Daily Papers

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.

Synthesis procedures play a critical role in materials research, as they directly affect material properties. With data-driven approaches increasingly accelerating materials discovery, there is growing interest in extracting synthesis procedures from scientific literature as structured data. However, existing studies often rely on rigid, domain-specific schemas with predefined fields for structuring synthesis procedures or assume that synthesis procedures are linear sequences of operations, which limits their ability to capture the structural complexity of real-world procedures. To address these limitations, we adopt PROV-DM, an international standard for provenance information, which supports flexible, graph-based modeling of procedures. We present MatPROV, a dataset of PROV-DM-compliant synthesis procedures extracted from scientific literature using large language models. MatPROV captures structural complexities and causal relationships among materials, operations, and conditions through visually intuitive directed graphs. This representation enables machine-interpretable synthesis knowledge, opening opportunities for future research such as automated synthesis planning and optimization.

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.

Large Language Models (LLMs) lack persistent memory for long-term personalized conversations. Existing graph-based memory systems suffer from information dilution, absent provenance tracking, and uniform retrieval that ignores query context. We introduce MemORAI (Memory Organization and Retrieval via Adaptive Graph Intelligence), a framework that integrates three innovations: selective memory filtering with dual-layer compression to retain user-persona-relevant content, a provenance-enriched multi-relational graph tracking factual origins at the turn level, and query-adaptive subgraph retrieval with Dynamic Weighted PageRank that applies query-conditioned edge weighting. Evaluated on LOCOMO and LongMemEval benchmarks, MemORAI achieves state-of-the-art performance in memory retrieval and personalized response generation, demonstrating that selective storage, enriched representation, and adaptive retrieval are essential for coherent, personalized LLM agents.

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.

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.

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.

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.

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.

Background. In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoption in bioinformatics due to their advantages for representing data in a generic graph format. For example, yummydata.org catalogs more than 60 knowledge graphs accessible through SPARQL, a technical query language. Although SPARQL allows powerful, expressive queries, even across physically distributed knowledge graphs, formulating such queries is a challenge for most users. Therefore, to guide users in retrieving the relevant data, many of these resources provide representative examples. These examples can also be an important source of information for machine learning, if a sufficiently large number of examples are provided and published in a common, machine-readable and standardized format across different resources. Findings. We introduce a large collection of human-written natural language questions and their corresponding SPARQL queries over federated bioinformatics knowledge graphs (KGs) collected for several years across different research groups at the SIB Swiss Institute of Bioinformatics. The collection comprises more than 1000 example questions and queries, including 65 federated queries. We propose a methodology to uniformly represent the examples with minimal metadata, based on existing standards. Furthermore, we introduce an extensive set of open-source applications, including query graph visualizations and smart query editors, easily reusable by KG maintainers who adopt the proposed methodology. Conclusions. We encourage the community to adopt and extend the proposed methodology, towards richer KG metadata and improved Semantic Web services.

Multi-agent systems powered by Large Language Models excel at complex tasks through coordinated collaboration, yet they face high failure rates in multi-turn deep search scenarios. Existing temporal attribution methods struggle to accurately diagnose root causes, particularly when errors propagate across multiple agents. Attempts to automate failure attribution by analyzing action sequences remain ineffective due to their inability to account for information dependencies that span agents. This paper identifies two core challenges: (i) distinguishing symptoms from root causes in multi-agent error propagation, and (ii) tracing information dependencies beyond temporal order. To address these issues, we introduce GraphTracer, a framework that redefines failure attribution through information flow analysis. GraphTracer constructs Information Dependency Graphs (IDGs) to explicitly capture how agents reference and build on prior outputs. It localizes root causes by tracing through these dependency structures instead of relying on temporal sequences. GraphTracer also uses graph-aware synthetic data generation to target critical nodes, creating realistic failure scenarios. Evaluations on the Who\&When benchmark and integration into production systems demonstrate that GraphTracer-8B achieves up to 18.18\% higher attribution accuracy compared to state-of-the-art models and enables 4.8\% to 14.2\% performance improvements in deployed multi-agent frameworks, establishing a robust solution for multi-agent system debugging.

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.

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.

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.

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.

Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction towards cognition and human-level intelligence. In this survey, we provide a comprehensive review of knowledge graph covering overall research topics about 1) knowledge graph representation learning, 2) knowledge acquisition and completion, 3) temporal knowledge graph, and 4) knowledge-aware applications, and summarize recent breakthroughs and perspective directions to facilitate future research. We propose a full-view categorization and new taxonomies on these topics. Knowledge graph embedding is organized from four aspects of representation space, scoring function, encoding models, and auxiliary information. For knowledge acquisition, especially knowledge graph completion, embedding methods, path inference, and logical rule reasoning, are reviewed. We further explore several emerging topics, including meta relational learning, commonsense reasoning, and temporal knowledge graphs. To facilitate future research on knowledge graphs, we also provide a curated collection of datasets and open-source libraries on different tasks. In the end, we have a thorough outlook on several promising research directions.

Knowledge graphs have been proven extremely useful in powering diverse applications in semantic search and natural language understanding. In this paper, we present GraphGen4Code, a toolkit to build code knowledge graphs that can similarly power various applications such as program search, code understanding, bug detection, and code automation. GraphGen4Code uses generic techniques to capture code semantics with the key nodes in the graph representing classes, functions, and methods. Edges indicate function usage (e.g., how data flows through function calls, as derived from program analysis of real code), and documentation about functions (e.g., code documentation, usage documentation, or forum discussions such as StackOverflow). Our toolkit uses named graphs in RDF to model graphs per program, or can output graphs as JSON. We show the scalability of the toolkit by applying it to 1.3 million Python files drawn from GitHub, 2,300 Python modules, and 47 million forum posts. This results in an integrated code graph with over 2 billion triples. We make the toolkit to build such graphs as well as the sample extraction of the 2 billion triples graph publicly available to the community for use.

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.

Given a node-attributed graph, and a graph task (link prediction or node classification), can we tell if a graph neural network (GNN) will perform well? More specifically, do the graph structure and the node features carry enough usable information for the task? Our goals are (1) to develop a fast tool to measure how much information is in the graph structure and in the node features, and (2) to exploit the information to solve the task, if there is enough. We propose NetInfoF, a framework including NetInfoF_Probe and NetInfoF_Act, for the measurement and the exploitation of network usable information (NUI), respectively. Given a graph data, NetInfoF_Probe measures NUI without any model training, and NetInfoF_Act solves link prediction and node classification, while two modules share the same backbone. In summary, NetInfoF has following notable advantages: (a) General, handling both link prediction and node classification; (b) Principled, with theoretical guarantee and closed-form solution; (c) Effective, thanks to the proposed adjustment to node similarity; (d) Scalable, scaling linearly with the input size. In our carefully designed synthetic datasets, NetInfoF correctly identifies the ground truth of NUI and is the only method being robust to all graph scenarios. Applied on real-world datasets, NetInfoF wins in 11 out of 12 times on link prediction compared to general GNN baselines.

Knowledge graph (KG) link prediction aims to infer new facts based on existing facts in the KG. Recent studies have shown that using the graph neighborhood of a node via graph neural networks (GNNs) provides more useful information compared to just using the query information. Conventional GNNs for KG link prediction follow the standard message-passing paradigm on the entire KG, which leads to superfluous computation, over-smoothing of node representations, and also limits their expressive power. On a large scale, it becomes computationally expensive to aggregate useful information from the entire KG for inference. To address the limitations of existing KG link prediction frameworks, we propose a novel retrieve-and-read framework, which first retrieves a relevant subgraph context for the query and then jointly reasons over the context and the query with a high-capacity reader. As part of our exemplar instantiation for the new framework, we propose a novel Transformer-based GNN as the reader, which incorporates graph-based attention structure and cross-attention between query and context for deep fusion. This simple yet effective design enables the model to focus on salient context information relevant to the query. Empirical results on two standard KG link prediction datasets demonstrate the competitive performance of the proposed method. Furthermore, our analysis yields valuable insights for designing improved retrievers within the framework.

The arXiv has collected 1.5 million pre-print articles over 28 years, hosting literature from scientific fields including Physics, Mathematics, and Computer Science. Each pre-print features text, figures, authors, citations, categories, and other metadata. These rich, multi-modal features, combined with the natural graph structure---created by citation, affiliation, and co-authorship---makes the arXiv an exciting candidate for benchmarking next-generation models. Here we take the first necessary steps toward this goal, by providing a pipeline which standardizes and simplifies access to the arXiv's publicly available data. We use this pipeline to extract and analyze a 6.7 million edge citation graph, with an 11 billion word corpus of full-text research articles. We present some baseline classification results, and motivate application of more exciting generative graph models.

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/.

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.

Graph Neural Networks (GNNs) are neural models that leverage the dependency structure in graphical data via message passing among the graph nodes. GNNs have emerged as pivotal architectures in analyzing graph-structured data, and their expansive application in sensitive domains requires a comprehensive understanding of their decision-making processes -- necessitating a framework for GNN explainability. An explanation function for GNNs takes a pre-trained GNN along with a graph as input, to produce a `sufficient statistic' subgraph with respect to the graph label. A main challenge in studying GNN explainability is to provide fidelity measures that evaluate the performance of these explanation functions. This paper studies this foundational challenge, spotlighting the inherent limitations of prevailing fidelity metrics, including Fid_+, Fid_-, and Fid_Delta. Specifically, a formal, information-theoretic definition of explainability is introduced and it is shown that existing metrics often fail to align with this definition across various statistical scenarios. The reason is due to potential distribution shifts when subgraphs are removed in computing these fidelity measures. Subsequently, a robust class of fidelity measures are introduced, and it is shown analytically that they are resilient to distribution shift issues and are applicable in a wide range of scenarios. Extensive empirical analysis on both synthetic and real datasets are provided to illustrate that the proposed metrics are more coherent with gold standard metrics. The source code is available at https://trustai4s-lab.github.io/fidelity.

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.

Graphs are a powerful tool for representing and analyzing complex relationships in real-world applications such as social networks, recommender systems, and computational finance. Reasoning on graphs is essential for drawing inferences about the relationships between entities in a complex system, and to identify hidden patterns and trends. Despite the remarkable progress in automated reasoning with natural text, reasoning on graphs with large language models (LLMs) remains an understudied problem. In this work, we perform the first comprehensive study of encoding graph-structured data as text for consumption by LLMs. We show that LLM performance on graph reasoning tasks varies on three fundamental levels: (1) the graph encoding method, (2) the nature of the graph task itself, and (3) interestingly, the very structure of the graph considered. These novel results provide valuable insight on strategies for encoding graphs as text. Using these insights we illustrate how the correct choice of encoders can boost performance on graph reasoning tasks inside LLMs by 4.8% to 61.8%, depending on the task.

