intermediate reasoning progress within a graph, rather than relying solely on final outcomes. Experiments on multi-hop question answering benchmarks demonstrate that HyperGraphPro consistently improves reasoning accuracy and generation quality over existing GraphRAG methods.

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

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.

When a data contributor requests removal, model trainers face a practical gap: unlearning algorithms require a forget set, yet no tool can locate which training records belong to a given author. Existing provenance systems operate at file or dataset level, forcing catastrophic over-deletion. We present ob, a record- and token-level data provenance system that propagates author identity through data processing pipelines and resolves revocation requests into precise forget sets via deterministic queries. Evaluation on 219,555 Wikipedia pages demonstrates that record-level provenance eliminates dataset-level over-deletion (from 101x to 1.3x), while integration adds 1.3-4.0% throughput overhead (HuggingFace) and 2.1-19.0% (Datatrove) on wiki data. On a 1.7B model, provenance-based forget sets improve unlearning by 42% over random baselines.

Advanced Persistent Threats (APTs) are stealthy cyberattacks that often evade detection in system-level audit logs. Provenance graphs model these logs as connected entities and events, revealing relationships that are missed by linear log representations. Existing systems apply anomaly detection to these graphs but often suffer from high false positive rates and coarse-grained alerts. Their reliance on node attributes like file paths or IPs leads to spurious correlations, reducing detection robustness and reliability. To fully understand an attack's progression and impact, security analysts need systems that can generate accurate, human-like narratives of the entire attack. To address these challenges, we introduce OCR-APT, a system for APT detection and reconstruction of human-like attack stories. OCR-APT uses Graph Neural Networks (GNNs) for subgraph anomaly detection, learning behavior patterns around nodes rather than fragile attributes such as file paths or IPs. This approach leads to a more robust anomaly detection. It then iterates over detected subgraphs using Large Language Models (LLMs) to reconstruct multi-stage attack stories. Each stage is validated before proceeding, reducing hallucinations and ensuring an interpretable final report. Our evaluations on the DARPA TC3, OpTC, and NODLINK datasets show that OCR-APT outperforms state-of-the-art systems in both detection accuracy and alert interpretability. Moreover, OCR-APT reconstructs human-like reports that comprehensively capture the attack story.

The exponential growth of data-driven systems and AI technologies has intensified the demand for high-quality web-sourced datasets. While existing datasets have proven valuable, conventional web data collection approaches face significant limitations in terms of human effort and scalability. Current data-collecting solutions fall into two categories: wrapper-based methods that struggle with adaptability and reproducibility, and large language model (LLM)-based approaches that incur substantial computational and financial costs. To address these challenges, we propose AutoData, a novel multi-agent system for Automated web Data collection, that requires minimal human intervention, i.e., only necessitating a natural language instruction specifying the desired dataset. In addition, AutoData is designed with a robust multi-agent architecture, featuring a novel oriented message hypergraph coordinated by a central task manager, to efficiently organize agents across research and development squads. Besides, we introduce a novel hypergraph cache system to advance the multi-agent collaboration process that enables efficient automated data collection and mitigates the token cost issues prevalent in existing LLM-based systems. Moreover, we introduce Instruct2DS, a new benchmark dataset supporting live data collection from web sources across three domains: academic, finance, and sports. Comprehensive evaluations over Instruct2DS and three existing benchmark datasets demonstrate AutoData's superior performance compared to baseline methods. Case studies on challenging tasks such as picture book collection and paper extraction from surveys further validate its applicability. Our source code and dataset are available at https://github.com/GraphResearcher/AutoData.

Hypergraph neural networks (HNNs) using neural networks to encode hypergraphs provide a promising way to model higher-order relations in data and further solve relevant prediction tasks built upon such higher-order relations. However, higher-order relations in practice contain complex patterns and are often highly irregular. So, it is often challenging to design an HNN that suffices to express those relations while keeping computational efficiency. Inspired by hypergraph diffusion algorithms, this work proposes a new HNN architecture named ED-HNN, which provably represents any continuous equivariant hypergraph diffusion operators that can model a wide range of higher-order relations. ED-HNN can be implemented efficiently by combining star expansions of hypergraphs with standard message passing neural networks. ED-HNN further shows great superiority in processing heterophilic hypergraphs and constructing deep models. We evaluate ED-HNN for node classification on nine real-world hypergraph datasets. ED-HNN uniformly outperforms the best baselines over these nine datasets and achieves more than 2\%uparrow in prediction accuracy over four datasets therein.

The burgeoning presence of multimodal content-sharing platforms propels the development of personalized recommender systems. Previous works usually suffer from data sparsity and cold-start problems, and may fail to adequately explore semantic user-product associations from multimodal data. To address these issues, we propose a novel Multi-Modal Hypergraph Contrastive Learning (MMHCL) framework for user recommendation. For a comprehensive information exploration from user-product relations, we construct two hypergraphs, i.e. a user-to-user (u2u) hypergraph and an item-to-item (i2i) hypergraph, to mine shared preferences among users and intricate multimodal semantic resemblance among items, respectively. This process yields denser second-order semantics that are fused with first-order user-item interaction as complementary to alleviate the data sparsity issue. Then, we design a contrastive feature enhancement paradigm by applying synergistic contrastive learning. By maximizing/minimizing the mutual information between second-order (e.g. shared preference pattern for users) and first-order (information of selected items for users) embeddings of the same/different users and items, the feature distinguishability can be effectively enhanced. Compared with using sparse primary user-item interaction only, our MMHCL obtains denser second-order hypergraphs and excavates more abundant shared attributes to explore the user-product associations, which to a certain extent alleviates the problems of data sparsity and cold-start. Extensive experiments have comprehensively demonstrated the effectiveness of our method. Our code is publicly available at: https://github.com/Xu107/MMHCL.

Higher-order interactions (HOIs) are ubiquitous in real-world complex systems and applications. Investigation of deep learning for HOIs, thus, has become a valuable agenda for the data mining and machine learning communities. As networks of HOIs are expressed mathematically as hypergraphs, hypergraph neural networks (HNNs) have emerged as a powerful tool for representation learning on hypergraphs. Given the emerging trend, we present the first survey dedicated to HNNs, with an in-depth and step-by-step guide. Broadly, the present survey overviews HNN architectures, training strategies, and applications. First, we break existing HNNs down into four design components: (i) input features, (ii) input structures, (iii) message-passing schemes, and (iv) training strategies. Second, we examine how HNNs address and learn HOIs with each of their components. Third, we overview the recent applications of HNNs in recommendation, bioinformatics and medical science, time series analysis, and computer vision. Lastly, we conclude with a discussion on limitations and future directions.

Foundation-model research increasingly needs data about people: user state, personal histories, relationships, contact-like fields, documents, and longitudinal updates. Real user data is difficult to share, perturb, audit, or redistribute responsibly, while independently generated fake fields rarely preserve the cross-field and temporal consistency needed for controlled evaluation. We present PROFILEFOUNDRY, a deterministic generator and fixed reference release of 100,000 adult synthetic Person Objects across eight locales. Each object combines a typed current snapshot, household, family, and employer links, snapshot-aligned events, normalized relational views, and generation provenance. The release contains 709,228 events, 40,338 households, 52,491 employers, and 518,564 directed relationship edges. We report evidence in separate categories: selected population-marginal comparisons, per-object invariant checks, release-wide referential and temporal closure, and coincidence/provenance screens. PROFILEFOUNDRY is not a population-fidelity model, a rendered-text corpus, or a formal privacy mechanism. Instead, it is a responsible synthetic source layer for constructing downstream foundation-model evaluations involving memory, privacy, document understanding, record linkage, and agent state while keeping the synthetic person behind each artifact inspectable

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.

Sustainability disclosure standards (e.g., GRI, SASB, TCFD, IFRS S2) are comprehensive yet lengthy, terminology-dense, and highly cross-referential, hindering structured analysis and downstream use. We present SSKG Hub (Sustainability Standards Knowledge Graph Hub), a research prototype and interactive web platform that transforms standards into auditable knowledge graphs (KGs) through an LLM-centered, expert-guided pipeline. The system integrates automatic standard identification, configurable chunking, standard-specific prompting, robust triple parsing, and provenance-aware Neo4j storage with fine-grained audit metadata. LLM extraction produces a provenance-linked Draft KG, which is reviewed, curated, and formally promoted to a Certified KG through meta-expert adjudication. A role-based governance framework covering read-only guest access, expert review and CRUD operations, meta-expert certification, and administrative oversight ensures traceability and accountability across draft and certified states. Beyond graph exploration and triple-level evidence tracing, SSKG Hub supports cross-KG fusion, KG-driven tasks, and dedicated modules for insights and curated resources. We validate the platform through a comprehensive expert-led KG review case study that demonstrates end-to-end curation and quality assurance. The web application is publicly available at www.sskg-hub.com.

Text-to-3D generation represents an exciting field that has seen rapid advancements, facilitating the transformation of textual descriptions into detailed 3D models. However, current progress often neglects the intricate high-order correlation of geometry and texture within 3D objects, leading to challenges such as over-smoothness, over-saturation and the Janus problem. In this work, we propose a method named ``3D Gaussian Generation via Hypergraph (Hyper-3DG)'', designed to capture the sophisticated high-order correlations present within 3D objects. Our framework is anchored by a well-established mainflow and an essential module, named ``Geometry and Texture Hypergraph Refiner (HGRefiner)''. This module not only refines the representation of 3D Gaussians but also accelerates the update process of these 3D Gaussians by conducting the Patch-3DGS Hypergraph Learning on both explicit attributes and latent visual features. Our framework allows for the production of finely generated 3D objects within a cohesive optimization, effectively circumventing degradation. Extensive experimentation has shown that our proposed method significantly enhances the quality of 3D generation while incurring no additional computational overhead for the underlying framework. (Project code: https://github.com/yjhboy/Hyper3DG)

Large language model (LLM) agents increasingly rely on external tools to complete complex real-world tasks. However, reliable tool-use planning remains challenging due to the limitations of implicit reasoning and the evolving nature of real-world execution environments. Existing tool-use agents typically rely on LLMs to infer tool compositions from textual descriptions, which can lead to inefficient exploration and unreliable execution in complex tasks. To address these challenges, we model tool relations at the schema level and construct a directed Tool--Schema Hypergraph, in which tools are represented as hyperedges from their required input-schema nodes to their output-schema nodes. Furthermore, we propose HyperAgent, a Tool--Schema Hypergraph-guided framework for dynamic planning and execution. Given a task, HyperAgent first extracts a task-relevant tool context graph and uses it to guide the construction of a schema-aware Task DAG. During execution, HyperAgent dynamically realizes each subtask by constructing a state-conditioned tool support graph through deficit-oriented expansion, which identifies unresolved requirements and retrieves supporting producer tools according to the current agent state. Experiments on AppWorld demonstrate that HyperAgent improves task completion performance while reducing redundant API calls, LLM interactions, and token consumption compared with existing agent baselines.

Visual fluency in generated video does not imply physical reliability, and a scalar quality score alone is incapable of indicating the obligation a clip violates or the moment it fails. We present VeriPhy, an auditable physical-verification system in which a text-only planner compiles the prompt into typed physical obligations and a statically validated execution plan before any frame is observed. During execution, observations gate and scope only declared calls to frozen low-level experts (e.g., segmentation and tracking, counting, eleven typed physical measurements over the resulting tracks, depth, OCR, and audio-event detection). Each action returns a provenance-carrying evidence record whose payload, when usable, is either a typed measurement or an explicitly tagged learned state. Typed resolvers and fixed composition map usable records to a three-valued state (supported, contradicted, or unknown, surfaced as plausible, implausible, or abstain) with full provenance, so that every verdict is traceable to the evidence that produced it. We anchor evaluation in a 1,500-clip corpus of human-annotated flaw records that localize real generation failures in prompt reference, space, and time. On a 149-clip core carrying 304 such records, VeriPhy accounts for 228, against 164 for a published question-decomposition evaluator given the same clips and the same claims. Recall alone does not separate it from prompting the same backbone monolithically, which reaches 222; what separates them is that each decision retains its evidence record and provenance, making the traces auditable one verdict at a time and usable as the interface through which a critic verdict could be written back into generation.

As agentic tasks grow in complexity, LLM agents increasingly rely on experiential memory to reuse procedural knowledge across tasks. Effective memory design must jointly address what to store, how memory is structured and retrieved, and how memory evolves. Existing systems tackle each only partially: they store trajectories, insights, or workflows as isolated entries, discarding compositional relationships among subtasks and reusable skills; retrieve by flat embedding similarity that ignores relational signals; and maintain memory without leveraging its relational structure. We propose HyperSkill, a hypergraph-based memory framework that jointly improves all three. HyperSkill represents memory as a hypergraph with two node types, subtask steps and reusable skills, where each hyperedge links the subtasks and skills from a single trajectory. Dual-path retrieval queries both subtask and trajectory levels, ranking skills by co-occurrence across retrieved trajectories. Periodic structure-informed maintenance prunes low-utility nodes and merges redundant skills via quality-weighted propagation. Across xBench, GAIA, and WebWalkerQA with GPT-4o and Qwen3-30B-A3B, HyperSkill outperforms ten memory baselines, yielding gains of up to +11.51 on GAIA and +11.18 on WebWalkerQA.