Public software repositories, like GitHub and Software Heritage Archive, store billions of files, yet extracting their implicit engineering knowledge ---i.e., the algorithms they implement, the paradigms they follow, the patterns they instantiate, and the application domains they serve--- remains challenging, as current tools are constrained to syntactic and token-level analysis. We present a pipeline for building an open-taxonomy semantic annotation of source code using a code-specialised Large Language Model. The extracted entities are grounded in Wikidata through a three-stage linking procedure: a deterministic SPARQL stage handles unambiguous entities, a Deep Research Agent resolves the residual long tail, and a hierarchy-rollup stage imports the parent-of closure of each resolved Wikidata identifier. The resulting annotations are materialised as a source-code-specific open-taxonomy knowledge graph. We further introduce a calibrated quality-assurance protocol that quantifies annotation precision by combining a small human gold set with an LLM-as-a-judge filter. We applied our pipeline to the 167 million files of the Stack-Edu corpus, creating the first known large-scale open-taxonomy knowledge graph for source code. Our graph, named CodeGraph, contains approximately 158 million nodes, which include around 145 million files, about 63,000 extracted concept entities (such as algorithms, paradigms, design patterns, and application domains), and roughly 19,800 grounded Wikidata entities. Furthermore, CodeGraph features approximately 1 billion typed edges that connect files to their respective concepts, link these concepts to their grounded Wikidata identifiers, and relate them to their parent categories, covering 14 programming languages.

Knowledge graphs have become a key resource for integrating heterogeneous data and powering downstream tasks such as question answering, entity linking, and semantic search. They are built and maintained incrementally, either (i) fully automated, e.g., YAGO, (ii) semiautomatically with community oversight, e.g., DBpedia, or (iii) manually through collaborative editing, e.g., Wikidata. Understanding the evolution of knowledge graphs is essential as changes may reflect real-world updates, error corrections, or noise introduced by vandalism, all of which affect the reliability of downstream applications. Among openly available knowledge graphs, Wikidata is the most challenging case to study evolution, with over 120 million entities edited by humans and bots and an edit history spanning more than a decade. Although Wikidata exposes change data in various formats (e.g., periodic dumps and real-time event streams), none support analytical queries over the complete edit history. Therefore, we present WiDiff, a tool that extracts changes from Wikidata's complete edit history and provides a unified interface for large-scale analytical queries over it.

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.

A research division plays an important role of driving innovation in an organization. Drawing insights, following trends, keeping abreast of new research, and formulating strategies are increasingly becoming more challenging for both researchers and executives as the amount of information grows in both velocity and volume. In this paper we present a use case of how a corporate research community, IBM Research, utilizes Semantic Web technologies to induce a unified Knowledge Graph from both structured and textual data obtained by integrating various applications used by the community related to research projects, academic papers, datasets, achievements and recognition. In order to make the Knowledge Graph more accessible to application developers, we identified a set of common patterns for exploiting the induced knowledge and exposed them as APIs. Those patterns were born out of user research which identified the most valuable use cases or user pain points to be alleviated. We outline two distinct scenarios: recommendation and analytics for business use. We will discuss these scenarios in detail and provide an empirical evaluation on entity recommendation specifically. The methodology used and the lessons learned from this work can be applied to other organizations facing similar challenges.

With the emergence of data marketplaces, the demand for methods to assess the value of data has increased significantly. While numerous techniques have been proposed for this purpose, none have specifically addressed graphs as the main data modality. Graphs are widely used across various fields, ranging from chemical molecules to social networks. In this study, we break down graphs into two main components: structural and featural, and we focus on evaluating data without relying on specific task-related metrics, making it applicable in practical scenarios where validation requirements may be lacking. We introduce a novel framework called blind message passing, which aligns the seller's and buyer's graphs using a shared node permutation based on graph matching. This allows us to utilize the graph Wasserstein distance to quantify the differences in the structural distribution of graph datasets, called the structural disparities. We then consider featural aspects of buyers' and sellers' graphs for data valuation and capture their statistical similarities and differences, referred to as relevance and diversity, respectively. Our approach ensures that buyers and sellers remain unaware of each other's datasets. Our experiments on real datasets demonstrate the effectiveness of our approach in capturing the relevance, diversity, and structural disparities of seller data for buyers, particularly in graph-based data valuation scenarios.

Artificial General Intelligence (AGI) has revolutionized numerous fields, yet its integration with graph data, a cornerstone in our interconnected world, remains nascent. This paper presents a pioneering survey on the emerging domain of graph prompts in AGI, addressing key challenges and opportunities in harnessing graph data for AGI applications. Despite substantial advancements in AGI across natural language processing and computer vision, the application to graph data is relatively underexplored. This survey critically evaluates the current landscape of AGI in handling graph data, highlighting the distinct challenges in cross-modality, cross-domain, and cross-task applications specific to graphs. Our work is the first to propose a unified framework for understanding graph prompt learning, offering clarity on prompt tokens, token structures, and insertion patterns in the graph domain. We delve into the intrinsic properties of graph prompts, exploring their flexibility, expressiveness, and interplay with existing graph models. A comprehensive taxonomy categorizes over 100 works in this field, aligning them with pre-training tasks across node-level, edge-level, and graph-level objectives. Additionally, we present, ProG, a Python library, and an accompanying website, to support and advance research in graph prompting. The survey culminates in a discussion of current challenges and future directions, offering a roadmap for research in graph prompting within AGI. Through this comprehensive analysis, we aim to catalyze further exploration and practical applications of AGI in graph data, underlining its potential to reshape AGI fields and beyond. ProG and the website can be accessed by https://github.com/WxxShirley/Awesome-Graph-Prompt, and https://github.com/sheldonresearch/ProG, respectively.

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.

Cyber threat intelligence (CTI) is being used to search for indicators of attacks that might have compromised an enterprise network for a long time without being discovered. To have a more effective analysis, CTI open standards have incorporated descriptive relationships showing how the indicators or observables are related to each other. However, these relationships are either completely overlooked in information gathering or not used for threat hunting. In this paper, we propose a system, called POIROT, which uses these correlations to uncover the steps of a successful attack campaign. We use kernel audits as a reliable source that covers all causal relations and information flows among system entities and model threat hunting as an inexact graph pattern matching problem. Our technical approach is based on a novel similarity metric which assesses an alignment between a query graph constructed out of CTI correlations and a provenance graph constructed out of kernel audit log records. We evaluate POIROT on publicly released real-world incident reports as well as reports of an adversarial engagement designed by DARPA, including ten distinct attack campaigns against different OS platforms such as Linux, FreeBSD, and Windows. Our evaluation results show that POIROT is capable of searching inside graphs containing millions of nodes and pinpoint the attacks in a few minutes, and the results serve to illustrate that CTI correlations could be used as robust and reliable artifacts for threat hunting.

As part of its scholarly data efforts, the Internet Archive (IA) releases a first version of a citation graph dataset, named refcat, derived from scholarly publications and additional data sources. It is composed of data gathered by the fatcat cataloging project (the catalog that underpins IA Scholar), related web-scale crawls targeting primary and secondary scholarly outputs, as well as metadata from the Open Library project and Wikipedia. This first version of the graph consists of over 1.3B citations. We release this dataset under a CC0 Public Domain Dedication, accessible through Internet Archive. The source code used for the derivation process, including exact and fuzzy citation matching, is released under an MIT license. The goal of this report is to describe briefly the current contents and the derivation of the dataset.

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.

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.

This paper studies the problem of embedding very large information networks into low-dimensional vector spaces, which is useful in many tasks such as visualization, node classification, and link prediction. Most existing graph embedding methods do not scale for real world information networks which usually contain millions of nodes. In this paper, we propose a novel network embedding method called the "LINE," which is suitable for arbitrary types of information networks: undirected, directed, and/or weighted. The method optimizes a carefully designed objective function that preserves both the local and global network structures. An edge-sampling algorithm is proposed that addresses the limitation of the classical stochastic gradient descent and improves both the effectiveness and the efficiency of the inference. Empirical experiments prove the effectiveness of the LINE on a variety of real-world information networks, including language networks, social networks, and citation networks. The algorithm is very efficient, which is able to learn the embedding of a network with millions of vertices and billions of edges in a few hours on a typical single machine. The source code of the LINE is available online.

We present CoDEx, a set of knowledge graph completion datasets extracted from Wikidata and Wikipedia that improve upon existing knowledge graph completion benchmarks in scope and level of difficulty. In terms of scope, CoDEx comprises three knowledge graphs varying in size and structure, multilingual descriptions of entities and relations, and tens of thousands of hard negative triples that are plausible but verified to be false. To characterize CoDEx, we contribute thorough empirical analyses and benchmarking experiments. First, we analyze each CoDEx dataset in terms of logical relation patterns. Next, we report baseline link prediction and triple classification results on CoDEx for five extensively tuned embedding models. Finally, we differentiate CoDEx from the popular FB15K-237 knowledge graph completion dataset by showing that CoDEx covers more diverse and interpretable content, and is a more difficult link prediction benchmark. Data, code, and pretrained models are available at https://bit.ly/2EPbrJs.

A variety of knowledge graph embedding approaches have been developed. Most of them obtain embeddings by learning the structure of the knowledge graph within a link prediction setting. As a result, the embeddings reflect only the semantics of a single knowledge graph, and embeddings for different knowledge graphs are not aligned, e.g., they cannot be used to find similar entities across knowledge graphs via nearest neighbor search. However, knowledge graph embedding applications such as entity disambiguation require a more global representation, i.e., a representation that is valid across multiple sources. We propose to learn universal knowledge graph embeddings from large-scale interlinked knowledge sources. To this end, we fuse large knowledge graphs based on the owl:sameAs relation such that every entity is represented by a unique identity. We instantiate our idea by computing universal embeddings based on DBpedia and Wikidata yielding embeddings for about 180 million entities, 15 thousand relations, and 1.2 billion triples. Moreover, we develop a convenient API to provide embeddings as a service. Experiments on link prediction show that universal knowledge graph embeddings encode better semantics compared to embeddings computed on a single knowledge graph. For reproducibility purposes, we provide our source code and datasets open access at https://github.com/dice-group/Universal_Embeddings

The research idea in a published paper is rarely the project's initial idea. Between the two lies a closed-loop process in which researchers run experiments, derive insights, identify challenges, explore the literature, and revise the idea, with each step motivated by evidence and reasoning they can articulate. We call the path one idea takes through this process, with the evidence and reasoning behind each step, its authentic research trajectory. Although it underlies every scientific contribution, it is rarely recorded. Existing LLM-based research agents generate an idea once, refine it against reviews, literature, or their own experimental results, or search over candidate ideas and experiments. In all of them the text of the idea evolves, while the evidence and reasoning that connected one version to the next are discarded. We propose the Research Progress Graph (RPG), a representation of authentic and complete research trajectories. An RPG records the evolution of an idea as typed research states connected by cognitive transitions, each annotated with a temporal index and the reasoning behind it, which makes this evolution an explicit object of study. We ground the representation in authentic trajectories whose steps their authors justify in annotations and papers. Comparing the representations of thirty-five research agents with the RPG, we find that each is an incomplete RPG; none keeps the state that changed, the evidence that changed it, and the reasoning connecting them as one evolving record. Modeling ideation with the RPG changes how research agents should be designed, evaluated, and trained. Agents predict the next research state instead of a complete idea, ideas are evaluated as trajectories instead of final texts, and authentic trajectories serve as training data. These directions shift research agents from generating static ideas to modeling how ideas evolve.