Temporal hypergraphs provide a powerful paradigm for modeling time-dependent, higher-order interactions in complex systems. Representation learning for hypergraphs is essential for extracting patterns of the higher-order interactions that are critically important in real-world problems in social network analysis, neuroscience, finance, etc. However, existing methods are typically designed only for specific tasks or static hypergraphs. We present CAT-Walk, an inductive method that learns the underlying dynamic laws that govern the temporal and structural processes underlying a temporal hypergraph. CAT-Walk introduces a temporal, higher-order walk on hypergraphs, SetWalk, that extracts higher-order causal patterns. CAT-Walk uses a novel adaptive and permutation invariant pooling strategy, SetMixer, along with a set-based anonymization process that hides the identity of hyperedges. Finally, we present a simple yet effective neural network model to encode hyperedges. Our evaluation on 10 hypergraph benchmark datasets shows that CAT-Walk attains outstanding performance on temporal hyperedge prediction benchmarks in both inductive and transductive settings. It also shows competitive performance with state-of-the-art methods for node classification. (https://github.com/ubc-systopia/CATWalk)

Real-world documents distribute evidence across text, tables, figures, and captions within complex page layouts. Answering complex questions over such documents therefore requires more than retrieving relevant passages: systems must recover the evidence topology that connects heterogeneous evidence units. Existing GraphRAG evaluations remain largely text-centered, while multimodal document RAG benchmarks assess cross-modal retrieval and generation without directly evaluating recovery of the intended evidence topology. We introduce TOPOGRAPHRAG-BENCH, a layout-grounded benchmark for multimodal evidence reasoning in GraphRAG, comprising 2,024 questions over 201 long, visually rich documents. Questions are constructed bottom-up from text, figure, and table evidence units under three controlled topologies: single-hop retrieval, bridge-chain reasoning, and multi-source synthesis. To ensure that questions preserve their intended structure, we apply counterfactual validation for shortcut resistance, modality necessity, and evidence necessity. We evaluate text-only GraphRAG, page-level visual retrieval, and multimodal GraphRAG systems using retrieval, generation, and topology-aware reasoning metrics. Multimodal GraphRAG systems achieve the strongest overall performance, but still fail when visual-textual evidence alignment or multi-unit composition is incomplete. Text-only GraphRAG struggles when key dependencies are grounded in figures or tables, while page-level visual retrieval lacks the fine-grained structure needed for topology recovery. These findings motivate GraphRAG systems that move beyond text-derived entity relation graphs to explicitly model document layouts, cross-modal evidence alignment, and the reasoning roles of evidence units. Code and data are available at https://richardlrc.github.io/TopoGraphRAG-Bench/.

Hyper-relational knowledge graphs (HKGs) extend standard knowledge graphs by associating attribute-value qualifiers to triples, which effectively represent additional fine-grained information about its associated triple. Hyper-relational knowledge graph completion (HKGC) aims at inferring unknown triples while considering its qualifiers. Most existing approaches to HKGC exploit a global-level graph structure to encode hyper-relational knowledge into the graph convolution message passing process. However, the addition of multi-hop information might bring noise into the triple prediction process. To address this problem, we propose HyperFormer, a model that considers local-level sequential information, which encodes the content of the entities, relations and qualifiers of a triple. More precisely, HyperFormer is composed of three different modules: an entity neighbor aggregator module allowing to integrate the information of the neighbors of an entity to capture different perspectives of it; a relation qualifier aggregator module to integrate hyper-relational knowledge into the corresponding relation to refine the representation of relational content; a convolution-based bidirectional interaction module based on a convolutional operation, capturing pairwise bidirectional interactions of entity-relation, entity-qualifier, and relation-qualifier. realize the depth perception of the content related to the current statement. Furthermore, we introduce a Mixture-of-Experts strategy into the feed-forward layers of HyperFormer to strengthen its representation capabilities while reducing the amount of model parameters and computation. Extensive experiments on three well-known datasets with four different conditions demonstrate HyperFormer's effectiveness. Datasets and code are available at https://github.com/zhiweihu1103/HKGC-HyperFormer.

The race to train language models on vast, diverse, and inconsistently documented datasets has raised pressing concerns about the legal and ethical risks for practitioners. To remedy these practices threatening data transparency and understanding, we convene a multi-disciplinary effort between legal and machine learning experts to systematically audit and trace 1800+ text datasets. We develop tools and standards to trace the lineage of these datasets, from their source, creators, series of license conditions, properties, and subsequent use. Our landscape analysis highlights the sharp divides in composition and focus of commercially open vs closed datasets, with closed datasets monopolizing important categories: lower resource languages, more creative tasks, richer topic variety, newer and more synthetic training data. This points to a deepening divide in the types of data that are made available under different license conditions, and heightened implications for jurisdictional legal interpretations of copyright and fair use. We also observe frequent miscategorization of licenses on widely used dataset hosting sites, with license omission of 72%+ and error rates of 50%+. This points to a crisis in misattribution and informed use of the most popular datasets driving many recent breakthroughs. As a contribution to ongoing improvements in dataset transparency and responsible use, we release our entire audit, with an interactive UI, the Data Provenance Explorer, which allows practitioners to trace and filter on data provenance for the most popular open source finetuning data collections: www.dataprovenance.org.

In this paper, we present a hypergraph neural networks (HGNN) framework for data representation learning, which can encode high-order data correlation in a hypergraph structure. Confronting the challenges of learning representation for complex data in real practice, we propose to incorporate such data structure in a hypergraph, which is more flexible on data modeling, especially when dealing with complex data. In this method, a hyperedge convolution operation is designed to handle the data correlation during representation learning. In this way, traditional hypergraph learning procedure can be conducted using hyperedge convolution operations efficiently. HGNN is able to learn the hidden layer representation considering the high-order data structure, which is a general framework considering the complex data correlations. We have conducted experiments on citation network classification and visual object recognition tasks and compared HGNN with graph convolutional networks and other traditional methods. Experimental results demonstrate that the proposed HGNN method outperforms recent state-of-the-art methods. We can also reveal from the results that the proposed HGNN is superior when dealing with multi-modal data compared with existing methods.

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.

LLM-based agents have demonstrated strong capabilities in data-intensive analytical tasks, yet their outputs are rarely verifiable: a reliance on linear text trajectories makes their reasoning difficult to audit. In particular, deterministic computations over raw data and semantic deductions over natural-language claims are often entangled in an unstructured stream, leaving numerical conclusions hard to reproduce and qualitative judgments hard to inspect. To address this, we propose VeriGraph, a traceable neuro-symbolic reasoning framework that enables agents to construct an explicit heterogeneous evidence directed acyclic graph (DAG) during execution. VeriGraph introduces three evidence-expansion primitives, namely computational, grounding, and derivational expansion, to connect raw data, interpreter variables, computed results, and natural-language claims in a unified graph. Under this formulation, structural traceability is reduced to graph reachability from raw data sources to terminal claims, while semantic support is measured by claim-level evidence evaluation. To improve graph construction, we further design a graph-based policy optimization strategy with a composite reward that jointly supervises answer correctness, computational integrity, and derivational coherence. Experiments on four benchmarks show that VeriGraph-8B achieves the highest overall score among all baselines. More importantly, VeriGraph produces auditable evidence graphs with substantially stronger claim grounding, achieving a 87.61\% Grounding Rate under our claim-level evidence support evaluation. These results suggest that explicit evidence-graph construction is a promising path toward verifiable data-analytic agents. Our code is available at https://github.com/ignorejjj/VeriGraph.

Mathematical knowledge is organized around statements and their dependencies, but this structure is exposed unevenly: informal papers cite mostly at the document level, while formal libraries record fine-grained dependencies over a much smaller body of mathematics. We introduce TheoremGraph, a unified statement-level dependency graph spanning both informal and formal mathematics. On the informal side, we parse 11.7M theorem-like environments from mathematics arXiv and recover 18.3M candidate directed dependencies, each labeled by the extractor that proposed it so downstream users can trade coverage for precision. On the formal side, we release LeanGraph, a Lean 4 elaborator-level extractor producing 388,105 declaration nodes and 11.3M typed edges across 25 Lean projects. We bridge the two graphs by embedding generated natural-language slogans into a shared semantic space, linking related statements across papers and across the informal/formal divide; an LLM judge affirms 47,952 such matches above a 0.8 cosine floor, with the judge-acceptance rate rising from 48% across the floor to 87% in the >=0.9 tier. On formal concept retrieval, our name-and-signature representation with graph expansion comes within 0.5pp of LeanSearch v2's reranked Recall@10 (0.775 vs. 0.780) without an LM reranker. We release the dataset, extractors, HTTP API, and MCP interface as infrastructure for mathematical search, attribution, and retrieval-augmented reasoning, available at theoremsearch.com and huggingface.co/datasets/uw-math-ai/theorem-matching.

Knowledge graph (KG) embeddings learn low-dimensional representations of entities and relations to predict missing facts. KGs often exhibit hierarchical and logical patterns which must be preserved in the embedding space. For hierarchical data, hyperbolic embedding methods have shown promise for high-fidelity and parsimonious representations. However, existing hyperbolic embedding methods do not account for the rich logical patterns in KGs. In this work, we introduce a class of hyperbolic KG embedding models that simultaneously capture hierarchical and logical patterns. Our approach combines hyperbolic reflections and rotations with attention to model complex relational patterns. Experimental results on standard KG benchmarks show that our method improves over previous Euclidean- and hyperbolic-based efforts by up to 6.1% in mean reciprocal rank (MRR) in low dimensions. Furthermore, we observe that different geometric transformations capture different types of relations while attention-based transformations generalize to multiple relations. In high dimensions, our approach yields new state-of-the-art MRRs of 49.6% on WN18RR and 57.7% on YAGO3-10.

Volume-based multimodal retrieval jointly scores a text query with a candidate's video, audio, and subtitle embeddings. While this approach captures higher-order within-candidate alignment, the score remains candidate-local, and semantically related training samples primarily serve as contrastive negatives. This work introduces Hypergraph-Regularized Gramian Volumes (HyVol), a training-time module that incorporates these semantic relations prior to evaluating the original volume loss. Document hyperedges connect the observed modalities of each candidate, whereas semantic hyperedges link candidates whose detached captions are mutual top-k neighbors. A shallow gated hyper-graph network applies residual corrections to the modality embeddings. Presence masks exclude unavailable streams from message passing, and identity padding preserves the determinant of the observed Gram submatrix without feature imputation. As refinement operates on embeddings rather than scores, the same construction applies to both Gram and HyperGram. We remove the hypergraph after training, leaving the backbone-only architecture, original scoring function, and retrieval cost unchanged. We train both backbones on a 150K-clip subset of VAST-27M and evaluate zero-shot performance on six benchmarks. Under the paired protocol, HyVol improves R@1 across all five retrieval benchmarks, with video-to-text gains reaching +8.3 on MSR-VTT and +7.6 on VATEX. Under missing-modality masking, the V2T margin remains positive in all experimental settings, although the T2V margin becomes slightly negative in four.

Reasoning ability is one of the most crucial capabilities of a foundation model, signifying its capacity to address complex reasoning tasks. Chain-of-Thought (CoT) technique is widely regarded as one of the effective methods for enhancing the reasoning ability of foundation models and has garnered significant attention. However, the reasoning process of CoT is linear, step-by-step, similar to personal logical reasoning, suitable for solving general and slightly complicated problems. On the contrary, the thinking pattern of an expert owns two prominent characteristics that cannot be handled appropriately in CoT, i.e., high-order multi-hop reasoning and multimodal comparative judgement. Therefore, the core motivation of this paper is transcending CoT to construct a reasoning paradigm that can think like an expert. The hyperedge of a hypergraph could connect various vertices, making it naturally suitable for modelling high-order relationships. Inspired by this, this paper innovatively proposes a multimodal Hypergraph-of-Thought (HoT) reasoning paradigm, which enables the foundation models to possess the expert-level ability of high-order multi-hop reasoning and multimodal comparative judgement. Specifically, a textual hypergraph-of-thought is constructed utilizing triple as the primary thought to model higher-order relationships, and a hyperedge-of-thought is generated through multi-hop walking paths to achieve multi-hop inference. Furthermore, we devise a visual hypergraph-of-thought to interact with the textual hypergraph-of-thought via Cross-modal Co-Attention Graph Learning for multimodal comparative verification. Experimentations on the ScienceQA benchmark demonstrate the proposed HoT-based T5 outperforms CoT-based GPT3.5 and chatGPT, which is on par with CoT-based GPT4 with a lower model size.

Scientific figures often encode the visual evidence behind scientific findings, yet figure plagiarism remains underexplored as a benchmarked multimodal evaluation problem. We present SciFigPlag-Bench, a benchmark for provenance-aware reasoning over scientific figures in scholarly documents. Unlike general image-similarity or image-forensics benchmarks, SciFigPlag-Bench evaluates whether a suspicious figure reuses evidence from a specific source figure, how the reused content has been transformed, and where the reused evidence appears. We introduce a factorized taxonomy that separates what is reused from how it is transformed, covering material-preserving reuse, such as full-figure and subfigure reuse, as well as abstract-content reuse, such as data re-expression and structural redraw. Guided by this taxonomy, we construct a hybrid benchmark with 2,582 positive pairs and 2,541 negative pairs, combining documented real-world cases, taxonomy-guided synthetic examples, and visually similar negatives. The benchmark supports four diagnostic tasks: pairwise detection, source attribution, hierarchical reuse-type classification, and reuse correspondence localization. Experiments with diverse vision-language models establish initial baselines and reveal persistent challenges in fine-grained provenance reasoning, reuse-type understanding, and spatial evidence grounding.

Knowledge graph foundation models such as ULTRA achieve zero-shot link prediction on unseen graphs through dedicated architectures that hard-code a transfer mechanism. In this work we move that mechanism out of the architecture and into the representation, by reifying the input graph: every fact becomes a node, connected to its subject, object, and relation type through a fixed vocabulary of six meta-relations, with relation types as anonymous shared nodes rather than model parameters. On this representation, five textbook GNNs (GAT, GINE with sum and with mean+max aggregation, GraphSAGE, R-GCN), each trained on a single knowledge graph of 4,245 triples for 30 minutes on one NVIDIA A100, transfer zero-shot to 40 inductive link-prediction benchmarks. The best of them, an off-the-shelf GAT, matches ULTRA, a dedicated foundation model pretrained on three graphs, across ULTRA's own evaluation suite. The same fixed vocabulary extends to relational databases, a row becoming an entity and a foreign-key column a relation type; a preliminary probe on two unseen databases, with no cell values, schema text or in-context labels, shows a model of this family pretrained on three knowledge graphs ranking foreign-key targets far above random-initialization and degree controls. We release the code, the checkpoints, and the evaluation pipeline for all 40 benchmarks.

Relation extraction has the potential for large-scale knowledge graph construction, but current methods do not consider the qualifier attributes for each relation triplet, such as time, quantity or location. The qualifiers form hyper-relational facts which better capture the rich and complex knowledge graph structure. For example, the relation triplet (Leonard Parker, Educated At, Harvard University) can be factually enriched by including the qualifier (End Time, 1967). Hence, we propose the task of hyper-relational extraction to extract more specific and complete facts from text. To support the task, we construct HyperRED, a large-scale and general-purpose dataset. Existing models cannot perform hyper-relational extraction as it requires a model to consider the interaction between three entities. Hence, we propose CubeRE, a cube-filling model inspired by table-filling approaches and explicitly considers the interaction between relation triplets and qualifiers. To improve model scalability and reduce negative class imbalance, we further propose a cube-pruning method. Our experiments show that CubeRE outperforms strong baselines and reveal possible directions for future research. Our code and data are available at github.com/declare-lab/HyperRED.

Tool-using LLM agents increasingly use the Model Context Protocol (MCP) to answer from heterogeneous evidence sources, including search, APIs, databases, clinical records, and formulary tools. Standard factuality metrics usually test whether an answer is supported by pooled evidence, missing a provenance-sensitive failure mode: a claim may be supported somewhere while being attributed to the wrong source. We call this cross-source conflation. We introduce ProvenanceGuard, a source-aware verifier for MCP-grounded answers. It consumes captured MCP traces with stable tool IDs, source IDs, and raw outputs; decomposes answers into atomic claims; routes claims to source-specific evidence; checks support with NLI and a token-alignment proxy; compares stated attribution with the routed source; and returns per-claim verdicts plus an answer-level allow/block decision. Blocked answers can be repaired with retrieval-augmented answer revision and re-verified. We evaluate on 281 medical-domain MCP-agent traces. A 266-trace adjudicated subset yields 2,325 LLM-assisted claim labels split by trace; 361 held-out labels are human-verified. On the 40-trace held-out split, ProvenanceGuard achieves block F1 0.802 and source accuracy 0.858 over 260 source-eligible claims, outperforming source-blind baselines that do not emit claim-to-source IDs. On a harder multi-source benchmark it reaches block F1 0.846, while source-plus-relation accuracy drops to 0.229, showing that exact source ownership remains difficult with semantically close sources. Repair-and-reverify resolves all blocked answers in the full trace set, often via conservative fallback. In 50 controlled clinical conflation probes, ProvenanceGuard detects all injected attribution swaps with no retained wrong attribution. These results show that source attribution is an independent axis for factuality verification in MCP-based agents.

Graph neural networks have recently achieved remarkable success in representing graph-structured data, with rapid progress in both the node embedding and graph pooling methods. Yet, they mostly focus on capturing information from the nodes considering their connectivity, and not much work has been done in representing the edges, which are essential components of a graph. However, for tasks such as graph reconstruction and generation, as well as graph classification tasks for which the edges are important for discrimination, accurately representing edges of a given graph is crucial to the success of the graph representation learning. To this end, we propose a novel edge representation learning framework based on Dual Hypergraph Transformation (DHT), which transforms the edges of a graph into the nodes of a hypergraph. This dual hypergraph construction allows us to apply message-passing techniques for node representations to edges. After obtaining edge representations from the hypergraphs, we then cluster or drop edges to obtain holistic graph-level edge representations. We validate our edge representation learning method with hypergraphs on diverse graph datasets for graph representation and generation performance, on which our method largely outperforms existing graph representation learning methods. Moreover, our edge representation learning and pooling method also largely outperforms state-of-the-art graph pooling methods on graph classification, not only because of its accurate edge representation learning, but also due to its lossless compression of the nodes and removal of irrelevant edges for effective message-passing.

Enterprise property graphs vary widely in schema structure, internal terminology, domain assumptions, governance constraints, and user interaction patterns. A deployment-relevant Text2Cypher benchmark therefore reflects the questions users and agents actually ask of that graph. Creating such a benchmark is difficult because schemas and values are unique, and graph structure changes over time. Each NL-query pair must also be executable, use real graph entities, preserve diversity, and remain balanced across query types and difficulty levels. We present PIPE-Cypher, a local benchmark-generation pipeline that turns a live property graph and optional seed queries from customer questions, analyst logs, or agent tool calls into balanced NL-to-Cypher benchmarks. PIPE-Cypher combines schema profiling, reverse-query grounding, constrained generation, deterministic Cypher governance, execution validation, redaction, diversity controls, and a calibrated local LLM judge. Using local Qwen3.5-9B generation and judging, PIPE-Cypher exports 3,000 accepted FinBench/SNB examples, completes three audited ablation suites, calibrates judge behavior with human labels, and evaluates 11 local downstream models. The resulting benchmark is deliberately discriminative: zero-shot transfer is weak, while a few-shot control shows that schema-specific example banks can help compatible model families. Together, PIPE-Cypher makes Text2Cypher benchmarking a repeatable process that evolves with the graph, its users, and its target workloads.

Code classification is a difficult issue in program understanding and automatic coding. Due to the elusive syntax and complicated semantics in programs, most existing studies use techniques based on abstract syntax tree (AST) and graph neural network (GNN) to create code representations for code classification. These techniques utilize the structure and semantic information of the code, but they only take into account pairwise associations and neglect the high-order correlations that already exist between nodes in the AST, which may result in the loss of code structural information. On the other hand, while a general hypergraph can encode high-order data correlations, it is homogeneous and undirected which will result in a lack of semantic and structural information such as node types, edge types, and directions between child nodes and parent nodes when modeling AST. In this study, we propose to represent AST as a heterogeneous directed hypergraph (HDHG) and process the graph by heterogeneous directed hypergraph neural network (HDHGN) for code classification. Our method improves code understanding and can represent high-order data correlations beyond paired interactions. We assess heterogeneous directed hypergraph neural network (HDHGN) on public datasets of Python and Java programs. Our method outperforms previous AST-based and GNN-based methods, which demonstrates the capability of our model.

Explaining an inferred fact under rule evaluation can require identifying the inclusion-minimal input sets that suffice for the inference and the deletions that make the fact disappear. For a fixed union of conjunctive queries, every minimal support is bounded by the query body. For recursive rules, the same answer may depend on large supports, and the number of minimal supports may be exponential in the input. We study the gap through deletion-based explanation, using inclusion-minimal endogenous input facts that entail the atom together with fixed background facts. We organize these supports as a hypergraph and prove that it determines actual causes, counterfactual causes, responsibility, and deletion robustness. The resulting view separates nonrecursive queries from recursive Datalog at the level of minimal input explanations. For positive-length reachability, minimal supports are exactly simple directed paths, and deletion robustness is the minimum directed edge cut. We also prove invariance under fixed-goal equivalent positive Datalog programs and an NP-hardness calibration for the robustness threshold problem.

When a multimodal AI agent is asked to forget a fact, current memory systems usually delete the text entry and report success. We find that the fact can remain recoverable from retained user images, including images tagged to entirely different facts, because VLMs use implicit visual cues at inference time. We introduce the Information Provenance Graph (IPG), a taxonomy that classifies memory representations by deletion affordance. The IPG reveals that deletion fails through multiple channels. Our benchmark, MemLeak, measures this across a deletion cascade: direct probing of deletion-capable systems yields <1%, but retained correlated text enables 18.3% recovery, and retained images enable 12.0% recovery (0.0% blind baseline, 0.3% FPR) -- with 47% of image leaks not text-recoverable. Content-aware semantic deletion reduces the image residual to 2.0%. The residual appears across multiple VLMs, a production memory system, and real Unsplash-licensed photographs. Dual-annotator human validation (kappa = 0.88) confirms judge reliability.

Higher-order models (e.g., hypergraph neural networks) often outperform lower-order baselines on hypergraph learning benchmarks, and their advantages are commonly attributed to their ability to exploit higher-order information. However, better performance alone does not establish this explanation. We therefore ask: Do higher-order models win for higher-order reasons? To investigate this question, we introduce a controlled performance-attribution framework that perturbs higher-order information while preserving the lower-order, i.e., pairwise, information. Across 25 commonly used hypergraph learning benchmarks spanning three tasks, we frequently observe an intriguing pattern: higher-order models originally outperform lower-order baselines, yet retain most of their advantage after perturbation. This suggests that much of the observed advantage remains achievable without the higher-order information. We then investigate potential lower-order explanations for these remaining gaps. We find that simple additions to a lower-order baseline, e.g., richer pairwise weighting, more steps of pairwise feature propagation, and normalization, reduce the remaining performance gaps, supporting lower-order explanations for part of the observed advantage. Our analysis calls for the hypergraph learning community to rethink performance attribution by distinguishing performance gains from their explanations, adopt stronger lower-order baselines, and use suitable benchmarks that better test the value of higher-order information.

Biomedical knowledge graphs (KGs) are widely used in the life sciences, yet many are derived from unstructured documents and therefore lack schema-level constrains, whereas graphs assembled from structured resources are difficult to harmonize into a unified representation. We present OptimusKG, a multimodal biomedical labeled property graph (LPG) built from structured and semi-structured resources to preserve factual, type-specific metadata across molecular, anatomical, clinical, and environmental domains. OptimusKG contains 190,531 nodes across 10 entity types, 21,813,816 edges across 26 relation types, and 67,249,863 property instances encoding 110,276,843 values across 150 distinct property keys, derived from 18 ontologies and controlled vocabularies. The graph enforces a top-level schema for nodes and edges and retains granular, type-specific properties, cross-references, and provenance across molecular, anatomical, clinical, and environmental domains. We assessed the validity of OptimusKG by evaluating whether graph relationships are supported by evidence from the scientific literature using a multimodal agent, PaperQA3. PaperQA3 identified supporting evidence for 70.0% of sampled edges, whereas 83.4% of sampled false edges received no supporting evidence. Edges without literature support were concentrated in associations derived from experimental and functional genomics resources, suggesting that OptimusKG captures biomedical knowledge that may precede synthesis in the scientific literature. OptimusKG is distributed as Apache Parquet files, providing a standardized resource for graph-based machine learning, knowledge-grounded retrieval with large language models, and biomedical discovery use cases such as hypothesis generation.

Machine-assisted theorem proving refers to the process of conducting structured reasoning to automatically generate proofs for mathematical theorems. Recently, there has been a surge of interest in using machine learning models in conjunction with proof assistants to perform this task. In this paper, we introduce Pantograph, a tool that provides a versatile interface to the Lean 4 proof assistant and enables efficient proof search via powerful search algorithms such as Monte Carlo Tree Search. In addition, Pantograph enables high-level reasoning by enabling a more robust handling of Lean 4's inference steps. We provide an overview of Pantograph's architecture and features. We also report on an illustrative use case: using machine learning models and proof sketches to prove Lean 4 theorems. Pantograph's innovative features pave the way for more advanced machine learning models to perform complex proof searches and high-level reasoning, equipping future researchers to design more versatile and powerful theorem provers.

E-commerce platforms should provide detailed product descriptions (attribute values) for effective product search and recommendation. However, attribute value information is typically not available for new products. To predict unseen attribute values, large quantities of labeled training data are needed to train a traditional supervised learning model. Typically, it is difficult, time-consuming, and costly to manually label large quantities of new product profiles. In this paper, we propose a novel method to efficiently and effectively extract unseen attribute values from new products in the absence of labeled data (zero-shot setting). We propose HyperPAVE, a multi-label zero-shot attribute value extraction model that leverages inductive inference in heterogeneous hypergraphs. In particular, our proposed technique constructs heterogeneous hypergraphs to capture complex higher-order relations (i.e. user behavior information) to learn more accurate feature representations for graph nodes. Furthermore, our proposed HyperPAVE model uses an inductive link prediction mechanism to infer future connections between unseen nodes. This enables HyperPAVE to identify new attribute values without the need for labeled training data. We conduct extensive experiments with ablation studies on different categories of the MAVE dataset. The results demonstrate that our proposed HyperPAVE model significantly outperforms existing classification-based, generation-based large language models for attribute value extraction in the zero-shot setting.