The volume of scientific output is creating an urgent need for automated tools to help scientists keep up with developments in their field. Semantic Scholar (S2) is an open data platform and website aimed at accelerating science by helping scholars discover and understand scientific literature. We combine public and proprietary data sources using state-of-the-art techniques for scholarly PDF content extraction and automatic knowledge graph construction to build the Semantic Scholar Academic Graph, the largest open scientific literature graph to-date, with 200M+ papers, 80M+ authors, 550M+ paper-authorship edges, and 2.4B+ citation edges. The graph includes advanced semantic features such as structurally parsed text, natural language summaries, and vector embeddings. In this paper, we describe the components of the S2 data processing pipeline and the associated APIs offered by the platform. We will update this living document to reflect changes as we add new data offerings and improve existing services.

Knowledge Graphs (KGs) are structured knowledge repositories containing entities and relations between them. In this paper, we investigate the problem of automatically updating KGs over time with respect to the evolution of knowledge in unstructured textual sources. This problem requires identifying a wide range of update operations based on the state of an existing KG at a specific point in time. This contrasts with traditional information extraction pipelines, which extract knowledge from text independently of the current state of a KG. To address this challenge, we propose a method for lifelong construction of a dataset consisting of Wikidata KG snapshots over time and Wikipedia passages paired with the corresponding edit operations that they induce in a particular KG snapshot. The resulting dataset comprises 376K Wikipedia passages aligned with a total of 1.25M KG edits over 10 different snapshots of Wikidata from 2019 to 2025. Our experimental results highlight challenges in updating KG snapshots based on emerging textual knowledge, positioning the dataset as a valuable benchmark for future research. We will publicly release our dataset and model implementations.

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.

Online misinformation poses an escalating threat, amplified by the Internet's open nature and increasingly capable LLMs that generate persuasive yet deceptive content. Existing misinformation detection methods typically focus on either textual content or network structure in isolation, failing to leverage the rich, dynamic interplay between website content and hyperlink relationships that characterizes real-world misinformation ecosystems. We introduce CrediBench: a large-scale data processing pipeline for constructing temporal web graphs that jointly model textual content and hyperlink structure for misinformation detection. Unlike prior work, our approach captures the dynamic evolution of general misinformation domains, including changes in both content and inter-site references over time. Our processed one-month snapshot extracted from the Common Crawl archive in December 2024 contains 45 million nodes and 1 billion edges, representing the largest web graph dataset made publicly available for misinformation research to date. From our experiments on this graph snapshot, we demonstrate the strength of both structural and webpage content signals for learning credibility scores, which measure source reliability. The pipeline and experimentation code are all available here, and the dataset is in this folder.

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.

Knowledge Graphs (KGs) have been used to support a wide range of applications, from web search to personal assistant. In this paper, we describe three generations of knowledge graphs: entity-based KGs, which have been supporting general search and question answering (e.g., at Google and Bing); text-rich KGs, which have been supporting search and recommendations for products, bio-informatics, etc. (e.g., at Amazon and Alibaba); and the emerging integration of KGs and LLMs, which we call dual neural KGs. We describe the characteristics of each generation of KGs, the crazy ideas behind the scenes in constructing such KGs, and the techniques developed over time to enable industry impact. In addition, we use KGs as examples to demonstrate a recipe to evolve research ideas from innovations to production practice, and then to the next level of innovations, to advance both science and business.

Knowledge graph (KG) embedding has been used to benefit the diagnosis of animal diseases by analyzing electronic medical records (EMRs), such as notes and veterinary records. However, learning representations to capture entities and relations with literal information in KGs is challenging as the KGs show heterogeneous properties and various types of literal information. Meanwhile, the existing methods mostly aim to preserve graph structures surrounding target nodes without considering different types of literals, which could also carry significant information. In this paper, we propose a knowledge graph embedding model for the efficient diagnosis of animal diseases, which could learn various types of literal information and graph structure and fuse them into unified representations, namely LiteralKG. Specifically, we construct a knowledge graph that is built from EMRs along with literal information collected from various animal hospitals. We then fuse different types of entities and node feature information into unified vector representations through gate networks. Finally, we propose a self-supervised learning task to learn graph structure in pretext tasks and then towards various downstream tasks. Experimental results on link prediction tasks demonstrate that our model outperforms the baselines that consist of state-of-the-art models. The source code is available at https://github.com/NSLab-CUK/LiteralKG.

User profiling has long been an important problem that investigates user interests in many real applications. Some recent works regard users and their interacted objects as entities of a graph and turn the problem into a node classification task. However, they neglect the difference of distinct interaction types, e.g. user clicks an item v.s.user purchases an item, and thus cannot incorporate such information well. To solve these issues, we propose to leverage the relation-aware heterogeneous graph method for user profiling, which also allows capturing significant meta relations. We adopt the query, key, and value mechanism in a transformer fashion for heterogeneous message passing so that entities can effectively interact with each other. Via such interactions on different relation types, our model can generate representations with rich information for the user profile prediction. We conduct experiments on two real-world e-commerce datasets and observe a significant performance boost of our approach.

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

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.

Information graphics are pivotal in effective information dissemination and storytelling. However, creating such graphics is extremely challenging for non-professionals, since the design process requires multifaceted skills and comprehensive knowledge. Thus, despite the many available authoring tools, a significant gap remains in enabling non-experts to produce compelling information graphics seamlessly, especially from scratch. Recent breakthroughs show that Large Language Models (LLMs), especially when tool-augmented, can autonomously engage with external tools, making them promising candidates for enabling innovative graphic design applications. In this work, we propose a LLM-centric interface with the agent GraphiMind for automatic generation, recommendation, and composition of information graphics design resources, based on user intent expressed through natural language. Our GraphiMind integrates a Textual Conversational Interface, powered by tool-augmented LLM, with a traditional Graphical Manipulation Interface, streamlining the entire design process from raw resource curation to composition and refinement. Extensive evaluations highlight our tool's proficiency in simplifying the design process, opening avenues for its use by non-professional users. Moreover, we spotlight the potential of LLMs in reshaping the domain of information graphics design, offering a blend of automation, versatility, and user-centric interactivity.

As economics scales, a key bottleneck is representing what papers claim in a comparable, aggregable form. We introduce evidence-annotated claim graphs that map each paper into a directed network of standardized economic concepts (nodes) and stated relationships (edges), with each edge labeled by evidentiary basis, including whether it is supported by causal inference designs or by non-causal evidence. Using a structured multi-stage AI workflow, we construct claim graphs for 44,852 economics papers from 1980-2023. The share of causal edges rises from 7.7% in 1990 to 31.7% in 2020. Measures of causal narrative structure and causal novelty are positively associated with top-five publication and long-run citations, whereas non-causal counterparts are weakly related or negative.

The exponential growth of scientific literature requires effective management and extraction of valuable insights. While existing scientific search engines excel at delivering search results based on relational databases, they often neglect the analysis of collaborations between scientific entities and the evolution of ideas, as well as the in-depth analysis of content within scientific publications. The representation of heterogeneous graphs and the effective measurement, analysis, and mining of such graphs pose significant challenges. To address these challenges, we present AceMap, an academic system designed for knowledge discovery through academic graph. We present advanced database construction techniques to build the comprehensive AceMap database with large-scale academic entities that contain rich visual, textual, and numerical information. AceMap also employs innovative visualization, quantification, and analysis methods to explore associations and logical relationships among academic entities. AceMap introduces large-scale academic network visualization techniques centered on nebular graphs, providing a comprehensive view of academic networks from multiple perspectives. In addition, AceMap proposes a unified metric based on structural entropy to quantitatively measure the knowledge content of different academic entities. Moreover, AceMap provides advanced analysis capabilities, including tracing the evolution of academic ideas through citation relationships and concept co-occurrence, and generating concise summaries informed by this evolutionary process. In addition, AceMap uses machine reading methods to generate potential new ideas at the intersection of different fields. Exploring the integration of large language models and knowledge graphs is a promising direction for future research in idea evolution. Please visit https://www.acemap.info for further exploration.

Legal documents including judgments and court orders require highly sophisticated legal knowledge for understanding. To disclose expert knowledge for non-experts, we explore the problem of visualizing legal texts with easy-to-understand diagrams and propose a novel dataset of LegalViz with 23 languages and 7,010 cases of legal document and visualization pairs, using the DOT graph description language of Graphviz. LegalViz provides a simple diagram from a complicated legal corpus identifying legal entities, transactions, legal sources, and statements at a glance, that are essential in each judgment. In addition, we provide new evaluation metrics for the legal diagram visualization by considering graph structures, textual similarities, and legal contents. We conducted empirical studies on few-shot and finetuning large language models for generating legal diagrams and evaluated them with these metrics, including legal content-based evaluation within 23 languages. Models trained with LegalViz outperform existing models including GPTs, confirming the effectiveness of our dataset.

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

To deduce new facts on a knowledge graph (KG), a link predictor learns from the graph structure and collects local evidence to find the answer to a given query. However, existing methods suffer from a severe scalability problem due to the utilization of the whole KG for prediction, which hinders their promise on large scale KGs and cannot be directly addressed by vanilla sampling methods. In this work, we propose the one-shot-subgraph link prediction to achieve efficient and adaptive prediction. The design principle is that, instead of directly acting on the whole KG, the prediction procedure is decoupled into two steps, i.e., (i) extracting only one subgraph according to the query and (ii) predicting on this single, query dependent subgraph. We reveal that the non-parametric and computation-efficient heuristics Personalized PageRank (PPR) can effectively identify the potential answers and supporting evidence. With efficient subgraph-based prediction, we further introduce the automated searching of the optimal configurations in both data and model spaces. Empirically, we achieve promoted efficiency and leading performances on five large-scale benchmarks. The code is publicly available at: https://github.com/tmlr-group/one-shot-subgraph.