Graph-based retrieval-augmented generation (RAG) methods, typically built on knowledge graphs (KGs) with binary relational facts, have shown promise in multi-hop open-domain QA. However, their rigid retrieval schemes and dense similarity search often introduce irrelevant context, increase computational overhead, and limit relational expressiveness. In contrast, n-ary hypergraphs encode higher-order relational facts that capture richer inter-entity dependencies and enable shallower, more efficient reasoning paths. To address this limitation, we propose HyperRAG, a RAG framework tailored for n-ary hypergraphs with two complementary retrieval variants: (i) HyperRetriever learns structural-semantic reasoning over n-ary facts to construct query-conditioned relational chains. It enables accurate factual tracking, adaptive high-order traversal, and interpretable multi-hop reasoning under context constraints. (ii) HyperMemory leverages the LLM's parametric memory to guide beam search, dynamically scoring n-ary facts and entities for query-aware path expansion. Extensive evaluations on WikiTopics (11 closed-domain datasets) and three open-domain QA benchmarks (HotpotQA, MuSiQue, and 2WikiMultiHopQA) validate HyperRAG's effectiveness. HyperRetriever achieves the highest answer accuracy overall, with average gains of 2.95% in MRR and 1.23% in Hits@10 over the strongest baseline. Qualitative analysis further shows that HyperRetriever bridges reasoning gaps through adaptive and interpretable n-ary chain construction, benefiting both open and closed-domain QA.

Visual recognition relies on understanding both the semantics of image tokens and the complex interactions among them. Mainstream self-attention methods, while effective at modeling global pair-wise relations, fail to capture high-order associations inherent in real-world scenes and often suffer from redundant computation. Hypergraphs extend conventional graphs by modeling high-order interactions and offer a promising framework for addressing these limitations. However, existing hypergraph neural networks typically rely on static and hard hyperedge assignments, leading to excessive and redundant hyperedges with hard binary vertex memberships that overlook the continuity of visual semantics. To overcome these issues, we present Soft Hypergraph Neural Networks (SoftHGNNs), which extend the methodology of hypergraph computation, to make it truly efficient and versatile in visual recognition tasks. Our framework introduces the concept of soft hyperedges, where each vertex is associated with hyperedges via continuous participation weights rather than hard binary assignments. This dynamic and differentiable association is achieved by using the learnable hyperedge prototype. Through similarity measurements between token features and the prototype, the model generates semantically rich soft hyperedges. SoftHGNN then aggregates messages over soft hyperedges to capture high-order semantics. To further enhance efficiency when scaling up the number of soft hyperedges, we incorporate a sparse hyperedge selection mechanism that activates only the top-k important hyperedges, along with a load-balancing regularizer to ensure balanced hyperedge utilization. Experimental results across three tasks on five datasets demonstrate that SoftHGNN efficiently captures high-order associations in visual scenes, achieving significant performance improvements.

Recent provenance-based intrusion detection systems (PIDSs) have demonstrated strong potential for detecting advanced persistent threats (APTs) by applying machine learning to system provenance graphs. However, evaluating and comparing PIDSs remains difficult: prior work uses inconsistent preprocessing pipelines, non-standard dataset splits, and incompatible ground-truth labeling and metrics. These discrepancies undermine reproducibility, impede fair comparison, and impose substantial re-implementation overhead on researchers. We present PIDSMaker, an open-source framework for developing and evaluating PIDSs under consistent protocols. PIDSMaker consolidates eight state-of-the-art systems into a modular, extensible architecture with standardized preprocessing and ground-truth labels, enabling consistent experiments and apples-to-apples comparisons. A YAML-based configuration interface supports rapid prototyping by composing components across systems without code changes. PIDSMaker also includes utilities for ablation studies, hyperparameter tuning, multi-run instability measurement, and visualization, addressing methodological gaps identified in prior work. We demonstrate PIDSMaker through concrete use cases and release it with preprocessed datasets and labels to support shared evaluation for the PIDS community.

As agentic applications increasingly route user tasks through official and third-party LLM APIs, provenance becomes an operational question: which model generated a given black-box response? We study Dynamic Black-Box LLM Provenance: identifying the source LLM from generations elicited by query-varying, non-predefined prompts rather than a fixed input set or benchmark suite. This setting is difficult because prompt semantics dominate the text, while model-specific authorship traces are weak and inconsistent at the surface level. We introduce READER (Robust Evidence-based Authorship Decoding via Extracted Representations), a lightweight provenance framework that treats a frozen proxy LLM as a reader of hidden authorship evidence. READER maps black-box outputs into proxy activation space, temporally filters token states within each response, and performs Bayesian Evidence Accumulation by summing single-response log-posterior evidence across independently sampled prompts. This avoids fragile mean-pooling of prompt-specific representations while preserving the query-wise evidence needed for calibrated confidence. On Agent500, a 50-target dataset built from agent-style prompts, READER reaches 31.0-42.4% top-1 accuracy from a single response and 70.0-84.0% from 50 responses, substantially outperforming sentence-encoder fingerprints. Scaling across nine proxy readers further shows that stronger LLMs expose more linearly decodable authorship structure, suggesting that authorship perception is already present in frozen LLM representations and can be converted into reliable multi-query attribution.

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

Link Prediction on Hyper-relational Knowledge Graphs (HKG) is a worthwhile endeavor. HKG consists of hyper-relational facts (H-Facts), composed of a main triple and several auxiliary attribute-value qualifiers, which can effectively represent factually comprehensive information. The internal structure of HKG can be represented as a hypergraph-based representation globally and a semantic sequence-based representation locally. However, existing research seldom simultaneously models the graphical and sequential structure of HKGs, limiting HKGs' representation. To overcome this limitation, we propose a novel Hierarchical Attention model for HKG Embedding (HAHE), including global-level and local-level attention. The global-level attention can model the graphical structure of HKG using hypergraph dual-attention layers, while the local-level attention can learn the sequential structure inside H-Facts via heterogeneous self-attention layers. Experiment results indicate that HAHE achieves state-of-the-art performance in link prediction tasks on HKG standard datasets. In addition, HAHE addresses the issue of HKG multi-position prediction for the first time, increasing the applicability of the HKG link prediction task. Our code is publicly available.

Provenance links keep the evidence behind an inherited belief reachable; an agent with a verification budget must still choose which links to inspect. We study a consolidated memory that states a decision constraint and whose source record has since been superseded by a record that withdraws it: provenance is immutable, the current record has changed, and the memory is stale. In a controlled six-memory scenario with a budget of two records, sixteen language models rarely re-verified a constraint that read as settled: they inspected its provenance path in about one episode in five and, once the constraint had been superseded, produced stale-consistent decisions in 77.3%, 74.7% and 74.7% of episodes across a primary run, a replication and a held-out domain. Re-assigning one of the same two slots to the critical path removed most of them: +74.0, +72.7 and +61.3 points (positive in every model), +80.7 in a prospectively frozen interleaved replication with a repaired non-critical control, and +62.0 on a panel of 10 models from 9 organisations; a corrected re-run of the held-out scenario gave +73.3. The forced-critical policy uses experimenter knowledge of the critical path: it quantifies how much stale-decision risk the same budget can recover and is not a scheduler. Two further deposited experiments locate the failure and a remedy: in this store the constraint's path is selected in 17.0% of episodes at two slots and 88.7% at four of six (above uniform allocation), and at two slots a one-sentence, target-blind rule (prefer memories that state a limit on a candidate direction) moved the agent's own allocation onto the constraint's path and recovered the oracle contrast on decisions (+89.3 points) where that constraint limits the tempting action, while a content-free freshness cue did not materially redirect allocation and a content-matched control rule changed neither selection nor decisions.

Khipus -- knotted cord devices -- were the primary recording medium of the Inka Empire (c. 1400-1532 CE), yet their system remains undeciphered. We present a reproducible machine-learning pipeline applied to the Open Khipu Repository (OKR), a public database of 619 khipus comprising 54,403 cords and 110,677 knots. We engineer 27 structural features per khipu and apply (i) unsupervised clustering via UMAP and HDBSCAN, recovering three structurally distinct groups (silhouette = 0.769); (ii) supervised provenance classification via gradient boosting, reaching F1 = 0.86 for the Inka Late Horizon imperial style; and (iii) SHAP-based interpretability, which identifies cord twist direction as the dominant structural discriminator of imperial khipus. We further report two findings of methodological interest. First, one cluster is dominated not by a geographic region but by nineteenth-century European museum collections, indicating that colonial acquisition and recording practices are structurally encoded in the corpus. Second, we provide an independent computational verification of the recto/verso (moiety) structure of the six Santa Valley khipus reported by Medrano and Urton (2018), reproducing both the aggregate attachment ratio and the identification of the single mixed specimen--using only the public OKR database, without physical access to the objects. We additionally report a negative result: knot-type sequence order, encoded as n-grams, adds no provenance signal beyond aggregate features. All code and data are openly available.

LLM agents reach users through resellers, who may rebrand a developer's agent or substitute a cheaper model. When provenance is disputed, attribution rests on the trajectory log (the record of tool calls, observations, and executed actions, not the model's reasoning), which the reseller stores and processes to meter usage. A watermark must therefore survive an adversary with full read/write access to the very evidence it is detected from; existing agent watermarks do not, as their attribution is read straight off that log. We present TRACE, to our knowledge the first agent watermark that is distortion-free in its action choices, self-synchronizing under deletion, and unconditionally invariant under rewriting. Deletion desynchronizes a position-derived key and rewriting alters content, so a deletion-robust key must come from content and a rewrite-robust key from position, and no single key serves both. A trajectory, however, has room for two watermarks. TRACE superposes a selection channel that sets which action is chosen, keyed on local content with a distortion-free sampler, so the agent's distribution is provably unchanged and detection resynchronizes after deletions, and a tally channel that sets how many records each decision group holds, keyed on the log's skeleton alone, which no rewriting can touch. We prove this behavioral watermark's signal is bought with decision entropy, each decision paying at least half its entropy and deterministic decisions nothing, and that erasing both channels forces the reseller to corrupt the trajectories it resells. On ToolBench and ALFWorld, TRACE matches the unwatermarked agent's success rate while its selection channel reaches detection scores near z = 100 on long-horizon trajectories, stays detectable under 70% step deletion, and keeps a tally channel exactly unchanged under LLM rewriting of any strength.

Recent advances in large language model-powered multi-agent systems have demonstrated remarkable collective intelligence through effective communication. However, existing approaches face two primary challenges: (i) Ineffective group collaboration modeling, as they rely on pairwise edge representations in graph structures, limiting their ability to capture relationships among multiple agents; and (ii) Limited task-adaptiveness in communication topology design, leading to excessive communication cost for simple tasks and insufficient coordination for complex scenarios. These issues restrict the scalability and practical deployment of adaptive collaboration frameworks. To address these challenges, we propose HyperAgent, a hypergraph-based framework that optimizes communication topologies and effectively captures group collaboration patterns using direct hyperedge representations. Unlike edge-based approaches, HyperAgent uses hyperedges to link multiple agents within the same subtask and employs hypergraph convolutional layers to achieve one-step information aggregation in collaboration groups. Additionally, it incorporates a variational autoencoder framework with sparsity regularization to dynamically adjust hypergraph topologies based on task complexity. Experiments highlight the superiority of HyperAgent in both performance and efficiency. For instance, on GSM8K, HyperAgent achieves 95.07\% accuracy while reducing token consumption by 25.33\%, demonstrating the potential of hypergraph-based optimization for multi-agent communication.

Ex-post harmonisation is one of many data preprocessing processes used to combine the increasingly vast and diverse sources of data available for research and analysis. Documenting provenance and ensuring the quality of multi-source datasets is vital for ensuring trustworthy scientific research and encouraging reuse of existing harmonisation efforts. However, capturing and communicating statistically relevant properties of harmonised datasets is difficult without a universal standard for describing harmonisation operations. Our paper combines mathematical and computer science perspectives to address this need. The Crossmaps Framework defines a new approach for transforming existing variables collected under a specific measurement or classification standard to an imputed counterfactual variable indexed by some target standard. It uses computational graphs to separate intended transformation logic from actual data transformations, and avoid the risk of syntactically valid data manipulation scripts resulting in statistically questionable data. In this paper, we introduce the Crossmaps Framework through the example of ex-post harmonisation of aggregated statistics in the social sciences. We define a new provenance task abstraction, the crossmap transform, and formalise two associated objects, the shared mass array and the crossmap. We further define graph, matrix and list encodings of crossmaps and discuss resulting implications for understanding statistical properties of ex-post harmonisation and designing error minimising workflows.