Rationale discovery is defined as finding a subset of the input data that maximally supports the prediction of downstream tasks. In graph machine learning context, graph rationale is defined to locate the critical subgraph in the given graph topology, which fundamentally determines the prediction results. In contrast to the rationale subgraph, the remaining subgraph is named the environment subgraph. Graph rationalization can enhance the model performance as the mapping between the graph rationale and prediction label is viewed as invariant, by assumption. To ensure the discriminative power of the extracted rationale subgraphs, a key technique named "intervention" is applied. The core idea of intervention is that given any changing environment subgraphs, the semantics from the rationale subgraph is invariant, which guarantees the correct prediction result. However, most, if not all, of the existing rationalization works on graph data develop their intervention strategies on the graph level, which is coarse-grained. In this paper, we propose well-tailored intervention strategies on graph data. Our idea is driven by the development of Transformer models, whose self-attention module provides rich interactions between input nodes. Based on the self-attention module, our proposed invariant graph Transformer (IGT) can achieve fine-grained, more specifically, node-level and virtual node-level intervention. Our comprehensive experiments involve 7 real-world datasets, and the proposed IGT shows significant performance advantages compared to 13 baseline methods.

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.

The database community has repeatedly advanced the state of the art by recognizing that new workloads demand new system architectures. We argue that long-horizon agentic tasks -- code generation, scientific discovery, hardware design -- are such a workload. These agents explore: they generate artifacts, execute tools, observe failures, branch, and repair over hundreds of steps. This search produces a structured object we call an experience graph: executable artifacts, tool outputs, rewards, sibling comparisons, and causal lineage. Yet existing agent frameworks treat this experience as disposable state -- JSON checkpoints and session logs that cannot be recovered after a crash, queried across users, or materialized into training data. We propose Trellis: a data foundation that treats the experience graph as first-class, governed, queryable database state. The core insight is that search over experience graphs is a database access pattern. Frontier selection is a query, cross-session reuse is vector-seeded graph retrieval, training-data extraction is a materialized view, and reconstructing what an agent knew at any past step is a time-travel query. When the database owns the experience graph, agents become stateless compute, and crash recovery, horizontal scaling, and a closed-loop training flywheel emerge as architectural byproducts. We ground the design in KernelEvolve, a production accelerator-kernel optimizer at Meta, where cross-session reuse reaches a target speedup roughly 10x faster at 52% lower token cost. More broadly, Trellis turns inference-time search from disposable computation into a durable institutional asset: logs made databases reliable; experience graphs may make agents cumulative.

Knowledge graph embedding involves learning representations of entities -- the vertices of the graph -- and relations -- the edges of the graph -- such that the resulting representations encode the known factual information represented by the knowledge graph and can be used in the inference of new relations. We show that knowledge graph embedding is naturally expressed in the topological and categorical language of cellular sheaves: a knowledge graph embedding can be described as an approximate global section of an appropriate knowledge sheaf over the graph, with consistency constraints induced by the knowledge graph's schema. This approach provides a generalized framework for reasoning about knowledge graph embedding models and allows for the expression of a wide range of prior constraints on embeddings. Further, the resulting embeddings can be easily adapted for reasoning over composite relations without special training. We implement these ideas to highlight the benefits of the extensions inspired by this new perspective.

For a broad range of research, governmental and commercial applications it is important to understand the allegiances, communities and structure of key players in society. One promising direction towards extracting this information is to exploit the rich relational data in digital social networks (the social graph). As social media data sets are very large, most approaches make use of distributed computing systems for this purpose. Distributing graph processing requires solving many difficult engineering problems, which has lead some researchers to look at single-machine solutions that are faster and easier to maintain. In this article, we present a single-machine real-time system for large-scale graph processing that allows analysts to interactively explore graph structures. The key idea is that the aggregate actions of large numbers of users can be compressed into a data structure that encapsulates user similarities while being robust to noise and queryable in real-time. We achieve single machine real-time performance by compressing the neighbourhood of each vertex using minhash signatures and facilitate rapid queries through Locality Sensitive Hashing. These techniques reduce query times from hours using industrial desktop machines operating on the full graph to milliseconds on standard laptops. Our method allows exploration of strongly associated regions (i.e. communities) of large graphs in real-time on a laptop. It has been deployed in software that is actively used by social network analysts and offers another channel for media owners to monetise their data, helping them to continue to provide free services that are valued by billions of people globally.

Knowledge Graphs (KG) provide us with a structured, flexible, transparent, cross-system, and collaborative way of organizing our knowledge and data across various domains in society and industrial as well as scientific disciplines. KGs surpass any other form of representation in terms of effectiveness. However, Knowledge Graph Engineering (KGE) requires in-depth experiences of graph structures, web technologies, existing models and vocabularies, rule sets, logic, as well as best practices. It also demands a significant amount of work. Considering the advancements in large language models (LLMs) and their interfaces and applications in recent years, we have conducted comprehensive experiments with ChatGPT to explore its potential in supporting KGE. In this paper, we present a selection of these experiments and their results to demonstrate how ChatGPT can assist us in the development and management of KGs.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

We present the task of modeling information propagation in literature, in which we seek to identify pieces of information passing from character A to character B to character C, only given a description of their activity in text. We describe a new pipeline for measuring information propagation in this domain and publish a new dataset for speaker attribution, enabling the evaluation of an important component of this pipeline on a wider range of literary texts than previously studied. Using this pipeline, we analyze the dynamics of information propagation in over 5,000 works of fiction, finding that information flows through characters that fill structural holes connecting different communities, and that characters who are women are depicted as filling this role much more frequently than characters who are men.

Knowledge graph reasoning (KGR), aiming to deduce new facts from existing facts based on mined logic rules underlying knowledge graphs (KGs), has become a fast-growing research direction. It has been proven to significantly benefit the usage of KGs in many AI applications, such as question answering, recommendation systems, and etc. According to the graph types, existing KGR models can be roughly divided into three categories, i.e., static models, temporal models, and multi-modal models. Early works in this domain mainly focus on static KGR, and recent works try to leverage the temporal and multi-modal information, which are more practical and closer to real-world. However, no survey papers and open-source repositories comprehensively summarize and discuss models in this important direction. To fill the gap, we conduct a first survey for knowledge graph reasoning tracing from static to temporal and then to multi-modal KGs. Concretely, the models are reviewed based on bi-level taxonomy, i.e., top-level (graph types) and base-level (techniques and scenarios). Besides, the performances, as well as datasets, are summarized and presented. Moreover, we point out the challenges and potential opportunities to enlighten the readers. The corresponding open-source repository is shared on GitHub https://github.com/LIANGKE23/Awesome-Knowledge-Graph-Reasoning.

Retrieval-augmented generation (RAG) is a powerful technique that enhances downstream task execution by retrieving additional information, such as knowledge, skills, and tools from external sources. Graph, by its intrinsic "nodes connected by edges" nature, encodes massive heterogeneous and relational information, making it a golden resource for RAG in tremendous real-world applications. As a result, we have recently witnessed increasing attention on equipping RAG with Graph, i.e., GraphRAG. However, unlike conventional RAG, where the retriever, generator, and external data sources can be uniformly designed in the neural-embedding space, the uniqueness of graph-structured data, such as diverse-formatted and domain-specific relational knowledge, poses unique and significant challenges when designing GraphRAG for different domains. Given the broad applicability, the associated design challenges, and the recent surge in GraphRAG, a systematic and up-to-date survey of its key concepts and techniques is urgently desired. Following this motivation, we present a comprehensive and up-to-date survey on GraphRAG. Our survey first proposes a holistic GraphRAG framework by defining its key components, including query processor, retriever, organizer, generator, and data source. Furthermore, recognizing that graphs in different domains exhibit distinct relational patterns and require dedicated designs, we review GraphRAG techniques uniquely tailored to each domain. Finally, we discuss research challenges and brainstorm directions to inspire cross-disciplinary opportunities. Our survey repository is publicly maintained at https://github.com/Graph-RAG/GraphRAG/.

Global challenges such as food supply chain disruptions, public health crises, and natural hazard responses require access to and integration of diverse datasets, many of which are geospatial. Over the past few years, a growing number of (geo)portals have been developed to address this need. However, most existing (geo)portals are stacked by separated or sparsely connected data "silos" impeding effective data consolidation. A new way of sharing and reusing geospatial data is therefore urgently needed. In this work, we introduce KnowWhereGraph, a knowledge graph-based data integration, enrichment, and synthesis framework that not only includes schemas and data related to human and environmental systems but also provides a suite of supporting tools for accessing this information. The KnowWhereGraph aims to address the challenge of data integration by building a large-scale, cross-domain, pre-integrated, FAIR-principles-based, and AI-ready data warehouse rooted in knowledge graphs. We highlight the design principles of KnowWhereGraph, emphasizing the roles of space, place, and time in bridging various data "silos". Additionally, we demonstrate multiple use cases where the proposed geospatial knowledge graph and its associated tools empower decision-makers to uncover insights that are often hidden within complex and poorly interoperable datasets.

Scientific paper evaluation often involves not only assessing a manuscript itself, but also relating it to contemporaneous research and prior literature. However, existing LLM-based methods typically model these signals separately and lack a unified mechanism for aggregating review evidence across papers. We propose GraphReview, a graph-based LLM framework that formulates paper evaluation as inference-time graph evidence expansion over a semantic paper graph. The graph jointly captures intrinsic quality, synchronic links among contemporaneous papers, and diachronic links to prior work. LLMs are used to estimate node-level quality priors and generate edge-level comparative evidence through pairwise paper comparisons, while Personalized PageRank integrates these structured signals for quality ranking, decision prediction, and review generation. To produce higher-quality graph evidence, we propose reward-induced maximum likelihood objectives for training the LLM backbones. Experiments show that GraphReview consistently outperforms the strongest baseline, achieving average improvements of 29.7% on decision and ranking metrics, including gains of 23.7% in Accuracy and 57.6% in Spearman's ρ. It also produces higher-quality review texts and generalizes effectively across time periods and conference venues.

Knowledge Graphs (KG) are of vital importance for multiple applications on the web, including information retrieval, recommender systems, and metadata annotation. Regardless of whether they are built manually by domain experts or with automatic pipelines, KGs are often incomplete. Recent work has begun to explore the use of textual descriptions available in knowledge graphs to learn vector representations of entities in order to preform link prediction. However, the extent to which these representations learned for link prediction generalize to other tasks is unclear. This is important given the cost of learning such representations. Ideally, we would prefer representations that do not need to be trained again when transferring to a different task, while retaining reasonable performance. In this work, we propose a holistic evaluation protocol for entity representations learned via a link prediction objective. We consider the inductive link prediction and entity classification tasks, which involve entities not seen during training. We also consider an information retrieval task for entity-oriented search. We evaluate an architecture based on a pretrained language model, that exhibits strong generalization to entities not observed during training, and outperforms related state-of-the-art methods (22% MRR improvement in link prediction on average). We further provide evidence that the learned representations transfer well to other tasks without fine-tuning. In the entity classification task we obtain an average improvement of 16% in accuracy compared with baselines that also employ pre-trained models. In the information retrieval task, we obtain significant improvements of up to 8.8% in NDCG@10 for natural language queries. We thus show that the learned representations are not limited KG-specific tasks, and have greater generalization properties than evaluated in previous work.

Scientific contributions rarely develop in isolation, but instead build upon prior discoveries. We formulate the task of automated technological roadmapping as extracting scientific contributions from scholarly articles and linking them to their prerequisites. We present the Scientific Contribution Graph, a large-scale resource containing 6 million detailed scientific contributions extracted from 655k open-access papers spanning computer science, medicine, biology, physics, chemistry, and other sciences, and connected by 36 million prerequisite edges. We further introduce scientific prerequisite prediction, a scientific discovery task in which models predict which existing technologies can enable future discoveries, and show that contemporary models are rapidly improving on this task, reaching 0.48 MAP when evaluated using temporally-filtered backtesting. We anticipate technological roadmapping resources such as this will support scientific impact assessment and automated scientific discovery.

Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches are inherently transductive and do not naturally generalize to unseen nodes. Here we present GraphSAGE, a general, inductive framework that leverages node feature information (e.g., text attributes) to efficiently generate node embeddings for previously unseen data. Instead of training individual embeddings for each node, we learn a function that generates embeddings by sampling and aggregating features from a node's local neighborhood. Our algorithm outperforms strong baselines on three inductive node-classification benchmarks: we classify the category of unseen nodes in evolving information graphs based on citation and Reddit post data, and we show that our algorithm generalizes to completely unseen graphs using a multi-graph dataset of protein-protein interactions.

Graph representations of programs are commonly a central element of machine learning for code research. We introduce an open source Python library python_graphs that applies static analysis to construct graph representations of Python programs suitable for training machine learning models. Our library admits the construction of control-flow graphs, data-flow graphs, and composite ``program graphs'' that combine control-flow, data-flow, syntactic, and lexical information about a program. We present the capabilities and limitations of the library, perform a case study applying the library to millions of competitive programming submissions, and showcase the library's utility for machine learning research.

In the past years, predictive process monitoring (PPM) techniques based on artificial neural networks have evolved as a method to monitor the future behavior of business processes. Existing approaches mostly focus on interpreting the processes as sequences, so-called traces, and feeding them to neural architectures designed to operate on sequential data such as recurrent neural networks (RNNs) or transformers. In this study, we investigate an alternative way to perform PPM: by transforming each process in its directly-follows-graph (DFG) representation we are able to apply graph neural networks (GNNs) for the prediction tasks. By this, we aim to develop models that are more suitable for complex processes that are long and contain an abundance of loops. In particular, we present different ways to create DFG representations depending on the particular GNN we use. The tested GNNs range from classical node-based to novel edge-based architectures. Further, we investigate the possibility of using multi-graphs. By these steps, we aim to design graph representations that minimize the information loss when transforming traces into graphs.

The task of Legal Statute Identification (LSI) aims to identify the legal statutes that are relevant to a given description of Facts or evidence of a legal case. Existing methods only utilize the textual content of Facts and legal articles to guide such a task. However, the citation network among case documents and legal statutes is a rich source of additional information, which is not considered by existing models. In this work, we take the first step towards utilising both the text and the legal citation network for the LSI task. We curate a large novel dataset for this task, including Facts of cases from several major Indian Courts of Law, and statutes from the Indian Penal Code (IPC). Modeling the statutes and training documents as a heterogeneous graph, our proposed model LeSICiN can learn rich textual and graphical features, and can also tune itself to correlate these features. Thereafter, the model can be used to inductively predict links between test documents (new nodes whose graphical features are not available to the model) and statutes (existing nodes). Extensive experiments on the dataset show that our model comfortably outperforms several state-of-the-art baselines, by exploiting the graphical structure along with textual features. The dataset and our codes are available at https://github.com/Law-AI/LeSICiN.

Open Information Extraction (OIE) methods extract facts from natural language text in the form of ("subject"; "relation"; "object") triples. These facts are, however, merely surface forms, the ambiguity of which impedes their downstream usage; e.g., the surface phrase "Michael Jordan" may refer to either the former basketball player or the university professor. Knowledge Graphs (KGs), on the other hand, contain facts in a canonical (i.e., unambiguous) form, but their coverage is limited by a static schema (i.e., a fixed set of entities and predicates). To bridge this gap, we need the best of both worlds: (i) high coverage of free-text OIEs, and (ii) semantic precision (i.e., monosemy) of KGs. In order to achieve this goal, we propose a new benchmark with novel evaluation protocols that can, for example, measure fact linking performance on a granular triple slot level, while also measuring if a system has the ability to recognize that a surface form has no match in the existing KG. Our extensive evaluation of several baselines show that detection of out-of-KG entities and predicates is more difficult than accurate linking to existing ones, thus calling for more research efforts on this difficult task. We publicly release all resources (data, benchmark and code) on https://github.com/nec-research/fact-linking.

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.

Graphs are a widely used paradigm for representing non-Euclidean data, with applications ranging from social network analysis to biomolecular prediction. While graph learning has achieved remarkable progress, real-world graph data presents a number of challenges that significantly hinder the learning process. In this survey, we focus on four fundamental data-centric challenges: (1) Incompleteness, real-world graphs have missing nodes, edges, or attributes; (2) Imbalance, the distribution of the labels of nodes or edges and their structures for real-world graphs are highly skewed; (3) Cross-domain Heterogeneity, graphs from different domains exhibit incompatible feature spaces or structural patterns; and (4) Dynamic Instability, graphs evolve over time in unpredictable ways. Recently, Large Language Models (LLMs) offer the potential to tackle these challenges by leveraging rich semantic reasoning and external knowledge. This survey focuses on how LLMs can address four fundamental data-centric challenges in graph-structured data, thereby improving the effectiveness of graph learning. For each challenge, we review both traditional solutions and modern LLM-driven approaches, highlighting how LLMs contribute unique advantages. Finally, we discuss open research questions and promising future directions in this emerging interdisciplinary field. To support further exploration, we have curated a repository of recent advances on graph learning challenges: https://github.com/limengran98/Awesome-Literature-Graph-Learning-Challenges.

Graph retrieval-augmented generation (GraphRAG) has effectively enhanced large language models in complex reasoning by organizing fragmented knowledge into explicitly structured graphs. Prior efforts have been made to improve either graph construction or graph retrieval in isolation, yielding suboptimal performance, especially when domain shifts occur. In this paper, we propose a vertically unified agentic paradigm, Youtu-GraphRAG, to jointly connect the entire framework as an intricate integration. Specifically, (i) a seed graph schema is introduced to bound the automatic extraction agent with targeted entity types, relations and attribute types, also continuously expanded for scalability over unseen domains; (ii) To obtain higher-level knowledge upon the schema, we develop novel dually-perceived community detection, fusing structural topology with subgraph semantics for comprehensive knowledge organization. This naturally yields a hierarchical knowledge tree that supports both top-down filtering and bottom-up reasoning with community summaries; (iii) An agentic retriever is designed to interpret the same graph schema to transform complex queries into tractable and parallel sub-queries. It iteratively performs reflection for more advanced reasoning; (iv) To alleviate the knowledge leaking problem in pre-trained LLM, we propose a tailored anonymous dataset and a novel 'Anonymity Reversion' task that deeply measures the real performance of the GraphRAG frameworks. Extensive experiments across six challenging benchmarks demonstrate the robustness of Youtu-GraphRAG, remarkably moving the Pareto frontier with up to 90.71% saving of token costs and 16.62% higher accuracy over state-of-the-art baselines. The results indicate our adaptability, allowing seamless domain transfer with minimal intervention on schema.

In this paper, we aim to develop a large language model (LLM) with the reasoning ability on complex graph data. Currently, LLMs have achieved very impressive performance on various natural language learning tasks, extensions of which have also been applied to study the vision tasks with multi-modal data. However, when it comes to the graph learning tasks, existing LLMs present very serious flaws due to their several inherited weaknesses in performing {multi-step logic reasoning}, {precise mathematical calculation} and {perception about the spatial and temporal factors}. To address such challenges, in this paper, we will investigate the principles, methodologies and algorithms to empower existing LLMs with graph reasoning ability, which will have tremendous impacts on the current research of both LLMs and graph learning. Inspired by the latest ChatGPT and Toolformer models, we propose the Graph-ToolFormer (Graph Reasoning oriented Toolformer) framework to teach LLMs themselves with prompts augmented by ChatGPT to use external graph reasoning API tools. Specifically, we will investigate to teach Graph-ToolFormer to handle various graph data reasoning tasks in this paper, including both (1) very basic graph data loading and graph property reasoning tasks, ranging from simple graph order and size to the graph diameter and periphery, and (2) more advanced reasoning tasks on real-world graph data, such as bibliographic networks, protein molecules, sequential recommender systems, social networks and knowledge graphs.

Identifying significant references within the complex interrelations of a citation knowledge graph is challenging, which encompasses connections through citations, authorship, keywords, and other relational attributes. The Paper Source Tracing (PST) task seeks to automate the identification of pivotal references for given scholarly articles utilizing advanced data mining techniques. In the KDD CUP 2024, we design a recommendation-based framework tailored for the PST task. This framework employs the Neural Collaborative Filtering (NCF) model to generate final predictions. To process the textual attributes of the papers and extract input features for the model, we utilize SciBERT, a pre-trained language model. According to the experimental results, our method achieved a score of 0.37814 on the Mean Average Precision (MAP) metric, outperforming baseline models and ranking 11th among all participating teams. The source code is publicly available at https://github.com/MyLove-XAB/KDDCupFinal.

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.

Recent advances in search-augmented large reasoning models (LRMs) enable the retrieval of external knowledge to reduce hallucinations in multistep reasoning. However, their ability to operate on graph-structured data, prevalent in domains such as e-commerce, social networks, and scientific citations, remains underexplored. Unlike plain text corpora, graphs encode rich topological signals that connect related entities and can serve as valuable priors for retrieval, enabling more targeted search and improved reasoning efficiency. Yet, effectively leveraging such structure poses unique challenges, including the difficulty of generating graph-expressive queries and ensuring reliable retrieval that balances structural and semantic relevance. To address this gap, we introduce GraphSearch, the first framework that extends search-augmented reasoning to graph learning, enabling zero-shot graph learning without task-specific fine-tuning. GraphSearch combines a Graph-aware Query Planner, which disentangles search space (e.g., 1-hop, multi-hop, or global neighbors) from semantic queries, with a Graph-aware Retriever, which constructs candidate sets based on topology and ranks them using a hybrid scoring function. We further instantiate two traversal modes: GraphSearch-R, which recursively expands neighborhoods hop by hop, and GraphSearch-F, which flexibly retrieves across local and global neighborhoods without hop constraints. Extensive experiments across diverse benchmarks show that GraphSearch achieves competitive or even superior performance compared to supervised graph learning methods, setting state-of-the-art results in zero-shot node classification and link prediction. These findings position GraphSearch as a flexible and generalizable paradigm for agentic reasoning over graphs.