Multi-hop logical reasoning is an established problem in the field of representation learning on knowledge graphs (KGs). It subsumes both one-hop link prediction as well as other more complex types of logical queries. Existing algorithms operate only on classical, triple-based graphs, whereas modern KGs often employ a hyper-relational modeling paradigm. In this paradigm, typed edges may have several key-value pairs known as qualifiers that provide fine-grained context for facts. In queries, this context modifies the meaning of relations, and usually reduces the answer set. Hyper-relational queries are often observed in real-world KG applications, and existing approaches for approximate query answering cannot make use of qualifier pairs. In this work, we bridge this gap and extend the multi-hop reasoning problem to hyper-relational KGs allowing to tackle this new type of complex queries. Building upon recent advancements in Graph Neural Networks and query embedding techniques, we study how to embed and answer hyper-relational conjunctive queries. Besides that, we propose a method to answer such queries and demonstrate in our experiments that qualifiers improve query answering on a diverse set of query patterns.

We enhance the calculus of string diagrams for monoidal categories with hierarchical features in order to capture closed monoidal (and cartesian closed) structure. Using this new syntax we formulate an automatic differentiation algorithm for (applied) simply typed lambda calculus in the style of [Pearlmutter and Siskind 2008] and we prove for the first time its soundness. To give an efficient yet principled implementation of the AD algorithm we define a sound and complete representation of hierarchical string diagrams as a class of hierarchical hypergraphs we call hypernets.

What kind of programming language would be most appropriate to serve the needs of integrative, multi-paradigm, multi-software-system approaches to AGI? This question is broached via exploring the more particular question of how to create a more scalable and usable version of the "Atomese" programming language that forms a key component of the OpenCog AGI design (an "Atomese 2.0") . It is tentatively proposed that the core of Atomese 2.0 should be a very flexible framework of rewriting rules for rewriting a metagraph (where the rules themselves are represented within the same metagraph, and some of the intermediate data created and used during the rule-interpretation process may be represented in the same metagraph). This framework should support concurrent rewriting of the metagraph according to rules that are labeled with various sorts of uncertainty-quantifications, and that are labeled with various sorts of types associated with various type systems. A gradual typing approach should be used to enable mixture of rules and other metagraph nodes/links associated with various type systems, and untyped metagraph nodes/links not associated with any type system. This must be done in a way that allows reasonable efficiency and scalability, including in concurrent and distributed processing contexts, in the case where a large percentage of of processing time is occupied with evaluating static pattern-matching queries on specific subgraphs of a large metagraph (including a rich variety of queries such as matches against nodes representing variables, and matches against whole subgraphs, etc.).

Organizing a large-scale knowledge graph into a typed property graph requires structural decisions -- which entities become nodes, which properties become edges, and what schema governs these choices. Existing approaches embed these decisions in pipeline code or extract relations ad hoc, producing schemas that are tightly coupled to their construction process and difficult to reuse for downstream ontology-level tasks. We present an ontology-oriented approach in which the schema is designed from the outset for ontology analysis, entity disambiguation, domain customization, and LLM-guided extraction -- not merely as a byproduct of graph building. The core mechanism is intrinsic-relational routing, which classifies every property as either intrinsic or relational and routes it to the corresponding schema module. This routing produces a declarative schema that is portable across storage backends and independently reusable. We instantiate the approach on the January 2026 Wikidata dump. A rule-based cleaning stage identifies a 34.6M-entity core set from the full dump, followed by iterative intrinsic-relational routing that assigns each property to one of 94 modules organized into 8 categories. With tool-augmented LLM support and human review, the schema reaches 93.3% category coverage and 98.0% module assignment among classified entities. Exporting this schema yields a property graph with 34.0M nodes and 61.2M edges across 38 relationship types. We validate the ontology-oriented claim through five applications that consume the schema independently of the construction pipeline: ontology structure analysis, benchmark annotation auditing, entity disambiguation, domain customization, and LLM-guided extraction.

Scientific discovery is not only answer generation but revision of the representational regime in which evidence, artifacts, operations, and verifiers are typed. We develop a category-theoretic account of agentic discovery for materials science. In a fixed regime b with schema category S_b, the system state is a copresheaf I_t: S_b -> Set, and provenance is the category of elements \int_{S_b} I_t. Fixed-regime operation is an update on such states, endofunctorial only when provenance-preserving refinements are specified and preserved. Discovery is instead a verified regime transition u: S_b -> S_b': old artifacts are preserved, transported by the left Kan extension Lan_u I_t, and compared with the post-transition state to identify residual content beyond functorial transport. This separates retrieval, search, and discovery without subjective novelty. We instantiate the framework in two systems. In Builder/Breaker, a protein-mechanics world model is revised under a Minimum Description Length gate; the accepted law expresses within-chain flexibility as all-mode elastic compliance conditioned by slow collective-mode participation, or mode-conditioned compliance. In CategoryScienceClaw, typed skills, artifacts, open needs, workflow mutation, gates, stress tests, and public discourse become a proof-carrying knowledge-computation graph. A fiber-network example records candidate models, rejected alternatives, an AIC gate, perturbation tests, and an accepted orientation-tensor anisotropic stiffness surrogate over an isotropic fiber-count descriptor. Together, the cases show how category theory can be both a mathematical language for discovery and an engineering specification for self-revising AI discovery systems.

Hypergraphs are widely being employed to represent complex higher-order relations in real-world applications. Most existing research on hypergraph learning focuses on node-level or edge-level tasks. A practically relevant and more challenging task, edge-dependent node classification (ENC), is still under-explored. In ENC, a node can have different labels across different hyperedges, which requires the modeling of node features unique to each hyperedge. The state-of-the-art ENC solution, WHATsNet, only outputs single node and edge representations, leading to the limitations of entangled edge-specific features and non-adaptive representation sizes when applied to ENC. Additionally, WHATsNet suffers from the common oversmoothing issue in most HGNNs. To address these limitations, we propose CoNHD, a novel HGNN architecture specifically designed to model edge-specific features for ENC. Instead of learning separate representations for nodes and edges, CoNHD reformulates within-edge and within-node interactions as a hypergraph diffusion process over node-edge co-representations. We develop a neural implementation of the proposed diffusion process, leveraging equivariant networks as diffusion operators to effectively learn the diffusion dynamics from data. Extensive experiments demonstrate that CoNHD achieves the best performance across all benchmark ENC datasets and several downstream tasks without sacrificing efficiency. Our implementation is available at https://github.com/zhengyijia/CoNHD.

Autonomous scientific agents now increasingly propose ideas, write code, run experiments, analyze results, and even draft papers. Observe and audit those agents are necessary but logging every model call is not enough, scientists also need to inspect the artifacts and claims that the systems produced and their relations. This is driven by the fact that failures in scientific agent systems are often distributed across several objects. A manuscript claim may cite the wrong evidence, a search process may select a degenerate candidate, a laboratory novelty claim may depend on an unstated rule, or a multi-agent plan may change without a visible trigger. Existing tracing, experiment tracking, and archival provenance tools are valuable, but their native objects do not make these scientific audit relations first-class. We argue that autonomous scientific systems should emit portable, claim-aware artifact lineage as a minimum audit layer. We propose a compact observability profile organized around individuals, operators, fitness records, lineage, archives, runs, streams, and steering commands. In this profile, scientific claims are ordinary individuals with explicit evidence bindings and verification records. The profile is intended as a semantic layer that complements current telemetry and provenance standards. Execution details can remain in OpenTelemetry. Final packages can export to PROV-O or RO-Crate standards.

Scene graph representations enable structured visual understanding by modeling objects and their relationships, and have been widely used for multiview and 3D scene reasoning. Existing methods such as MSG learn scene graph embeddings in Euclidean space using contrastive learning and attention based association. However, Euclidean geometry does not explicitly capture hierarchical entailment relationships between places and objects, limiting the structural consistency of learned representations. To address this, we propose Hyperbolic Scene Graph (HSG), which learns scene graph embeddings in hyperbolic space where hierarchical relationships are naturally encoded through geometric distance. Our results show that HSG improves hierarchical structure quality while maintaining strong retrieval performance. The largest gains are observed in graph level metrics: HSG achieves a PP IoU of 33.17 and the highest Graph IoU of 33.51, outperforming the best AoMSG variant (25.37) by 8.14, highlighting the effectiveness of hyperbolic representation learning for scene graph modeling. Code: https://github.com/AIGeeksGroup/HSG.

Hyperbolic vision-language models are designed to encode abstraction geometrically: general concepts near the origin, specific ones farther out, and entailment cones representing directed order. We ask whether trained MERU, HyCoCLIP, and PHyCLIP models actually use these mechanisms. We audit seven released checkpoints and matched from-scratch interventions, using diagnostics that distinguish active hyperbolic geometry from angular structure and supervision effects. All audited converged checkpoints remain near-Euclidean in the dimensionless radius u=cρ, which measures how strongly embeddings experience hyperbolic geometry: the largest observed image-side value is 0.37 -- well below uapprox0.84, where local metric distortion reaches 10%. Releasing the curvature floor changes curvature and norms but not this regime, with mixed, generally modest downstream shifts. Trained entailment cones are saturated or nearly saturated, so low violation rates can arise from trivially wide cones rather than learned order. Preregistered semantic traversal detects weak within-branch order but no operative full-hierarchy readout. Shuffle-controlled tests detect no pair-specific radial ordering in released checkpoints, and no positive result is consistent across all three matched ViT-B seeds. We trace this to a low-curvature shortcut: lowering curvature widens entailment cones and suppresses violations without learning order. In the probed trajectories, gradient decomposition identifies entailment as the dominant curvature-lowering pressure during collapse. Yet curvature contracts even when entailment is removed, so the shortcut is not the sole cause. Under our diagnostics, the audited formulations do not demonstrate an operative radial or cone-based hierarchy. We distill the audit into a five-number geometry report for evaluating future hierarchy claims.

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats and emphasizes model designs. This approach is inherently limited in real-world applications due to the unavoidable information loss in simple undirected graphs and the model optimization challenges that arise when exceeding the upper bounds of this sub-optimal data representational capacity. As a result, there has been a shift toward data-centric methods that prioritize improving graph quality and representation. Specifically, various types of graphs can be derived from naturally structured data, including heterogeneous graphs, hypergraphs, and directed graphs. Among these, directed graphs offer distinct advantages in topological systems by modeling causal relationships, and directed GNNs have been extensively studied in recent years. However, a comprehensive survey of this emerging topic is still lacking. Therefore, we aim to provide a comprehensive review of directed graph learning, with a particular focus on a data-centric perspective. Specifically, we first introduce a novel taxonomy for existing studies. Subsequently, we re-examine these methods from the data-centric perspective, with an emphasis on understanding and improving data representation. It demonstrates that a deep understanding of directed graphs and their quality plays a crucial role in model performance. Additionally, we explore the diverse applications of directed GNNs across 10+ domains, highlighting their broad applicability. Finally, we identify key opportunities and challenges within the field, offering insights that can guide future research and development in directed graph learning.

Discharge summaries require extracting critical information from lengthy electronic health records (EHRs), a process that is labor-intensive when performed manually. Large language models (LLMs) can improve generation efficiency; however, they are prone to producing faithfulness hallucinations, statements that contradict source records, posing direct risks to patient safety. To address this, we present CuraView, a multi-agent framework for sentence-level detection and evidence-grounded explanation of faithfulness hallucinations in discharge summaries. CuraView constructs a GraphRAG-based knowledge graph from patient-level EHRs and implements a closed-loop generation-detection pipeline with sentence-level evidence retrieval and classification spanning four evidence grades from strong support to direct contradiction (E1-E4), yielding structured and interpretable evidence chains. We evaluate CuraView on a subset of 250 patients from the Discharge-Me benchmark, with 50 patients held out for testing. Our fine-tuned Qwen3-14B detection model achieves an F1 of 0.831 on the safety-critical E4 metric (90.9% recall, 76.5% precision) and an F1 of 0.823 on E3+E4, representing a 50.0% relative improvement over the base model and outperforming RAGTruth-style and QAGS-style baselines. These results demonstrate that evidence-chain-based graph retrieval verification substantially improves the factual reliability of clinical documentation, while simultaneously producing reusable annotated datasets for downstream model training and distillation.

Structural fidelity is essential to scientific methodology diagrams. To communicate research logic, these diagrams must faithfully render components, directional relations, and textual annotations. Since a single error, such as a reversed arrow or an unreadable equation, can invalidate the entire figure, structural fidelity is inherently conjunctive: correctness on one axis cannot compensate for failure on another. Current open-source models fail to satisfy this criterion. Supervised fine-tuning (SFT) learns plausible layouts but cannot reliably ensure structural correctness, while scalar reward-based post-training obscures which structural dimension has failed. To address this, we introduce SciForma, a framework for the structure faithful generation of scientific methodology diagrams. Specifically, SciForma decomposes diagram quality into three structural axes: Component, Arrow, and Text, guided by a structural inventory. Built on this foundation, we curate SciFormaData-700K for structured training and SciFormaBench-2K for logic-verified evaluation. To close the gap left by SFT, we develop Multi-Dimensional Conjunctive Preference Optimization (M-DPO), which enforces simultaneous correctness across all axes and adaptively routes gradients to the most deficient dimension in post-training. The same structural inventory also enables iterative editing at inference time to correct residual errors. This combination allows SciForma-9B to exceed all open-source baselines and GPT-Image-1.5 on both SciFormaBench-2K and AIBench, bringing open scientific diagram generation close to proprietary-level structural fidelity. Our code and data will be available at: https://github.com/microsoft/SciForma.