Knowledge Graphs (KGs) are symbolically structured storages of facts. The KG embedding contains concise data used in NLP tasks requiring implicit information about the real world. Furthermore, the size of KGs that may be useful in actual NLP assignments is enormous, and creating embedding over it has memory cost issues. We represent KG as a 3rd-order binary tensor and move beyond the standard CP decomposition by using a data-specific generalized version of it. The generalization of the standard CP-ALS algorithm allows obtaining optimization gradients without a backpropagation mechanism. It reduces the memory needed in training while providing computational benefits. We propose a MEKER, a memory-efficient KG embedding model, which yields SOTA-comparable performance on link prediction tasks and KG-based Question Answering.

There has been a surge of interest in harnessing the reasoning capabilities of Large Language Models (LLMs) to accelerate scientific discovery. While existing approaches rely on grounding the discovery process within the relevant literature, effectiveness varies significantly with the quality and nature of the retrieved literature. We address the challenge of retrieving prior work whose concepts can inspire solutions for a given research problem, a task we define as Methodology Inspiration Retrieval (MIR). We construct a novel dataset tailored for training and evaluating retrievers on MIR, and establish baselines. To address MIR, we build the Methodology Adjacency Graph (MAG); capturing methodological lineage through citation relationships. We leverage MAG to embed an "intuitive prior" into dense retrievers for identifying patterns of methodological inspiration beyond superficial semantic similarity. This achieves significant gains of +5.4 in Recall@3 and +7.8 in Mean Average Precision (mAP) over strong baselines. Further, we adapt LLM-based re-ranking strategies to MIR, yielding additional improvements of +4.5 in Recall@3 and +4.8 in mAP. Through extensive ablation studies and qualitative analyses, we exhibit the promise of MIR in enhancing automated scientific discovery and outline avenues for advancing inspiration-driven retrieval.

Large language models (LLMs) augmented with tools are emerging as autonomous agents capable of using Web engine, APIs, and code to solve complex, long-horizon tasks. Current tool-using benchmarks for information seeking on academic graphs rely on synthetic templates, simplified solution spaces, or narrow tasks such as paper-centric tasks, leaving key challenges underexplored - realistic user intent, complex multi-step API planning, rich parameter filling for APIs, grounded answers with references, and comprehensive evaluation of both the process and the outcome. We introduce AISE-Bench, a real-world, full-cycle annotated benchmark for information seeking on academic knowledge graphs. AISE-Bench release contains 1,133 QA pairs, including query taxonomies, full API execution trajectories, validated parameters, and source-grounded answers with reference links. To support high-quality annotation, we design a customized agent workflow to enable annotators to plan, execute, and revise complex API workflows efficiently. We develop a comprehensive evaluation protocol measuring answer quality, reference grounding, API-planning correctness, and execution success. Among the 14 evaluated methods, even the strongest model (PLAY2PROMPT with Gemini-3-Pro) achieves only moderate performance and often struggles with API planning and execution. AISE-Bench establishes a challenging new testbed for quantitatively evaluating and improving the stepwise correctness, grounded summarization, and traceable reasoning of multi-step API-using LLM agents. Our code and data are available at https://aise-bench.github.io/.

Information extraction (IE) is an important task in Natural Language Processing (NLP), involving the extraction of named entities and their relationships from unstructured text. In this paper, we propose a novel approach to this task by formulating it as graph structure learning (GSL). By formulating IE as GSL, we enhance the model's ability to dynamically refine and optimize the graph structure during the extraction process. This formulation allows for better interaction and structure-informed decisions for entity and relation prediction, in contrast to previous models that have separate or untied predictions for these tasks. When compared against state-of-the-art baselines on joint entity and relation extraction benchmarks, our model, GraphER, achieves competitive results.

Knowledge Graphs (KGs) are valuable tools for representing relationships between entities in a structured format. Traditionally, these knowledge bases are queried to extract specific information. However, question-answering (QA) over such KGs poses a challenge due to the intrinsic complexity of natural language compared to the structured format and the size of these graphs. Despite these challenges, the structured nature of KGs can provide a solid foundation for grounding the outputs of Large Language Models (LLMs), offering organizations increased reliability and control. Recent advancements in LLMs have introduced reasoning methods at inference time to improve their performance and maximize their capabilities. In this work, we propose integrating these reasoning strategies with KGs to anchor every step or "thought" of the reasoning chains in KG data. Specifically, we evaluate both agentic and automated search methods across several reasoning strategies, including Chain-of-Thought (CoT), Tree-of-Thought (ToT), and Graph-of-Thought (GoT), using GRBench, a benchmark dataset for graph reasoning with domain-specific graphs. Our experiments demonstrate that this approach consistently outperforms baseline models, highlighting the benefits of grounding LLM reasoning processes in structured KG data.

Cross-Chart Retrieval-Augmented Generation (RAG) is critical for complex multi-modal analytical tasks in scientific, business, and political domains. However, existing benchmarks either focus on tables, which are well-structured and textualized, or generate cross-chart questions by simply extracting key points, which often induces lexical overlap between queries and evidence and yields logically inconsistent reasoning chains. To address this, we introduce ChartWalker, a novel framework for constructing challenging cross-chart RAG tasks. ChartWalker features a hierarchical knowledge graph construction method tailored to charts, which organizes entities and relations by granularity to preserve analytical structure. We then propose a structure-aware sampling algorithm that synthesizes semantically coherent, multi-hop reasoning paths, enabling explicit control over query difficulty and granularity for QA generation. Built with this framework, we release ChartWalker-Bench, a comprehensive benchmark spanning diverse domains and cross-chart query types. Extensive evaluations across major RAG paradigms reveal significant performance gaps, underscoring the benchmark's difficulty and utility. Furthermore, we provide ChartWalker-Agent, an agentic baseline to facilitate analysis and inspire future system design.

In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.

Knowledge graphs (KGs) have garnered significant attention for their vast potential across diverse domains. However, the issue of outdated facts poses a challenge to KGs, affecting their overall quality as real-world information evolves. Existing solutions for outdated fact detection often rely on manual recognition. In response, this paper presents DEAN (Deep outdatEd fAct detectioN), a novel deep learning-based framework designed to identify outdated facts within KGs. DEAN distinguishes itself by capturing implicit structural information among facts through comprehensive modeling of both entities and relations. To effectively uncover latent out-of-date information, DEAN employs a contrastive approach based on a pre-defined Relations-to-Nodes (R2N) graph, weighted by the number of entities. Experimental results demonstrate the effectiveness and superiority of DEAN over state-of-the-art baseline methods.

Large Language Models (LLMs) reasoning processes are challenging to analyze due to their complexity and the lack of organized visualization tools. We present ReasonGraph, a web-based platform for visualizing and analyzing LLM reasoning processes. It supports both sequential and tree-based reasoning methods while integrating with major LLM providers and over fifty state-of-the-art models. ReasonGraph incorporates an intuitive UI with meta reasoning method selection, configurable visualization parameters, and a modular framework that facilitates efficient extension. Our evaluation shows high parsing reliability, efficient processing, and strong usability across various downstream applications. By providing a unified visualization framework, ReasonGraph reduces cognitive load in analyzing complex reasoning paths, improves error detection in logical processes, and enables more effective development of LLM-based applications. The platform is open-source, promoting accessibility and reproducibility in LLM reasoning analysis.

AI agents have experienced a paradigm shift, from early dominance by reinforcement learning (RL) to the rise of agents powered by large language models (LLMs), and now further advancing towards a synergistic fusion of RL and LLM capabilities. This progression has endowed AI agents with increasingly strong abilities. Despite these advances, to accomplish complex real-world tasks, agents are required to plan and execute effectively, maintain reliable memory, and coordinate smoothly with other agents. Achieving these capabilities involves contending with ever-present intricate information, operations, and interactions. In light of this challenge, data structurization can play a promising role by transforming intricate and disorganized data into well-structured forms that agents can more effectively understand and process. In this context, graphs, with their natural advantage in organizing, managing, and harnessing intricate data relationships, present a powerful data paradigm for structurization to support the capabilities demanded by advanced AI agents. To this end, this survey presents a first systematic review of how graphs can empower AI agents. Specifically, we explore the integration of graph techniques with core agent functionalities, highlight notable applications, and identify prospective avenues for future research. By comprehensively surveying this burgeoning intersection, we hope to inspire the development of next-generation AI agents equipped to tackle increasingly sophisticated challenges with graphs. Related resources are collected and continuously updated for the community in the Github link.

Artificial general intelligence on graphs has shown significant advancements across various applications, yet the traditional 'Pre-train & Fine-tune' paradigm faces inefficiencies and negative transfer issues, particularly in complex and few-shot settings. Graph prompt learning emerges as a promising alternative, leveraging lightweight prompts to manipulate data and fill the task gap by reformulating downstream tasks to the pretext. However, several critical challenges still remain: how to unify diverse graph prompt models, how to evaluate the quality of graph prompts, and to improve their usability for practical comparisons and selection. In response to these challenges, we introduce the first comprehensive benchmark for graph prompt learning. Our benchmark integrates SIX pre-training methods and FIVE state-of-the-art graph prompt techniques, evaluated across FIFTEEN diverse datasets to assess performance, flexibility, and efficiency. We also present 'ProG', an easy-to-use open-source library that streamlines the execution of various graph prompt models, facilitating objective evaluations. Additionally, we propose a unified framework that categorizes existing graph prompt methods into two main approaches: prompts as graphs and prompts as tokens. This framework enhances the applicability and comparison of graph prompt techniques. The code is available at: https://github.com/sheldonresearch/ProG.

Knowledge graphs are useful tools to organize, recommend and sort data. Hierarchies in knowledge graphs provide significant benefit in improving understanding and compartmentalization of the data within a knowledge graph. This work leverages large language models to generate and augment hierarchies in an existing knowledge graph. For small (<100,000 node) domain-specific KGs, we find that a combination of few-shot prompting with one-shot generation works well, while larger KG may require cyclical generation. We present techniques for augmenting hierarchies, which led to coverage increase by 98% for intents and 99% for colors in our knowledge graph.

Large language models are increasingly deployed as agents that plan over long horizons and act through external tools. Most agents select actions through unconstrained generation over an accumulating history, leaving implicit the procedural knowledge of what to do, in what order, and under which conditions. As trajectories lengthen, agents can lose track of their objectives, invoke tools out of order, and repeat unproductive actions. We introduce the Procedural Graph: just as a knowledge graph organizes factual knowledge into (entity, relation, entity) triplets for what-is questions, a Procedural Graph organizes procedural knowledge into (procedure, relation, procedure) triplets for what-to-do questions. At each decision step, the framework localizes the agent's active node, and a guidance model translates the surrounding subgraph into step-level situational guidance that biases the solver's next action without dictating it. The graph is self-evolving: an LLM refiner contrasts failed trajectories with successful ones and edits the graph's topology and attributes, committing edits that preserve or improve held-out validation performance while retaining rejected ones to discourage repetition. Starting from a minimal skeleton, the loop builds graphs that match or surpass hand-designed ones. It can also repair a flawed expert prior. Across multiple datasets, task types, and LLMs, the Procedural Graph delivers consistent gains over memory-based baselines, and self-evolution further improves performance without manual engineering.