HAL (Hyper Articles en Ligne) is the French national publication repository, used by most higher education and research organizations for their open science policy. As a digital library, it is a rich repository of scholarly documents, but its potential for advanced research has been underutilized. We present HALvest, a unique dataset that bridges the gap between citation networks and the full text of papers submitted on HAL. We craft our dataset by filtering HAL for scholarly publications, resulting in approximately 700,000 documents, spanning 34 languages across 13 identified domains, suitable for language model training, and yielding approximately 16.5 billion tokens (with 8 billion in French and 7 billion in English, the most represented languages). We transform the metadata of each paper into a citation network, producing a directed heterogeneous graph. This graph includes uniquely identified authors on HAL, as well as all open submitted papers, and their citations. We provide a baseline for authorship attribution using the dataset, implement a range of state-of-the-art models in graph representation learning for link prediction, and discuss the usefulness of our generated knowledge graph structure.

In this paper, we study the problem of inference in high-order structured prediction tasks. In the context of Markov random fields, the goal of a high-order inference task is to maximize a score function on the space of labels, and the score function can be decomposed into sum of unary and high-order potentials. We apply a generative model approach to study the problem of high-order inference, and provide a two-stage convex optimization algorithm for exact label recovery. We also provide a new class of hypergraph structural properties related to hyperedge expansion that drives the success in general high-order inference problems. Finally, we connect the performance of our algorithm and the hyperedge expansion property using a novel hypergraph Cheeger-type inequality.

Creating static visualizations for presentations and publications requires granular refinements of visual details, even for simple charts. Existing data-driven visualization tools offer limited interactive control for such refinements, forcing users to export charts to external graphic editors and breaking the critical link between data and visual representation. To address this gap, we propose an extended InfoVis Reference Model to account for post-render design refinement. A formative study with 18 visualization practitioners and a follow-up survey of 35 respondents confirmed that this stage is pervasive yet unsupported in current practice. Based on these findings, we present TailVis, a visualization authoring system that enables expressive visual customization while preserving data-binding integrity. TailVis supports element-level direct selection and scope expansion, allowing users to define a data-aware scope ranging from a single mark to a data-driven category with a simple selection. For modifications beyond predefined controls, TailVis blends natural language input with dynamically generated GUI widgets, where deictic interaction lets users reference elements simply by clicking them, keeping even open-ended edits bound to the data. To support rigorous exploration and comparison of design alternatives, TailVis implements a provenance history that enables users to capture diverse design iterations while ensuring data-visual integrity. A user study with 12 participants verified that TailVis effectively supports expressive, granular refinement without sacrificing data binding, significantly reducing repetitive manual processes in an integrated environment.

Large language model (LLM) agents increasingly rely on invoking external tools to complete real-world tasks. Tool retrieval, which selects a small task-relevant subset from a library of thousands of tools before the agent acts, has therefore become a critical component of LLM agent pipelines. However, existing retrievers either score each tool in isolation or assemble the tool set sequentially, so the joint utility of a candidate set is never evaluated as a whole. In this paper, we propose HYSET, short for HYperedge-based SEt-level Tool retrieval. Our contributions are threefold: (i) we formulate tool retrieval as query-conditioned hyperedge prediction on a tool co-invocation hypergraph, under which the tool set itself becomes the unit of scoring and most existing retrieval paradigms reduce to restricted instances; (ii) we capture size-dependent tool compatibility through cardinality-specific interactions; and (iii) we design HYSET as a pre-selection module requiring no modification to the downstream agent. Experiments on ToolBench demonstrate that HYSET consistently outperforms state-of-the-art baselines in both tool retrieval performance and end-to-end task success. Beyond the in-domain setting, HYSET further supports zero-shot/few-shot transfer, generalizing to held-out tools/categories and unseen domains with minimal supervision.

For a long-horizon LLM agent, the memory question is not what was once recorded but what currently holds. Most designs answer it only indirectly: every interaction is stored, and the present is reconstructed at query time by retrieving and reconciling records, so stale values re-enter and the same conflicts are re-litigated. Committing the current value at write time avoids this, but existing write-time (CRUD) memories overwrite, so a wrong update is unrecoverable and prior state is lost. We take the missing combination---commit on arrival while retaining what is displaced---and formalize it as Memory of Memory (MoM): memory tracks not only content but the provenance, status, and history of its own entries. We instantiate MoM as Provenant Memory (P-Mem), a typed provenance graph whose active frontier exposes one current value per resolved key while displaced values are retained as provenance; typed operations decide whether a new observation supports, supersedes, contests, rejects, revokes, or resolves an existing value. P-Mem's decisive gain is validity rather than accuracy: its turn-level read matches the strongest retrieval memory in accuracy at sim4times fewer read tokens---a retrieval-granularity effect---while graph-guided turn pruning cuts the knowledge-update stale-answer rate (19.4\%rightarrow10.9\%); on revision chains it stays at 100\% where query-time reading collapses to 25\%, and, because displaced values are retained rather than overwritten, it recovers committed errors a CRUD memory cannot (100\% vs.\ 0\%).

When reading a document, glancing at the spatial layout of a document is an initial step to understand it roughly. Traditional document layout analysis (DLA) methods, however, offer only a superficial parsing of documents, focusing on basic instance detection and often failing to capture the nuanced spatial and logical relations between instances. These limitations hinder DLA-based models from achieving a gradually deeper comprehension akin to human reading. In this work, we propose a novel graph-based Document Structure Analysis (gDSA) task. This task requires that model not only detects document elements but also generates spatial and logical relations in form of a graph structure, allowing to understand documents in a holistic and intuitive manner. For this new task, we construct a relation graph-based document structure analysis dataset (GraphDoc) with 80K document images and 4.13M relation annotations, enabling training models to complete multiple tasks like reading order, hierarchical structures analysis, and complex inter-element relation inference. Furthermore, a document relation graph generator (DRGG) is proposed to address the gDSA task, which achieves performance with 57.6% at mAP_g@0.5 for a strong benchmark baseline on this novel task and dataset. We hope this graphical representation of document structure can mark an innovative advancement in document structure analysis and understanding. The new dataset and code will be made publicly available at https://yufanchen96.github.io/projects/GraphDoc.

Repeated training on model-generated data can degrade later models. One possible response is to use provenance when deciding which generated examples to reuse. We test both how reliably that provenance can be recovered and whether it helps identify better training data. Using financial-risk text, we first identify the source of generated passages and then repeat the test after rewriting them. Generator attribution is 98.7% accurate on the original passages but falls to 53.1% after paraphrasing and 29.0% after style rewriting. Generated-versus-human detection remains close to perfect against the tested human comparison set. We then compare two ways of selecting generated examples over three rounds of generation and retraining. One uses source information. The other uses a score from a separate reference model. The two rules select different examples, but the planned comparison does not detect a stable difference in the degradation of the resulting models. The results show that identifying where data came from and identifying which data are useful for training are separate problems. The experiment therefore separates source identity, criterion-facing selection, and recursive training outcome: neither the provenance score nor the tested criterion-facing proxy is established as sufficient for future recursive behaviour.

Advanced Persistent Threats (APT) attacks have plagued modern enterprises, causing significant financial losses. To counter these attacks, researchers propose techniques that capture the complex and stealthy scenarios of APT attacks by using provenance graphs to model system entities and their dependencies. Particularly, to accelerate attack detection and reduce financial losses, online provenance-based detection systems that detect and investigate APT attacks under the constraints of timeliness and limited resources are in dire need. Unfortunately, existing online systems usually sacrifice detection granularity to reduce computational complexity and produce provenance graphs with more than 100,000 nodes, posing challenges for security admins to interpret the detection results. In this paper, we design and implement NodLink, the first online detection system that maintains high detection accuracy without sacrificing detection granularity. Our insight is that the APT attack detection process in online provenance-based detection systems can be modeled as a Steiner Tree Problem (STP), which has efficient online approximation algorithms that recover concise attack-related provenance graphs with a theoretically bounded error. To utilize STP approximation algorithm frameworks for APT attack detection, we propose a novel design of in-memory cache, an efficient attack screening method, and a new STP approximation algorithm that is more efficient than the conventional one in APT attack detection while maintaining the same complexity. We evaluate NodLink in a production environment. The open-world experiment shows that NodLink outperforms two state-of-the-art (SOTA) online provenance analysis systems by achieving magnitudes higher detection and investigation accuracy while having the same or higher throughput.

Graph foundation models represent a transformative paradigm for learning transferable representations across diverse graph domains. Recent methods leverage large language models to unify graph and text modalities into a shared representation space using contrastive learning. However, systematic evaluations reveal significant performance degradation at structural boundaries where distinct topological patterns converge, with accuracy losses exceeding 20 percentage points. This issue arises from a key limitation: current methods assume all graph structures can be encoded within a single Euclidean space. In reality, tree structures require hyperbolic geometry to preserve hierarchical branching, while cyclic patterns depend on spherical geometry for closure properties. At structural boundaries, nodes experience conflicting geometric constraints that uniform encoding spaces cannot resolve. This raises a crucial challenge: Can alignment frameworks be designed to respect the intrinsic geometric diversity of graph structures? We introduce GraphShaper, a geometry-aware framework that enhances graph encoding through multi-geometric specialization. Our approach employs expert networks tailored to different geometric spaces, dynamically computing fusion weights to adaptively integrate geometric properties based on local structural characteristics. This adaptive fusion preserves structural integrity before alignment with text embeddings. Extensive experiments demonstrate that GraphShaper achieves 9.47\% accuracy improvements on citation networks and 7.63\% on social networks in zero-shot settings.

Working agents need to read diverse files, coordinate tools, and produce deliverables. Training such agents requires tasks built on many real files with verifiable results, but few pipelines exist to synthesize this kind of data. Existing pipelines either generate files with models, which lack realism and diversity, or build tasks on real files without task-specific verifiers, leaving result quality unchecked. We introduce GraphForge, an evidence-graph based framework that grounds both the task and its verification in real files. Starting from occupation-grounded seeds for controlled diversity, GraphForge assembles a workspace of real files for each seed and builds an evidence graph over their relations. Since the task statement and rubrics are both derived from this graph, task requirements are backed by the workspace files and each criterion is anchored to the files needed to verify it. An initial rollout further tests executability, and a revision agent repairs the task and rubrics against the original files before trajectories are collected. Fine-tuning Qwen3.6-27B on 2,169 GraphForge trajectories brings GDPVal to 1445.7 (+65.7) under OpenHands, and Workspace-Bench-Lite and SpreadsheetBench II to 63.7 (+7.7) and 24.0 (+13.7) under Claude Code. Rejection fine-tuning on the SFT model's own rollouts, with candidates selected by the evidence-anchored rubrics, yields further improvements on all three benchmarks, suggesting that the rubrics provide a useful selection signal. The data and models are available.

We introduce Darshana Graph, a corpus of over 125,000 text records spanning classical Hindu, Buddhist, and Jain philosophical traditions, drawn from public-domain and openly licensed translations of sources including the Bhagavad Gita, Brahma Sutras, principal Upanishads, the Pali Canon, and core Jain texts. Its distinctive contribution lies in a structurally unique subset of roughly 8,500 Hindu and Jain records in which the same root verse or sutra is aligned across eighteen historical commentators representing five schools of Vedanta and other darshanas, enabling direct comparison of how independent interpretive traditions read identical source material. To our knowledge, no publicly available resource provides comparable cross-commentator alignment at this scale. We present two analyses built on this corpus. First, a transparent stylometric comparison requiring no machine learning measures argumentative style through scriptural citation density, explicit refutation rate, and sentence complexity. It finds a moderate negative correlation between citation density and refutation rate, a marked increase in refutation rate across three commentators in a related doctrinal lineage, and measurable genre-level differences within the Pali Canon itself. Second, we describe a constrained large language model pipeline that extracts typed philosophical relationships between concepts using a predefined relation vocabulary and deterministic post-hoc validation. The resulting graph surfaces cross-school disagreement patterns while also revealing important extraction limitations, including cases where an independent embedding-based analysis disagrees with the graph-derived findings. We release the full corpus, extracted relationship graph, and all source code.

Multi-hop reasoning over financial disclosures is often a retrieval problem before it becomes a reasoning or generation problem: relevant facts are dispersed across sections, filings, companies, and years, and LLMs often expend excessive tokens navigating noisy context. Without precise Knowledge Graph (KG)-guided selection of relevant context, even strong reasoning models either fail to answer or consume excessive tokens, whereas KG-linked evidence enables models to focus their reasoning on composing already retrieved facts. We present FinReflectKG - MultiHop, a benchmark built on FinReflectKG, a temporally indexed financial KG that links audited triples to source chunks from S&P 100 filings (2022-2024). Mining frequent 2-3 hop subgraph patterns across sectors (via GICS taxonomy), we generate financial analyst style questions with exact supporting evidence from the KG. A two-phase pipeline first creates QA pairs via pattern-specific prompts, followed by a multi-criteria quality control evaluation to ensure QA validity. We then evaluate three controlled retrieval scenarios: (S1) precise KG-linked paths; (S2) text-only page windows centered on relevant text spans; and (S3) relevant page windows with randomizations and distractors. Across both reasoning and non-reasoning models, KG-guided precise retrieval yields substantial gains on the FinReflectKG - MultiHop QA benchmark dataset, boosting correctness scores by approximately 24 percent while reducing token utilization by approximately 84.5 percent compared to the page window setting, which reflects the traditional vector retrieval paradigm. Spanning intra-document, inter-year, and cross-company scopes, our work underscores the pivotal role of knowledge graphs in efficiently connecting evidence for multi-hop financial QA. We also release a curated subset of the benchmark (555 QA Pairs) to catalyze further research.

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

The need to analyze graphs is ubiquitous across various fields, from social networks to biological research and recommendation systems. Therefore, enabling the ability of large language models (LLMs) to process graphs is an important step toward more advanced general intelligence. However, current LLM benchmarks on graph analysis require models to directly reason over the prompts describing graph topology, and are thus limited to small graphs with only a few dozens of nodes. In contrast, human experts typically write programs based on popular libraries for task solving, and can thus handle graphs with different scales. To this end, a question naturally arises: can LLMs analyze graphs like professionals? In this paper, we introduce ProGraph, a manually crafted benchmark containing 3 categories of graph tasks. The benchmark expects solutions based on programming instead of directly reasoning over raw inputs. Our findings reveal that the performance of current LLMs is unsatisfactory, with the best model achieving only 36% accuracy. To bridge this gap, we propose LLM4Graph datasets, which include crawled documents and auto-generated codes based on 6 widely used graph libraries. By augmenting closed-source LLMs with document retrieval and fine-tuning open-source ones on the codes, we show 11-32% absolute improvements in their accuracies. Our results underscore that the capabilities of LLMs in handling structured data are still under-explored, and show the effectiveness of LLM4Graph in enhancing LLMs' proficiency of graph analysis. The benchmark, datasets and enhanced open-source models are available at https://github.com/BUPT-GAMMA/ProGraph.

Answering complex questions over long documents frequently requires integrating evidence that the source itself disperses naturally across distant passages. In an incident report, the operating condition, design flaw, and missed safety check that jointly explain a disaster may appear dozens of sections apart; in a novel, a character's true motive may surface only through scenes far removed from the moment it becomes relevant. This source-internal evidence integration is central to real-world long-document analysis, yet existing benchmarks largely sidestep it. Needle probes, planted facts, and reverse-engineered multi-hop chains embed evidence that may differ from the host text in distribution, placement, or register, making it unclear whether strong performance reflects genuine source reasoning or distributional artifacts. We introduce WILDTRACE, a benchmark of 481 tasks over 214 naturally occurring long-form sources such as technical incident reports and lesser-known literary narratives, where all evidence trails arise from the document's own causal, temporal, and narrative logic. Drawing on Pearl's causal hierarchy and prior multi-hop reasoning typologies, we define seven source-internal evidence geometries that characterize the distinct relational demands of analytical reading in long documents. A source-first construction pipeline mines candidate trails from document structure before writing questions; each item then undergoes multi-stage validation covering clue necessity, answer groundedness, rubric fidelity, contamination resistance and answerability. As models are increasingly entrusted with real-world high-stakes analytical tasks, this gap between accessing information and reasoning over naturally dispersed evidence emerges as a defining challenge for the next stage of long-context research.

Text-attributed graphs are widely used across domains, offering rich opportunities for zero-shot learning via graph-text alignment. However, existing methods struggle with tasks requiring fine-grained pattern recognition, particularly on heterophilic graphs. Through empirical and theoretical analysis, we identify an over-abstraction problem: current approaches operate at excessively large hyperbolic radii, compressing multi-scale structural information into uniform high-level abstractions. This abstraction-induced information loss obscures critical local patterns essential for accurate predictions. By analyzing embeddings in hyperbolic space, we demonstrate that optimal graph learning requires faithful preservation of fine-grained structural details, better retained by representations positioned closer to the origin. To address this, we propose H4G, a framework that systematically reduces embedding radii using learnable block-diagonal scaling matrices and M\"obius matrix multiplication. This approach restores access to fine-grained patterns while maintaining global receptive ability with minimal computational overhead. Experiments show H4G achieves state-of-the-art zero-shot performance with 12.8\% improvement on heterophilic graphs and 8.4\% on homophilic graphs, confirming that radius reduction enables faithful multi-scale representation for advancing zero-shot graph learning.

We introduce a novel graph-based Retrieval-Augmented Generation (RAG) framework specifically designed for the medical domain, called MedGraphRAG, aimed at enhancing Large Language Model (LLM) capabilities and generating evidence-based results, thereby improving safety and reliability when handling private medical data. Our comprehensive pipeline begins with a hybrid static-semantic approach to document chunking, significantly improving context capture over traditional methods. Extracted entities are used to create a three-tier hierarchical graph structure, linking entities to foundational medical knowledge sourced from medical papers and dictionaries. These entities are then interconnected to form meta-graphs, which are merged based on semantic similarities to develop a comprehensive global graph. This structure supports precise information retrieval and response generation. The retrieval process employs a U-retrieve method to balance global awareness and indexing efficiency of the LLM. Our approach is validated through a comprehensive ablation study comparing various methods for document chunking, graph construction, and information retrieval. The results not only demonstrate that our hierarchical graph construction method consistently outperforms state-of-the-art models on multiple medical Q\&A benchmarks, but also confirms that the responses generated include source documentation, significantly enhancing the reliability of medical LLMs in practical applications. Code will be at: https://github.com/MedicineToken/Medical-Graph-RAG/tree/main

Graph-based Retrieval-Augmented Generation (GraphRAG) organizes external knowledge as a hierarchical graph, enabling efficient retrieval and aggregation of scattered evidence across multiple documents. However, many existing benchmarks for GraphRAG rely on short, curated passages as external knowledge, failing to adequately evaluate systems in realistic settings involving long contexts and large-scale heterogeneous documents. To bridge this gap, we introduce WildGraphBench, a benchmark designed to assess GraphRAG performance in the wild. We leverage Wikipedia's unique structure, where cohesive narratives are grounded in long and heterogeneous external reference documents, to construct a benchmark reflecting real-word scenarios. Specifically, we sample articles across 12 top-level topics, using their external references as the retrieval corpus and citation-linked statements as ground truth, resulting in 1,100 questions spanning three levels of complexity: single-fact QA, multi-fact QA, and section-level summarization. Experiments across multiple baselines reveal that current GraphRAG pipelines help on multi-fact aggregation when evidence comes from a moderate number of sources, but this aggregation paradigm may overemphasize high-level statements at the expense of fine-grained details, leading to weaker performance on summarization tasks. Project page:https://github.com/BstWPY/WildGraphBench.

Computational knowledge graphs assign philosophical concepts to traditions based on corpus frequency: the school that mentions a concept most becomes its attributed tradition. We argue this conflates three measurements: textual power, historical priority, and philosophical significance, demonstrated using the darshana-graph, a knowledge graph of 28,322 relationships across Hindu, Buddhist, and Jain traditions. Seven of the top 25 concepts by betweenness centrality predate their attributed school by 288 to 2,288 years. Moksha, attributed to Advaita Vedanta, appears first in Jain sources over 1,200 years earlier. The most reliable snapshot, at 300 BCE using only explicitly dated sources, shows a genuinely pluralistic structure: 59% Vedic, 24% Jain, 18% Buddhist. We also quantify a critical distortion in the temporal method: between 300 CE and 800 CE the network grows from 18 to 1,028 nodes, with 97.4% carrying Advaita proxy dates, revealing that apparent dominance reflects textual survival, not philosophical history. Beyond correcting attribution bias, the temporally grounded graph enables structural homology analysis across traditions. Ego-network feature vectors applied to 48 temporally labelled concepts across eight traditions identify cross-tradition concept pairs with high structural similarity. The method recovers known correspondences including purusha-jiva (Samkhya/Jain, sim 0.990) and prakriti-maya (Samkhya/Vedic, sim 0.972), and surfaces novel homologies. Nibbana and samsara score 0.954 despite being doctrinal opposites: both function as the ultimate reference concept in their tradition's soteriology. Cetana (Buddhist intention) and ajiva (Jain non-living matter) score 0.923, a pairing absent from the literature. These are not claims of doctrinal equivalence but of measurable structural homology: different philosophical vocabularies navigating a shared conceptual space.

Electronic Health Records (EHR) are high-dimensional data with implicit connections among thousands of medical concepts. These connections, for instance, the co-occurrence of diseases and lab-disease correlations can be informative when only a subset of these variables is documented by the clinician. A feasible approach to improving the representation learning of EHR data is to associate relevant medical concepts and utilize these connections. Existing medical ontologies can be the reference for EHR structures, but they place numerous constraints on the data source. Recent progress on graph neural networks (GNN) enables end-to-end learning of topological structures for non-grid or non-sequential data. However, there are problems to be addressed on how to learn the medical graph adaptively and how to understand the effect of the medical graph on representation learning. In this paper, we propose a variationally regularized encoder-decoder graph network that achieves more robustness in graph structure learning by regularizing node representations. Our model outperforms the existing graph and non-graph based methods in various EHR predictive tasks based on both public data and real-world clinical data. Besides the improvements in empirical experiment performances, we provide an interpretation of the effect of variational regularization compared to standard graph neural network, using singular value analysis.

Existing research infrastructure is fundamentally document-centric, providing citation links between papers but lacking explicit representations of methodological evolution. In particular, it does not capture the structured relationships that explain how and why research methods emerge, adapt, and build upon one another. With the rise of AI-driven research agents as a new class of consumers of scientific knowledge, this limitation becomes increasingly consequential, as such agents cannot reliably reconstruct method evolution topologies from unstructured text. We introduce Intern-Atlas, a methodological evolution graph that automatically identifies method-level entities, infers lineage relationships among methodologies, and captures the bottlenecks that drive transitions between successive innovations. Built from 1,030,314 papers spanning AI conferences, journals, and arXiv preprints, the resulting graph comprises 9,410,201 semantically typed edges, each grounded in verbatim source evidence, forming a queryable causal network of methodological development. To operationalize this structure, we further propose a self-guided temporal tree search algorithm for constructing evolution chains that trace the progression of methods over time. We evaluate the quality of the resulting graph against expert-curated ground-truth evolution chains and observe strong alignment. In addition, we demonstrate that Intern-Atlas enables downstream applications in idea evaluation and automated idea generation. We position methodological evolution graphs as a foundational data layer for the emerging automated scientific discovery.

Epilepsy diagnosis and treatment require evidence-intensive reasoning across heterogeneous clinical knowledge, including biosignal patterns, genetic mechanisms, pharmacogenomics, treatment strategies, and patient outcomes. In this work, we present EpiGraph, a large-scale epilepsy knowledge graph and benchmark for evaluating knowledge-augmented clinical reasoning. EpiGraph integrates 48,166 peer-reviewed papers and seven clinical resources into a heterogeneous graph containing 24,324 entities and 32,009 evidence-grounded triplets across five clinical layers. Built upon this graph, EpiBench defines five clinically motivated tasks spanning clinical decision-making, EEG report generation, pharmacogenomic precision medicine, treatment recommendation, and deep research planning. We evaluate six LLMs under both standard and Graph-RAG settings. Results show that integrating EpiGraph consistently improves performance across all tasks, with the largest gains observed in pharmacogenomic reasoning (+30--41\%). Our findings demonstrate that structured epilepsy knowledge substantially enhances evidence-grounded clinical reasoning and provides a practical benchmark framework for evaluating knowledge-augmented LLMs in real-world neurological settings. Our code is available at: https://github.com/LabRAI/EEG-KG.

Retrieval from graph data is crucial for augmenting large language models (LLM) with both open-domain knowledge and private enterprise data, and it is also a key component in the recent GraphRAG system (edge et al., 2024). Despite decades of research on knowledge graphs and knowledge base question answering, leading LLM frameworks (e.g. Langchain and LlamaIndex) have only minimal support for retrieval from modern encyclopedic knowledge graphs like Wikidata. In this paper, we analyze the root cause and suggest that modern RDF knowledge graphs (e.g. Wikidata, Freebase) are less efficient for LLMs due to overly large schemas that far exceed the typical LLM context window, use of resource identifiers, overlapping relation types and lack of normalization. As a solution, we propose property graph views on top of the underlying RDF graph that can be efficiently queried by LLMs using Cypher. We instantiated this idea on Wikidata and introduced CypherBench, the first benchmark with 11 large-scale, multi-domain property graphs with 7.8 million entities and over 10,000 questions. To achieve this, we tackled several key challenges, including developing an RDF-to-property graph conversion engine, creating a systematic pipeline for text-to-Cypher task generation, and designing new evaluation metrics.

Large Language Models (LLMs) have demonstrated their potential in hardware design tasks, such as Hardware Description Language (HDL) generation and debugging. Yet, their performance in real-world, repository-level HDL projects with thousands or even tens of thousands of code lines is hindered. To this end, we propose HDLxGraph, a novel framework that integrates Graph Retrieval Augmented Generation (Graph RAG) with LLMs, introducing HDL-specific graph representations by incorporating Abstract Syntax Trees (ASTs) and Data Flow Graphs (DFGs) to capture both code graph view and hardware graph view. HDLxGraph utilizes a dual-retrieval mechanism that not only mitigates the limited recall issues inherent in similarity-based semantic retrieval by incorporating structural information, but also enhances its extensibility to various real-world tasks by a task-specific retrieval finetuning. Additionally, to address the lack of comprehensive HDL search benchmarks, we introduce HDLSearch, a multi-granularity evaluation dataset derived from real-world repository-level projects. Experimental results demonstrate that HDLxGraph significantly improves average search accuracy, debugging efficiency and completion quality by 12.04%, 12.22% and 5.04% compared to similarity-based RAG, respectively. The code of HDLxGraph and collected HDLSearch benchmark are available at https://github.com/Nick-Zheng-Q/HDLxGraph.