Previous works on knowledge-to-text generation take as input a few RDF triples or key-value pairs conveying the knowledge of some entities to generate a natural language description. Existing datasets, such as WIKIBIO, WebNLG, and E2E, basically have a good alignment between an input triple/pair set and its output text. However, in practice, the input knowledge could be more than enough, since the output description may only cover the most significant knowledge. In this paper, we introduce a large-scale and challenging dataset to facilitate the study of such a practical scenario in KG-to-text. Our dataset involves retrieving abundant knowledge of various types of main entities from a large knowledge graph (KG), which makes the current graph-to-sequence models severely suffer from the problems of information loss and parameter explosion while generating the descriptions. We address these challenges by proposing a multi-graph structure that is able to represent the original graph information more comprehensively. Furthermore, we also incorporate aggregation methods that learn to extract the rich graph information. Extensive experiments demonstrate the effectiveness of our model architecture.

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.

We propose a methodology that allows communication with Piping and Instrumentation Diagrams (P&IDs) using natural language. In particular, we represent P&IDs through the DEXPI data model as labeled property graphs and integrate them with Large Language Models (LLMs). The approach consists of three main parts: 1) P&IDs are cast into a graph representation from the DEXPI format using our pyDEXPI Python package. 2) A tool for generating P&ID knowledge graphs from pyDEXPI. 3) Integration of the P&ID knowledge graph to LLMs using graph-based retrieval augmented generation (graph-RAG). This approach allows users to communicate with P&IDs using natural language. It extends LLM's ability to retrieve contextual data from P&IDs and mitigate hallucinations. Leveraging the LLM's large corpus, the model is also able to interpret process information in PIDs, which could help engineers in their daily tasks. In the future, this work will also open up opportunities in the context of other generative Artificial Intelligence (genAI) solutions on P&IDs, and AI-assisted HAZOP studies.

Knowledge Graph Embedding (KGE) models are used to learn continuous representations of entities and relations. A key task in the literature is predicting missing links between entities. However, Knowledge Graphs are not just sets of links but also have semantics underlying their structure. Semantics is crucial in several downstream tasks, such as query answering or reasoning. We introduce the subgraph inference task, where a model has to generate likely and semantically valid subgraphs. We propose IntelliGraphs, a set of five new Knowledge Graph datasets. The IntelliGraphs datasets contain subgraphs with semantics expressed in logical rules for evaluating subgraph inference. We also present the dataset generator that produced the synthetic datasets. We designed four novel baseline models, which include three models based on traditional KGEs. We evaluate their expressiveness and show that these models cannot capture the semantics. We believe this benchmark will encourage the development of machine learning models that emphasize semantic understanding.

Graph is powerful for representing various types of real-world data. The topology (edges' presence) and edges' features of a graph decides the message passing mechanism among vertices within the graph. While most existing approaches only manually define a single-value edge to describe the connectivity or strength of association between a pair of vertices, task-specific and crucial relationship cues may be disregarded by such manually defined topology and single-value edge features. In this paper, we propose the first general graph representation learning framework (called GRATIS) which can generate a strong graph representation with a task-specific topology and task-specific multi-dimensional edge features from any arbitrary input. To learn each edge's presence and multi-dimensional feature, our framework takes both of the corresponding vertices pair and their global contextual information into consideration, enabling the generated graph representation to have a globally optimal message passing mechanism for different down-stream tasks. The principled investigation results achieved for various graph analysis tasks on 11 graph and non-graph datasets show that our GRATIS can not only largely enhance pre-defined graphs but also learns a strong graph representation for non-graph data, with clear performance improvements on all tasks. In particular, the learned topology and multi-dimensional edge features provide complementary task-related cues for graph analysis tasks. Our framework is effective, robust and flexible, and is a plug-and-play module that can be combined with different backbones and Graph Neural Networks (GNNs) to generate a task-specific graph representation from various graph and non-graph data. Our code is made publicly available at https://github.com/SSYSteve/Learning-Graph-Representation-with-Task-specific-Topology-and-Multi-dimensional-Edge-Features.

Deep graph generative modeling has proven capable of learning the distribution of complex, multi-scale structures characterizing real-world graphs. However, one of the main limitations of existing methods is their large output space, which limits generation scalability and hinders accurate modeling of the underlying distribution. To overcome these limitations, we propose a novel approach that significantly reduces the output space of existing graph generative models. Specifically, starting from the observation that many real-world graphs have low graph bandwidth, we restrict graph bandwidth during training and generation. Our strategy improves both generation scalability and quality without increasing architectural complexity or reducing expressiveness. Our approach is compatible with existing graph generative methods, and we describe its application to both autoregressive and one-shot models. We extensively validate our strategy on synthetic and real datasets, including molecular graphs. Our experiments show that, in addition to improving generation efficiency, our approach consistently improves generation quality and reconstruction accuracy. The implementation is made available.

Dependency graph, as a heterogeneous graph representing the intrinsic relationships between different pairs of system entities, is essential to many data analysis applications, such as root cause diagnosis, intrusion detection, etc. Given a well-trained dependency graph from a source domain and an immature dependency graph from a target domain, how can we extract the entity and dependency knowledge from the source to enhance the target? One way is to directly apply a mature dependency graph learned from a source domain to the target domain. But due to the domain variety problem, directly using the source dependency graph often can not achieve good performance. Traditional transfer learning methods mainly focus on numerical data and are not applicable. In this paper, we propose ACRET, a knowledge transfer based model for accelerating dependency graph learning from heterogeneous categorical event streams. In particular, we first propose an entity estimation model to filter out irrelevant entities from the source domain based on entity embedding and manifold learning. Only the entities with statistically high correlations are transferred to the target domain. On the surviving entities, we propose a dependency construction model for constructing the unbiased dependency relationships by solving a two-constraint optimization problem. The experimental results on synthetic and real-world datasets demonstrate the effectiveness and efficiency of ACRET. We also apply ACRET to a real enterprise security system for intrusion detection. Our method is able to achieve superior detection performance at least 20 days lead lag time in advance with more than 70% accuracy.

Explainable recommendation has demonstrated significant advantages in informing users about the logic behind recommendations, thereby increasing system transparency, effectiveness, and trustworthiness. To provide personalized and interpretable explanations, existing works often combine the generation capabilities of large language models (LLMs) with collaborative filtering (CF) information. CF information extracted from the user-item interaction graph captures the user behaviors and preferences, which is crucial for providing informative explanations. However, due to the complexity of graph structure, effectively extracting the CF information from graphs still remains a challenge. Moreover, existing methods often struggle with the integration of extracted CF information with LLMs due to its implicit representation and the modality gap between graph structures and natural language explanations. To address these challenges, we propose G-Refer, a framework using graph retrieval-augmented large language models (LLMs) for explainable recommendation. Specifically, we first employ a hybrid graph retrieval mechanism to retrieve explicit CF signals from both structural and semantic perspectives. The retrieved CF information is explicitly formulated as human-understandable text by the proposed graph translation and accounts for the explanations generated by LLMs. To bridge the modality gap, we introduce knowledge pruning and retrieval-augmented fine-tuning to enhance the ability of LLMs to process and utilize the retrieved CF information to generate explanations. Extensive experiments show that G-Refer achieves superior performance compared with existing methods in both explainability and stability. Codes and data are available at https://github.com/Yuhan1i/G-Refer.

Graph-structured data are the commonly used and have wide application scenarios in the real world. For these diverse applications, the vast variety of learning tasks, graph domains, and complex graph learning procedures present challenges for human experts when designing versatile graph learning approaches. Facing these challenges, large language models (LLMs) offer a potential solution due to the extensive knowledge and the human-like intelligence. This paper proposes a novel conceptual prototype for designing versatile graph learning methods with LLMs, with a particular focus on the "where" and "how" perspectives. From the "where" perspective, we summarize four key graph learning procedures, including task definition, graph data feature engineering, model selection and optimization, deployment and serving. We then explore the application scenarios of LLMs in these procedures across a wider spectrum. In the "how" perspective, we align the abilities of LLMs with the requirements of each procedure. Finally, we point out the promising directions that could better leverage the strength of LLMs towards versatile graph learning methods.

Graph Neural Networks (GNNs) have demonstrated superior performance on various graph learning tasks, including recommendation, where they leverage user-item collaborative filtering signals in graphs. However, theoretical formulations of their capability are scarce, despite their empirical effectiveness in state-of-the-art recommender models. Recently, research has explored the expressiveness of GNNs in general, demonstrating that message passing GNNs are at most as powerful as the Weisfeiler-Lehman test, and that GNNs combined with random node initialization are universal. Nevertheless, the concept of "expressiveness" for GNNs remains vaguely defined. Most existing works adopt the graph isomorphism test as the metric of expressiveness, but this graph-level task may not effectively assess a model's ability in recommendation, where the objective is to distinguish nodes of different closeness. In this paper, we provide a comprehensive theoretical analysis of the expressiveness of GNNs in recommendation, considering three levels of expressiveness metrics: graph isomorphism (graph-level), node automorphism (node-level), and topological closeness (link-level). We propose the topological closeness metric to evaluate GNNs' ability to capture the structural distance between nodes, which aligns closely with the objective of recommendation. To validate the effectiveness of this new metric in evaluating recommendation performance, we introduce a learning-less GNN algorithm that is optimal on the new metric and can be optimal on the node-level metric with suitable modification. We conduct extensive experiments comparing the proposed algorithm against various types of state-of-the-art GNN models to explore the explainability of the new metric in the recommendation task. For reproducibility, implementation codes are available at https://github.com/HKUDS/GTE.

The exponential growth of scientific literature necessitates advanced tools for effective knowledge exploration. We present Knowledge Navigator, a system designed to enhance exploratory search abilities by organizing and structuring the retrieved documents from broad topical queries into a navigable, two-level hierarchy of named and descriptive scientific topics and subtopics. This structured organization provides an overall view of the research themes in a domain, while also enabling iterative search and deeper knowledge discovery within specific subtopics by allowing users to refine their focus and retrieve additional relevant documents. Knowledge Navigator combines LLM capabilities with cluster-based methods to enable an effective browsing method. We demonstrate our approach's effectiveness through automatic and manual evaluations on two novel benchmarks, CLUSTREC-COVID and SCITOC. Our code, prompts, and benchmarks are made publicly available.

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.