Enterprise question answering is framed as retrieving internal documents and generating grounded answers. Routine enterprise records, however, are work by-products in which required organizational relations remain implicit across heterogeneous sources. Existing benchmarks provide realistic multi-source evidence, but often materialize a predefined answer path and therefore test the composition of stated facts rather than recovery of a target relation absent from the corpus. We call the latter capability latent organizational reasoning. We introduce ENTLORE, a graph-grounded benchmark construction framework that reconstructs an audited enterprise world from routine documents, authoritative organizational tables, and operational records. Versioned organizational conventions certify derived relations in a truth graph, enabling complete golden answers and proof certificates. The aligned anonymized release exposes only the document corpus while withholding private structure and target relations. ENTLORE contains 2,341 documents from three source types and 907 questions spanning explicit lookup, cross-source composition, and latent organizational reasoning, evaluated across 56 model and access configurations. Structuring the released world as an induced entity graph or navigable knowledge base gives the strongest deployable results. Yet supplying gold documents still leaves 30.4% of latent questions unanswered, versus 12.6% and 6.2% for explicit and compositional questions. Enterprise QA therefore depends not only on document recall, but also on whether implicit organizational relations become usable. The benchmark, data, and code are publicly available at ENTLORE.

This work aims to tackle the challenging heterogeneous graph encoding problem in the text-to-SQL task. Previous methods are typically node-centric and merely utilize different weight matrices to parameterize edge types, which 1) ignore the rich semantics embedded in the topological structure of edges, and 2) fail to distinguish local and non-local relations for each node. To this end, we propose a Line Graph Enhanced Text-to-SQL (LGESQL) model to mine the underlying relational features without constructing meta-paths. By virtue of the line graph, messages propagate more efficiently through not only connections between nodes, but also the topology of directed edges. Furthermore, both local and non-local relations are integrated distinctively during the graph iteration. We also design an auxiliary task called graph pruning to improve the discriminative capability of the encoder. Our framework achieves state-of-the-art results (62.8% with Glove, 72.0% with Electra) on the cross-domain text-to-SQL benchmark Spider at the time of writing.

Deploying Large Language Models (LLMs) for regulatory compliance demands rigorous traceability via comprehensive citations across multi-tiered authority structures. Unlike traditional multi-hop or legal QA, this task requires structured procedural lookups and evidence-set closure rather than entity resolution or case-law reasoning. Existing RAG systems struggle here due to flattened citation edges, fragmented retrieval expansions, and fragile post-hoc attribution. We formalize Regulatory Compliance QA with RegOps-Bench, a novel benchmark featuring an Operational Knowledge Graph derived from complex national R\&D regulations. To address these bottlenecks, we propose RefWalk, a unified framework driven by a shared topic anchor. RefWalk traverses cross-document citations, fuses multi-view candidates via max-based aggregation, and enforces per-rule attribution to explicitly map claims to sources. We establish a strong baseline with substantial improvements in retrieval recall and citation accuracy. Finally, a contrastive evaluation on a U.S. health compliance dataset (HIPAA) reveals that existing systems exhibit saturation on flat-structure rules, underscoring the need for RegOps-Bench. Our code is available at https://github.com/yeongjoonJu/RefWalk.

Hieroglyphs, as logographic writing systems, encode rich semantic and cultural information within their internal structural composition. Yet, current advanced Large Language Models (LLMs) and Multimodal LLMs (MLLMs) usually remain structurally blind to this information. LLMs process characters as textual tokens, while MLLMs additionally view them as raw pixel grids. Both fall short to model the underlying logic of character strokes. Furthermore, existing structural analysis methods are often script-specific and labor-intensive. In this paper, we propose Hieroglyphic Stroke Analyzer (HieroSA), a novel and generalizable framework that enables MLLMs to automatically derive stroke-level structures from character bitmaps without handcrafted data. It transforms modern logographic and ancient hieroglyphs character images into explicit, interpretable line-segment representations in a normalized coordinate space, allowing for cross-lingual generalization. Extensive experiments demonstrate that HieroSA effectively captures character-internal structures and semantics, bypassing the need for language-specific priors. Experimental results highlight the potential of our work as a graphematics analysis tool for a deeper understanding of hieroglyphic scripts. View our code at https://github.com/THUNLP-MT/HieroSA.

Modern multi-agent knowledge systems increasingly accumulate knowledge through chains of autonomous transformations rather than direct retrieval. Existing provenance work records what happened - execution traces, tool calls, evidence links - and source-reliability estimation is long established (truth discovery, reputation systems). What is missing is an operational framework that attaches graded, per-domain transmitter reliability to claim-level transmission chains, with completeness semantics, transformation-typed aggregation, decoupled content criticism, and serve/review/quarantine routing. Classical Islamic hadith science confronted a structurally similar problem: deciding whether knowledge transmitted through chains of human narrators should be accepted. Over centuries it developed a rigorous methodology - isnad (a complete transmission chain attached to every claim), rijal (systematic grading of each narrator's integrity and precision), weakest-link chain evaluation, corroboration through independent chains, and matn criticism (content evaluated independently of chain quality). This paper transfers that methodology to AI system design. We contribute a formal mapping from hadith-science concepts to multi-agent pipelines, a relational schema implementing claim chains and a graded narrator registry, a decision matrix combining chain grade with content criticism, and an evaluation on 20,000 claims from real physics textbooks. The evaluation validates weakest-link quarantine and independent-chain corroboration; reports a partial failure of the grade-recovery loop, which missed the highest-fault narrator; and reports two analyses as inconclusive, including a matched-coverage comparison the framework could not reach with the reference content critic. The paper is explicit throughout about which claims the evidence does and does not yet support.

Personalizing language models by effectively incorporating user interaction history remains a central challenge in the development of adaptive AI systems. While large language models (LLMs), combined with Retrieval-Augmented Generation (RAG), have improved factual accuracy, they often lack structured memory and fail to scale in complex, long-term interactions. To address this, we propose a flexible external memory framework based on a knowledge graph that is constructed and updated automatically by the LLM. Building upon the AriGraph architecture, we introduce a novel hybrid graph design that supports both standard edges and two types of hyper-edges, enabling rich and dynamic semantic and temporal representations. Our framework also supports diverse retrieval mechanisms, including A*, WaterCircles traversal, beam search, and hybrid methods, making it adaptable to different datasets and LLM capacities. We evaluate our system on TriviaQA, HotpotQA, DiaASQ benchmarks and demonstrate that different memory and retrieval configurations yield optimal performance depending on the task. Additionally, we extend the DiaASQ benchmark with temporal annotations and internally contradictory statements, showing that our system remains robust and effective in managing temporal dependencies and context-aware reasoning

Knowledge Graph-based Question Answering (KGQA) plays a pivotal role in complex reasoning tasks but remains constrained by two persistent challenges: the structural heterogeneity of Knowledge Graphs(KGs) often leads to semantic mismatch during retrieval, while existing reasoning path retrieval methods lack a global structural perspective. To address these issues, we propose Structure-Tracing Evidence Mining (STEM), a novel framework that reframes multi-hop reasoning as a schema-guided graph search task. First, we design a Semantic-to-Structural Projection pipeline that leverages KG structural priors to decompose queries into atomic relational assertions and construct an adaptive query schema graph. Subsequently, we execute globally-aware node anchoring and subgraph retrieval to obtain the final evidence reasoning graph from KG. To more effectively integrate global structural information during the graph construction process, we design a Triple-Dependent GNN (Triple-GNN) to generate a Global Guidance Subgraph (Guidance Graph) that guides the construction. STEM significantly improves both the accuracy and evidence completeness of multi-hop reasoning graph retrieval, and achieves State-of-the-Art performance on multiple multi-hop benchmarks.

Evaluating retrieval-augmented generation (RAG) pipelines requires corpora where ground truth is knowable, temporally structured, and cross-artifact properties that real-world datasets rarely provide cleanly. Existing resources such as the Enron corpus carry legal ambiguity, demographic skew, and no structured ground truth. Purely LLM-generated synthetic data solves the legal problem but introduces a subtler one: the generating model cannot be prevented from hallucinating facts that contradict themselves across documents.We present OrgForge, an open-source multi-agent simulation framework that enforces a strict physics-cognition boundary: a deterministic Python engine maintains a SimEvent ground truth bus; large language models generate only surface prose, constrained by validated proposals. An actor-local clock enforces causal timestamp correctness across all artifact types, eliminating the class of timeline inconsistencies that arise when timestamps are sampled independently per document. We formalize three graph-dynamic subsystems stress propagation via betweenness centrality, temporal edge-weight decay, and Dijkstra escalation routing that govern organizational behavior independently of any LLM. Running a configurable N-day simulation, OrgForge produces interleaved Slack threads, JIRA tickets, Confluence pages, Git pull requests, and emails, all traceable to a shared, immutable event log. We additionally describe a causal chain tracking subsystem that accumulates cross-artifact evidence graphs per incident, a hybrid reciprocal-rank-fusion recurrence detector for identifying repeated failure classes, and an inbound/outbound email engine that routes vendor alerts, customer complaints, and HR correspondence through gated causal chains with probabilistic drop simulation. OrgForge is available under the MIT license.

Graph mining workloads aim to extract structural properties of a graph by exploring its subgraph structures. General purpose graph mining systems provide a generic runtime to explore subgraph structures of interest with the help of user-defined functions that guide the overall exploration process. However, the state-of-the-art graph mining systems remain largely oblivious to the shape (or pattern) of the subgraphs that they mine. This causes them to: (a) explore unnecessary subgraphs; (b) perform expensive computations on the explored subgraphs; and, (c) hold intermediate partial subgraphs in memory; all of which affect their overall performance. Furthermore, their programming models are often tied to their underlying exploration strategies, which makes it difficult for domain users to express complex mining tasks. In this paper, we develop Peregrine, a pattern-aware graph mining system that directly explores the subgraphs of interest while avoiding exploration of unnecessary subgraphs, and simultaneously bypassing expensive computations throughout the mining process. We design a pattern-based programming model that treats "graph patterns" as first class constructs and enables Peregrine to extract the semantics of patterns, which it uses to guide its exploration. Our evaluation shows that Peregrine outperforms state-of-the-art distributed and single machine graph mining systems, and scales to complex mining tasks on larger graphs, while retaining simplicity and expressivity with its "pattern-first" programming approach.

Hop-constrained s-t simple path (HC-s-t path) enumeration is a fundamental problem in graph analysis. Existing solutions for this problem focus on optimizing the processing performance of a single query. However, in practice, it is more often that multiple HC-s-t path queries are issued simultaneously and processed as a batch. Therefore, we study the problem of batch HC-s-t path query processing in this paper and aim to compute the results of all queries concurrently and efficiently as a batch. To achieve this goal, we first propose the concept of HC-s path query which can precisely characterize the common computation among different queries.We then devise a two-phase HC-s path query detection algorithm to identify the common HC-s path queries for the given HC-s-t path queries. Based on the detected HC-s path queries, we further devise an efficient HC-s-t path enumeration algorithm in which the common computation represented by HC-s path queries are effectively shared. We conduct extensive experiments on real-world graphs and the experimental results demonstrate that our proposed algorithm is efficient and scalable regarding processing multiple HC-s-t path queries in large graphs at billion-scale.

Mechanistic interpretability aims to understand neural networks by identifying which learned features mediate specific behaviors. Attribution graphs reveal these feature pathways, but interpreting them requires extensive manual analysis -- a single prompt can take approximately 2 hours for an experienced circuit tracer. We present probe prompting, an automated pipeline that transforms attribution graphs into compact, interpretable subgraphs built from concept-aligned supernodes. Starting from a seed prompt and target logit, we select high-influence features, generate concept-targeted yet context-varying probes, and group features by cross-prompt activation signatures into Semantic, Relationship, and Say-X categories using transparent decision rules. Across five prompts including classic "capitals" circuits, probe-prompted subgraphs preserve high explanatory coverage while compressing complexity (Completeness 0.83, mean across circuits; Replacement 0.54). Compared to geometric clustering baselines, concept-aligned groups exhibit higher behavioral coherence: 2.3x higher peak-token consistency (0.425 vs 0.183) and 5.8x higher activation-pattern similarity (0.762 vs 0.130), despite lower geometric compactness. Entity-swap tests reveal a layerwise hierarchy: early-layer features transfer robustly (64% transfer rate, mean layer 6.3), while late-layer Say-X features specialize for output promotion (mean layer 16.4), supporting a backbone-and-specialization view of transformer computation. We release code (https://github.com/peppinob-ol/attribution-graph-probing), an interactive demo (https://huggingface.co/spaces/Peppinob/attribution-graph-probing), and minimal artifacts enabling immediate reproduction and community adoption.