Tabular data, ubiquitous and rich in informational value, is an increasing focus for deep representation learning, yet progress is hindered by studies centered on single tables or isolated databases, which limits model capabilities due to data scale. While collaborative learning approaches such as federated learning, transfer learning, split learning, and tabular foundation models aim to learn from multiple correlated databases, they are challenged by a scarcity of real-world interconnected tabular resources. Current data lakes and corpora largely consist of isolated databases lacking defined inter-database correlations. To overcome this, we introduce WikiDBGraph, a large-scale graph of 100,000 real-world tabular databases from WikiData, interconnected by 17 million edges and characterized by 13 node and 12 edge properties derived from its database schema and data distribution. WikiDBGraph's weighted edges identify both instance- and feature-overlapped databases. Experiments on these newly identified databases confirm that collaborative learning yields superior performance, thereby offering considerable promise for structured foundation model training while also exposing key challenges and future directions for learning from interconnected tabular data.

Clinical case formulation organizes patient symptoms and psychosocial factors into causal models, often using the 5P framework. However, constructing such graphs from therapy transcripts is time consuming and varies across clinicians. We present InsightFlow, an LLM based approach that automatically generates 5P aligned causal graphs from patient-therapist dialogues. Using 46 psychotherapy intake transcripts annotated by clinical experts, we evaluate LLM generated graphs against human formulations using structural (NetSimile), semantic (embedding similarity), and expert rated clinical criteria. The generated graphs show structural similarity comparable to inter annotator agreement and high semantic alignment with human graphs. Expert evaluations rate the outputs as moderately complete, consistent, and clinically useful. While LLM graphs tend to form more interconnected structures compared to the chain like patterns of human graphs, overall complexity and content coverage are similar. These results suggest that LLMs can produce clinically meaningful case formulation graphs within the natural variability of expert practice. InsightFlow highlights the potential of automated causal modeling to augment clinical workflows, with future work needed to improve temporal reasoning and reduce redundancy.

Temporal knowledge graphs represent temporal facts (s,p,o,tau) relating a subject s and an object o via a relation label p at time tau, where tau could be a time point or time interval. Temporal knowledge graphs may exhibit static temporal patterns at distinct points in time and dynamic temporal patterns between different timestamps. In order to learn a rich set of static and dynamic temporal patterns and apply them for inference, several embedding approaches have been suggested in the literature. However, as most of them resort to single underlying embedding spaces, their capability to model all kinds of temporal patterns was severely limited by having to adhere to the geometric property of their one embedding space. We lift this limitation by an embedding approach that maps temporal facts into a product space of several heterogeneous geometric subspaces with distinct geometric properties, i.e.\ Complex, Dual, and Split-complex spaces. In addition, we propose a temporal-geometric attention mechanism to integrate information from different geometric subspaces conveniently according to the captured relational and temporal information. Experimental results on standard temporal benchmark datasets favorably evaluate our approach against state-of-the-art models.

Wikidata is the largest collaborative general knowledge graph supported by a worldwide community. It includes many helpful topics for knowledge exploration and data science applications. However, due to the enormous size of Wikidata, it is challenging to retrieve a large amount of data with millions of results, make complex queries requiring large aggregation operations, or access too many statement references. This paper introduces our preliminary works on Wikidata-lite, a toolkit to build a database offline for knowledge extraction and exploration, e.g., retrieving item information, statements, provenances, or searching entities by their keywords and attributes. Wikidata-lite has high performance and memory efficiency, much faster than the official Wikidata SPARQL endpoint for big queries. The Wikidata-lite repository is available at https://github.com/phucty/wikidb.

Schema graphs are an upstream bottleneck of schema-grounded information extraction and knowledge graph construction, yet most extraction systems assume the schema is already available. We introduce SCOPE (Schema Construction and Ontology-induction Pipeline Evaluation), a train-text-only benchmark for corpus-to-schema induction and optional schema fusion from raw text, built from 24 public information extraction sources (15 RE and 9 EE) normalized into evaluation-only gold schema graphs; its core event-extraction target covers event types and within-event argument roles, with inter-event links reported separately. We present SCION (Schema Construction and Induction with Ontology Normalization), an auditable reference pipeline rather than a new extraction architecture; it constructs candidate spaces from train text and restricts naming, merging, filtering, validation, and conservative fusion to candidate-linked evidence under strict JSON contracts. On the SCOPE core suite, SCION-lite attains the highest F1 among released source-schema references, Text2Onto-style, LLM-only, and matched extract-then-aggregate baselines under Literal, Fuzzy, Continuous, and Graph schema-graph metrics, while the compact open-model SCION-RL variant reduces reliance on proprietary LLM schema engineers. These results are reported against normalized typed-edge targets rather than as claims that induced schemas surpass human ontology design; the release includes evidence-linked outputs, parse/fallback logs, candidate retention/merging logs, run manifests, code, and benchmark packages at https://github.com/wandugu/paper_scion.

Large language models (LLMs) have demonstrated remarkable success across a wide range of tasks; however, they still encounter challenges in reasoning tasks that require understanding and inferring relationships between distinct pieces of information within text sequences. This challenge is particularly pronounced in tasks involving multi-step processes, such as logical reasoning and multi-hop question answering, where understanding implicit relationships between entities and leveraging multi-hop connections in the given context are crucial. Graphs, as fundamental data structures, explicitly represent pairwise relationships between entities, thereby offering the potential to enhance LLMs' reasoning capabilities. External graphs have proven effective in supporting LLMs across multiple tasks. However, in many reasoning tasks, no pre-existing graph structure is provided. Can we structure implicit knowledge derived from context into graphs to assist LLMs in reasoning? In this paper, we propose Reasoning with Graphs (RwG) by first constructing explicit graphs from the context and then leveraging these graphs to enhance LLM reasoning performance on reasoning tasks. Extensive experiments demonstrate the effectiveness of the proposed method in improving both logical reasoning and multi-hop question answering tasks.

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.

Multi-relational temporal graphs are powerful tools for modeling real-world data, capturing the evolving and interconnected nature of entities over time. Recently, many novel models are proposed for ML on such graphs intensifying the need for robust evaluation and standardized benchmark datasets. However, the availability of such resources remains scarce and evaluation faces added complexity due to reproducibility issues in experimental protocols. To address these challenges, we introduce Temporal Graph Benchmark 2.0 (TGB 2.0), a novel benchmarking framework tailored for evaluating methods for predicting future links on Temporal Knowledge Graphs and Temporal Heterogeneous Graphs with a focus on large-scale datasets, extending the Temporal Graph Benchmark. TGB 2.0 facilitates comprehensive evaluations by presenting eight novel datasets spanning five domains with up to 53 million edges. TGB 2.0 datasets are significantly larger than existing datasets in terms of number of nodes, edges, or timestamps. In addition, TGB 2.0 provides a reproducible and realistic evaluation pipeline for multi-relational temporal graphs. Through extensive experimentation, we observe that 1) leveraging edge-type information is crucial to obtain high performance, 2) simple heuristic baselines are often competitive with more complex methods, 3) most methods fail to run on our largest datasets, highlighting the need for research on more scalable methods.

Graphs are ubiquitous structures found in numerous real-world applications, such as drug discovery, recommender systems, and social network analysis. To model graph-structured data, graph neural networks (GNNs) have become a popular tool. However, existing GNN architectures encounter challenges in cross-graph learning where multiple graphs have different feature spaces. To address this, recent approaches introduce text-attributed graphs (TAGs), where each node is associated with a textual description, which can be projected into a unified feature space using textual encoders. While promising, this method relies heavily on the availability of text-attributed graph data, which is difficult to obtain in practice. To bridge this gap, we propose a novel method named Topology-Aware Node description Synthesis (TANS), leveraging large language models (LLMs) to convert existing graphs into text-attributed graphs. The key idea is to integrate topological information into LLMs to explain how graph topology influences node semantics. We evaluate our TANS on text-rich, text-limited, and text-free graphs, demonstrating its applicability. Notably, on text-free graphs, our method significantly outperforms existing approaches that manually design node features, showcasing the potential of LLMs for preprocessing graph-structured data in the absence of textual information. The code and data are available at https://github.com/Zehong-Wang/TANS.

Relational databases (RDBs) are composed of interconnected tables, where relationships between them are defined through foreign keys. Recent research on applying machine learning to RDBs has explored graph-based representations of RDBs, where rows of tables are modeled as nodes, and foreign key relationships are modeled as edges. RDB-to-graph modeling helps capture cross-table dependencies, ultimately leading to enhanced performance across diverse tasks. However, there are numerous ways to model RDBs as graphs, and performance varies significantly depending on the chosen graph model. In our analysis, applying a common heuristic rule for graph modeling leads to up to a 10% drop in performance compared to the best-performing graph model, which remains non-trivial to identify. To foster research on intelligent RDB-to-graph modeling, we introduce RDB2G-Bench, the first benchmark framework for evaluating such methods. We construct extensive datasets covering 5 real-world RDBs and 12 predictive tasks, resulting in around 50k graph-performance pairs for efficient and reproducible evaluations. Thanks to our precomputed datasets, we were able to benchmark 9 automatic RDB-to-graph modeling methods on the 12 tasks over 600x faster than on-the-fly evaluation, which requires repeated model training. Our analysis of the datasets and benchmark results reveals key structural patterns affecting graph model effectiveness, along with practical implications for effective graph modeling.

Even for a conservative estimate, 80% of enterprise data reside in unstructured files, stored in data lakes that accommodate heterogeneous formats. Classical search engines can no longer meet information seeking needs, especially when the task is to browse and explore for insight formulation. In other words, there are no obvious search keywords to use. Knowledge graphs, due to their natural visual appeals that reduce the human cognitive load, become the winning candidate for heterogeneous data integration and knowledge representation. In this paper, we introduce Docs2KG, a novel framework designed to extract multimodal information from diverse and heterogeneous unstructured documents, including emails, web pages, PDF files, and Excel files. Dynamically generates a unified knowledge graph that represents the extracted key information, Docs2KG enables efficient querying and exploration of document data lakes. Unlike existing approaches that focus on domain-specific data sources or pre-designed schemas, Docs2KG offers a flexible and extensible solution that can adapt to various document structures and content types. The proposed framework unifies data processing supporting a multitude of downstream tasks with improved domain interpretability. Docs2KG is publicly accessible at https://docs2kg.ai4wa.com, and a demonstration video is available at https://docs2kg.ai4wa.com/Video.

Large language models have been extensively studied as neural knowledge bases for their knowledge access, editability, reasoning, and explainability. However, few works focus on the structural patterns of their knowledge. Motivated by this gap, we investigate these structural patterns from a graph perspective. We quantify the knowledge of LLMs at both the triplet and entity levels, and analyze how it relates to graph structural properties such as node degree. Furthermore, we uncover the knowledge homophily, where topologically close entities exhibit similar levels of knowledgeability, which further motivates us to develop graph machine learning models to estimate entity knowledge based on its local neighbors. This model further enables valuable knowledge checking by selecting triplets less known to LLMs. Empirical results show that using selected triplets for fine-tuning leads to superior performance.